PREFIX obo:
PREFIX rdf:
PREFIX rdfs:
PREFIX xsd:
obo:MI_0079 a rdfs:Class ;
rdfs:label "other biochemical technologies" ;
rdfs:comment """Experimental methods that could not be assigned to the other large group of technologies.
OBSOLETE use biochemical (MI:0401) instead.""" .
obo:MI_2407 a rdfs:Class ;
rdfs:label "Uberon" ;
rdfs:comment """Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage.
https://www.ebi.ac.uk/ols/ontologies/uberon""" ;
rdfs:subClassOf obo:MI_0473 .
obo:MI_2047 a rdfs:Class ;
rdfs:label "percentage of plasma protein binding" ;
rdfs:comment "Percentage of the drug that is bound in plasma proteins" ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_2394 a rdfs:Class ;
rdfs:label "negative genetic interaction" ;
rdfs:comment "An effect in which two genetic perturbations, when combined, result in a fitness that is less than expected given the fitness resulting from the individual perturbations." ;
rdfs:subClassOf obo:MI_0933 .
obo:MI_0233 a rdfs:Class ;
rdfs:label "protein dna complex" ;
rdfs:comment "A stable set of interacting protein and DNA that can be copurified and operate as a functional unit." ;
rdfs:subClassOf obo:MI_1299 .
obo:MI_1170 a rdfs:Class ;
rdfs:label "pre-assembly response" ;
rdfs:comment "This term describes the way in which preformation of a molecular complex has a non-allosteric cooperative effect on subsequent interactions of its components." ;
rdfs:subClassOf obo:MI_1149 .
obo:MI_0516 a rdfs:Class ;
rdfs:label "methyltransferase radiometric assay" ;
rdfs:comment "Measures the transfer of a radiolabelled methyl group of a donor, for example S-adenosyl-L-methionine (SAM) to a carboxyl group of an acceptor." ;
rdfs:subClassOf obo:MI_0515 .
obo:MI_0047 a rdfs:Class ;
rdfs:label "far western blotting" ;
rdfs:comment "Proteins are fractionated by PAGE (SDS-polyacrylamide gel electrophoresis), transferred to a nitrocellulose membrane and tested for the ability to bind to a protein, a peptide, or any other ligand. Cell lysates can also be fractionated before gel electrophoresis to increase the sensitivity of the method for detecting interactions with rare proteins. Denaturants are removed during the blotting procedure, which allows many proteins to recover (or partially recover) activity. However, if biological activity is not recoverable, the proteins can be fractionated by a non denaturing gel system. This variation of the method eliminates the problem of activity regeneration and allows the detection of binding when the presence of a protein complex is required for binding. The protein probe can be prepared by any one of several procedures, while fusion affinity tags greatly facilitate purification. Synthesis in E. coli with a GST fusion, epitope tag, or other affinity tag is most commonly used. The protein of interest can then be radioactively labelled, biotinylated, or used in the blotting procedure as an unlabeled probe that is detected by a specific antibody." ;
rdfs:subClassOf obo:MI_0892 .
obo:MI_0391 a rdfs:Class ;
rdfs:label "alexa 594 label" ;
rdfs:comment "Alexa fluorescent dye analogue to Texas Red-X with an approximate excitation wavelength maximum of 594nm." ;
rdfs:subClassOf obo:MI_0384 .
obo:MI_2155 a rdfs:Class ;
rdfs:label "average molecular weight" ;
rdfs:comment "Molecular weight in g/mol, determined from molecular formula or sequence." ;
rdfs:subClassOf obo:MI_2025 .
obo:MI_1311 a rdfs:Class ;
rdfs:label "differential scanning calorimetry" ;
rdfs:comment "Differential scanning calorimetry (DSC) is a thermoanalytical technique in which the difference in the amount of heat required to increase the temperature of a sample and reference in solution is measured as a function of temperature. By measuring the temperature dependence of this partial heat capacity, a basic thermodynamic property, DSC gives immediate access to the thermodynamic mechanism that governs a conformational equilibrium, for example between a protein complex and its individual participants." ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_2304 a rdfs:Class ;
rdfs:label "carbohydrate chemical modification disrupting interaction rate" ;
rdfs:comment "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate." ;
rdfs:subClassOf obo:MI_2302 .
obo:MI_1140 a rdfs:Class ;
rdfs:label "decarboxylation reaction" ;
rdfs:comment "Decarboxylation is a chemical reaction that releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. Enzymes that catalyze decarboxylations are called decarboxylases or, the more formal term, carboxy-lyases (EC number 4.1.1)." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0657 a rdfs:Class ;
rdfs:label "systematic evolution of ligands by exponential enrichment" ;
rdfs:comment "RNA and cDNA constructs with variable central sequences and a constant flanking region are collected in a complex library. The library is then screened to select either specific binding partners of a bait molecule (generally a protein) or particular enzymatic activities of the nucleic acid molecules themselves. The selected nucleic acids are amplified using the constant flanking regions to increase their abundance. Cycles of selection-amplification can be repeated to increase the specificity of the targets that, at the end, are individually identified by sequencing." ;
rdfs:subClassOf obo:MI_0400 .
obo:MI_1031 a rdfs:Class ;
rdfs:label "protein folding/unfolding" ;
rdfs:comment "A change in the rate of protein folding/unfolding is taken as a measure of chaperone protein binding." ;
rdfs:subClassOf obo:MI_0400 .
obo:MI_0897 a rdfs:Class ;
rdfs:label "protein modification ontology" ;
rdfs:comment "Catalogue of covalent modification of, or a change resulting in an alteration of the measured molecular mass of, a peptide or protein amino acid residue." ;
rdfs:subClassOf obo:MI_0447 .
obo:MI_1051 a rdfs:Class ;
rdfs:label "evidence" ;
rdfs:comment "Binary pair is defined by a single piece of experimental evidence." ;
rdfs:subClassOf obo:MI_1050 .
obo:MI_0739 a rdfs:Class ;
rdfs:label "penetrating tag" ;
rdfs:comment "Membrane shuttling peptide derived from the Drosophila homeobox protein Antennapedia: RQIKIWFQNRRMKWKK" ;
rdfs:subClassOf obo:MI_0740 .
obo:MI_0446 a rdfs:Class ;
rdfs:label "pubmed" ;
rdfs:comment """PubMed is designed to provide access to citations from biomedical literature. The data can be found at both NCBI PubMed and Europe PubMed Central.
http://www.ncbi.nlm.nih.gov/pubmed
http://europepmc.org""" ;
rdfs:subClassOf obo:MI_0445 .
obo:MI_2361 a rdfs:Class ;
rdfs:label "Split Intein-Mediated Protein Ligation" ;
rdfs:comment "Bait protein is fused to a standard protein fusion tag and an intein fragment, prey a with a different protein fusion tag and the complementary intein fragment. The bait and prey are co-expressed in a cell line where the association of bait and prey brings the intein fragments into close proximity, allowing them to reconstitute a fully functional intein, which then catalyzes its own excision and the concurrent ligation of the bait and the prey peptides (as well as the standard protein fusion tags). The resulting spliced protein can be resolved by regular western blot analysis due to its altered mobility, while the presence of the standard protein fusion tags allows visualization or purification of protein using regular biochemical techniques." ;
rdfs:subClassOf obo:MI_0090 .
obo:MI_0508 a rdfs:Class ;
rdfs:label "deacetylase radiometric assay" ;
rdfs:comment "Measures the release of radiolabelled acetic acid from a pre-labeled molecule." ;
rdfs:subClassOf obo:MI_0406 .
obo:MI_0523 a rdfs:Class ;
rdfs:label "t7 tag" ;
rdfs:comment "The protein of interest is expressed as a fusion to the peptide MASMTGGQQMG for which antibodies are commercially available." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_0086 a rdfs:Class ;
rdfs:label "polyclonal antibody western blot" ;
rdfs:comment "Western blot assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest." ;
rdfs:subClassOf obo:MI_0113 .
obo:MI_0519 a rdfs:Class ;
rdfs:label "glutathione s tranferase tag" ;
rdfs:comment "The protein is expressed and purified as a fusion to the glutathione S-tranferase protein." ;
rdfs:subClassOf obo:MI_0365 .
obo:MI_0222 a rdfs:Class ;
rdfs:label "physiological level" ;
rdfs:comment "A molecule whose synthesis is under control of its natural gene promoter or estimated to be expressed at a similar rate." ;
rdfs:subClassOf obo:MI_0221 .
obo:MI_2316 a rdfs:Class ;
rdfs:label "attached carbohydrate disrupting interaction strength" ;
rdfs:comment "Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction strength when compared with the non-glycosylated molecule." ;
rdfs:subClassOf obo:MI_2311 , obo:MI_2317 .
obo:MI_1185 a rdfs:Class ;
rdfs:label "tag visualisation by dna adenine methyltransferase" ;
rdfs:comment "Proteins of interest are tagged with Escherichia coli DNA adenine methyltransferase (dam). Expression of this fusion protein in vivo leads to preferential methylation of adenines in DNA surrounding the native binding sites of the dam fusion partner. Because adenine methylation does not occur endogenously in most eukaryotes, it provides a unique tag to mark protein interaction sites. The adenine-methylated DNA fragments are isolated by selective polymerase chain reaction amplification and can be identified by microarray hybridization." ;
rdfs:subClassOf obo:MI_0980 .
obo:MI_1089 a rdfs:Class ;
rdfs:label "nuclear translocation assay" ;
rdfs:comment "Method to detect interaction by inducing nuclear localization of one participant, which would then pull an interacting participant along with it into the nucleus. As both participants are labeled, the difference in nuclear localization between the induced and non-induced states provides an indication of the interaction between the two molecules." ;
rdfs:subClassOf obo:MI_1088 .
obo:MI_2175 a rdfs:Class ;
rdfs:label "genedb" ;
rdfs:comment """The GeneDB project is a core part of the Sanger Institute's Pathogen Genomics activities. Its primary goals are:
-to provide reliable access to the latest sequence data and annotation/curation for the whole range of organisms sequenced by the Pathogen group.
-to develop the website and other tools to aid the community in accessing and obtaining the maximum value from these data.
GeneDB currently provides access to more than 40 genomes, at various stages of completion, from early access to partial genomes with automatic annotation through to complete genomes with extensive manual curation.
www.genedb.org""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0558 a rdfs:Class ;
rdfs:label "deglycosylation reaction" ;
rdfs:comment "Reaction catalyzed by PNGase, a deglycosylating enzyme that promotes the hydrolysis of the beta-aspartylglycosylamine bond of aspargine-linked glycopeptides and glycoproteins." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0330 a rdfs:Class ;
rdfs:label "molecular source" ;
rdfs:comment "Defines whether molecule is endogenously expressed or has in any way been altered, in sequence or expression level, from its native state. For a complete description of the experimental molecule form use the orthogonal CVs expression level, delivery method, and sample process." ;
rdfs:subClassOf obo:MI_0346 .
obo:MI_2222 a rdfs:Class ;
rdfs:label "inference by socio-affinity scoring" ;
rdfs:comment "Socio-affinity index provides a single measure of the association between each pair of proteins based on an entire AP-MS dataset, considering both the spoke (when one protein retrieves another when tagged) and the matrix (when two proteins are retrieved by another) evidence, and the overall frequency of each protein in the data set." ;
rdfs:subClassOf obo:MI_0363 .
obo:MI_1078 a rdfs:Class ;
rdfs:label "plantgdb" ;
rdfs:comment "PlantGDB develops plant species-specific EST and GSS databases, to provide web-accessible tools and inter-species query capabilities, and to provide genome browsing and annotation capabilities." ;
rdfs:subClassOf obo:MI_1094 .
obo:MI_1231 a rdfs:Class ;
rdfs:label "aminomethylcoumarin label" ;
rdfs:comment "AMC (aminomethylcoumarin ) is a blue fluorescent tag with reactive derivatives that are used as contrasting probes for double- and triple-labeling in immunofluorescence microscopy, arrays and in situ hybridization and can be attached to proteins or small molecules for reaction monitoring." ;
rdfs:subClassOf obo:MI_1328 .
obo:MI_1264 a rdfs:Class ;
rdfs:label "ntnu" ;
rdfs:comment "Norwegian University of Science and Technology. www.ntnu.no/home." ;
rdfs:subClassOf obo:MI_0489 .
obo:MI_2260 a rdfs:Class ;
rdfs:label "stimulus" ;
rdfs:comment "Any detectable change in the internal or external environment of a cell, tissue, organ, or organism." ;
rdfs:subClassOf obo:MI_2259 .
obo:MI_1212 a rdfs:Class ;
rdfs:label "checksum" ;
rdfs:comment "A fixed-size datum calculated (by using a hash function) for a molecular sequence or structure, typically for purposes of error detection or indexing." ;
rdfs:subClassOf obo:MI_0666 .
obo:MI_2341 a rdfs:Class ;
rdfs:label "luminescence transmitter" ;
rdfs:comment "Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific luminescence donor and then act as a donor via re-emission of its own characteristic fluorescence. The luminescence donor may or may not be a fluorophore itself." ;
rdfs:subClassOf obo:MI_0495 .
obo:MI_2127 a rdfs:Class ;
rdfs:label "tmax/cmax" ;
rdfs:comment "Ratio between the time value at Cmax (maximum concentration) in a dose response curve, and the Cmax value itself." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_2315 a rdfs:Class ;
rdfs:label "attached carbohydrate disrupting interaction rate" ;
rdfs:comment "Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule." ;
rdfs:subClassOf obo:MI_2311 , obo:MI_2317 .
obo:MI_2285 a rdfs:Class ;
rdfs:label "miRNA interference luciferase reporter assay" ;
rdfs:comment "The method is based on the functional effect of the binding of the microRNA on the target (mRNA or LncRNA), which is the repression of the expression of the target. To validate a sequence as a direct target of a microRNA, a luciferase reporter gene carrying the wt candidate sequence or its mutated form is used, and the expression of the target is evaluated with a luciferase assay. If the wt is significantly less expressed than the mutant, the binding occurs." ;
rdfs:subClassOf obo:MI_0255 .
obo:MI_1202 a rdfs:Class ;
rdfs:label "one-strep-tag" ;
rdfs:comment "Synthetic peptide tag (SAWSHPQFEK-(GGGS)2-SAWSHPQFEK)" ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_2435 a rdfs:Class ;
rdfs:label "polypeptide cleavage site" ;
rdfs:comment "The location on a polypeptide chain where peptide bonds are broken down by hydrolysis." ;
rdfs:subClassOf obo:MI_2434 .
obo:MI_2046 a rdfs:Class ;
rdfs:label "lethal dose 50" ;
rdfs:comment "The LD50 is the dose that kills half (50%) of the animals tested" ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_2267 a rdfs:Class ;
rdfs:label "de-sumoylated residue" ;
rdfs:comment "A protein modification that effectively cleaves the G-K bond and releases SUMO proteins." ;
rdfs:subClassOf obo:MI_2262 .
obo:MI_0378 a rdfs:Class ;
rdfs:label "rare isotope label" ;
rdfs:comment "Molecule can be labelled including rare isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule." ;
rdfs:subClassOf obo:MI_0253 .
obo:MI_1322 a rdfs:Class ;
rdfs:label "atto 465" ;
rdfs:comment "Fluorescent tag - maleimide couples to thiols." ;
rdfs:subClassOf obo:MI_1092 .
obo:MI_0418 a rdfs:Class ;
rdfs:label "genetic" ;
rdfs:comment """methods supporting genetic interactions.
OBSOLETE as too unspecific use Genetic interference instead MI:0254.""" .
obo:MI_0586 a rdfs:Class ;
rdfs:label "inhibitor" ;
rdfs:comment "Molecule inhibiting an interaction by interacting with one or more of its participants." ;
rdfs:subClassOf obo:MI_2274 .
obo:MI_1042 a rdfs:Class ;
rdfs:label "pubmed central" ;
rdfs:comment "PubMed Central is the US National Institute of Health free digital archive of biomedical and life science journals." ;
rdfs:subClassOf obo:MI_0445 .
obo:MI_0457 a rdfs:Class ;
rdfs:label "smart" ;
rdfs:comment """SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures.
http://smart.embl-heidelberg.de/""" ;
rdfs:subClassOf obo:MI_0449 .
obo:MI_2424 a rdfs:Class ;
rdfs:label "HuMap" ;
rdfs:comment "HuMap is a machine learning framework to identify protein complexes from mass spectrometry and other large-scale interaction experiments. HuMap 3.0 is presented as a searchable web resource (https://humap3.proteincomplexes.org/) using data from >25,000 mass spectrometry experiments to identify nearly >15,000 human protein complexes." ;
rdfs:subClassOf obo:MI_0489 .
obo:MI_0979 a rdfs:Class ;
rdfs:label "oxidoreductase assay" ;
rdfs:comment "Catalysis of oxido-reductions. The substrate oxidized is regarded as the hydrogen or electron donor. The classification is based on 'donor:acceptor oxidoreductase'. The common name is 'dehydrogenase', wherever this is possible; as an alternative, 'acceptor reductase' can be used. 'Oxidase' is used only where O2 is an acceptor." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0534 a rdfs:Class ;
rdfs:label "glycosyl-cysteine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00131.""" .
obo:MI_2263 a rdfs:Class ;
rdfs:label "s-nitrosylation" ;
rdfs:comment "Reaction that create a covalent bond between a nitrogen monoxide group and the thiol group of cysteine." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0968 a rdfs:Class ;
rdfs:label "biosensor" ;
rdfs:comment "A biosensor is a device for the detection of an analyte that combines a biological component with a physicochemical detector component" ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_2426 a rdfs:Class ;
rdfs:label "orthology-group" ;
rdfs:comment "Reference to an orthology database group. Gathers orthologous entities across species in a single identifier for their group" ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_0861 a rdfs:Class ;
rdfs:label "protein a tag" ;
rdfs:comment "The protein A is a bacterial cell wall isolated from Staphylococcus aureus that binds to mammalian IgGs mainly through Fc regions. The protein A can be use to retaint antibodies or as fusion tag of a protein under analysis." ;
rdfs:subClassOf obo:MI_0240 .
obo:MI_2043 a rdfs:Class ;
rdfs:label "pharmacology" ;
rdfs:comment "Text description of how the drug works at a clinical or physiological level." ;
rdfs:subClassOf obo:MI_2089 .
obo:MI_2245 a rdfs:Class ;
rdfs:label "causal regulatory mechanism" ;
rdfs:comment "Type of relationship between entities involved in a causal interaction. This term is to be used only to describe the effect of a modulator entity A on a modulated entity B when A is not immediately upstream of B." ;
rdfs:subClassOf obo:MI_2233 .
obo:MI_2357 a rdfs:Class ;
rdfs:label "kcat/km" ;
rdfs:comment "This parameter represents the rate of the reaction at negligible substrate concentration, indicating how the velocity varies according to how often enzyme and substrate combine." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_2015 a rdfs:Class ;
rdfs:label "pharmgkb" ;
rdfs:comment "Pharmacogenomics Knowledge Base identification number (if molecule is in PharmGKB)" ;
rdfs:subClassOf obo:MI_2054 .
obo:MI_0872 a rdfs:Class ;
rdfs:label "atomic force microscopy" ;
rdfs:comment """The atomic force microscope (AFM) is a very high-resolution type of scanning probe microscope, with demonstrated resolution of fractions of a nanometer, more than 1000 times better than the optical diffraction limit. The AFM was invented by Binnig, Quate and Gerber in 1986, and is one of the foremost tools for imaging, measuring and manipulating matter at the nanoscale.The term 'microscope' in the name is actually a misnomer because it implies looking, while in fact the information is gathered by feeling out the surface with a mechanical feeler.
http://en.wikipedia.org/wiki/Atomic_force_microscope""" ;
rdfs:subClassOf obo:MI_0428 .
obo:MI_1144 a rdfs:Class ;
rdfs:label "protein a tag visualisation" ;
rdfs:comment "Protein A tag is visualized by interacting with IgG antibodies (or their derivatives) that are specifically recognized by protein A." ;
rdfs:subClassOf obo:MI_0866 .
obo:MI_1357 a rdfs:Class ;
rdfs:label "RNAcentral" ;
rdfs:comment "Provides unified access to the ncRNA sequence data supplied by the expert databases." ;
rdfs:subClassOf obo:MI_0683 .
obo:MI_2233 a rdfs:Class ;
rdfs:label "causal interaction" ;
rdfs:comment "Binary causative relationships between biological entities. CV terms belonging to this term allow the description of causal interactions using the current PSI-MI schema." ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_0058 a rdfs:Class ;
rdfs:label "genome based prediction" ;
rdfs:comment "Methods that require fully sequenced genomes either because they are based on the comparison of genome topology or on the identification of orthologous sequences in different genomes." ;
rdfs:subClassOf obo:MI_0063 .
obo:MI_1293 a rdfs:Class ;
rdfs:label "monophenotypic genetic suppression (complete)" ;
rdfs:comment """An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the complete suppression (to wild type) of the mutant phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a < ab = b = wt [E = a]
OR
wt = b = ab < a [E = a]
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1290 , obo:MI_1292 .
obo:MI_0886 a rdfs:Class ;
rdfs:label "publication year" ;
rdfs:comment "Year of publication of a paper." ;
rdfs:subClassOf obo:MI_1093 .
obo:MI_1242 a rdfs:Class ;
rdfs:label "fc-igg1" ;
rdfs:comment "A fusion protein tag consisting of a portion of the constant region of IgG1." ;
rdfs:subClassOf obo:MI_0975 .
obo:MI_0728 a rdfs:Class ;
rdfs:label "gal4 vp16 complementation" ;
rdfs:comment "A chimeric protein consisting of the GAL4 DNA-binding domain (aa 1-147 of GAL4) and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) can specifically activate transcription of a reporter gene located downstream ofGAL4 DNA binding sites and the E1B minimal promoter. Similarly, two chimeric proteins, one encoding a chimeric GAL4 protein and the other encoding a chimeric VP16 protein, can activate the reporter gene, if the domains fused to the GAL4 and VP16 sequences can complex with appropriate conformation. However, if the domains fused to the GAL4 and VP16 sequences do not interact specifically to form a + complex that reconstitutes GAL4 function, the reporter gene cannot be activated." ;
rdfs:subClassOf obo:MI_0018 .
obo:MI_0505 a rdfs:Class ;
rdfs:label "experimental feature" ;
rdfs:comment "The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number." ;
rdfs:subClassOf obo:MI_0116 .
obo:MI_0742 a rdfs:Class ;
rdfs:label "gpm" ;
rdfs:comment """Global Proteome Machine aim to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results.
http://www.thegpm.org""" ;
rdfs:subClassOf obo:MI_0737 .
obo:MI_0309 a rdfs:Class ;
rdfs:label "genomic tagging" ;
rdfs:comment """A cassette coding for a protein tag is inserted by homologous recombination onto the genomic copy of an open reading frame. The advantage of this delivery method is that the resulting engineered protein is expressed under its natural promoter control.
OBSOLETE redundant term. Map to feature type : tag (MI:0507).""" .
obo:MI_1253 a rdfs:Class ;
rdfs:label "atto 532" ;
rdfs:comment "Fluorescent tag - maleimide couples to thiols." ;
rdfs:subClassOf obo:MI_1092 .
obo:MI_0646 a rdfs:Class ;
rdfs:label "Kd" ;
rdfs:comment "The equilibrium dissociation constant of a receptor/ligand or proteinA/proteinB complex. Unit Molar (generally M-1)." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_1104 a rdfs:Class ;
rdfs:label "solid state nmr" ;
rdfs:comment """Solid-state NMR (ssNMR) does not require that the sample be soluble or form a crystal, and the approach can be used to study molecules larger than 100 kD. Solid-state NMR spectra are very broad, as the full
effects of anisotropic or orientation-dependent interactions are observed in the spectrum.""" ;
rdfs:subClassOf obo:MI_0077 .
obo:MI_2256 a rdfs:Class ;
rdfs:label "relocalization" ;
rdfs:comment "Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location." .
obo:MI_0007 a rdfs:Class ;
rdfs:label "anti tag coimmunoprecipitation" ;
rdfs:comment "A specific antibody for the molecule of interest is not available, therefore the bait protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient and specific antibodies or a specific ligand are available." ;
rdfs:subClassOf obo:MI_0019 .
obo:MI_2352 a rdfs:Class ;
rdfs:label "enhanced gene" ;
rdfs:comment "A gene whose genetic perturbation phenotype is enhanced by a different genetic perturbation." ;
rdfs:subClassOf obo:MI_0495 .
obo:MI_2194 a rdfs:Class ;
rdfs:label "crac" ;
rdfs:comment "Combination of UV cross-linking and affinity purification where the protein of interest bears a tag used for pull-down or immunoprecipitation. As in CLIP, unspecific proteins are digested via proteinase K treatment and RNAs are tagged with oligonucleotide linkers. RNA can be then identified via Northern blotting or using RT-PCR and then sequencing of the generated cDNA." ;
rdfs:subClassOf obo:MI_0430 .
obo:MI_2383 a rdfs:Class ;
rdfs:label "phenotype result" ;
rdfs:comment "The expression of a phenotype in an organism or a population of organisms resulting from one or more organismal perturbations, including genetic perturbations and environmental (including chemical/drug exposure) perturbations." ;
rdfs:subClassOf obo:MI_0190 .
obo:MI_0880 a rdfs:Class ;
rdfs:label "atpase assay" ;
rdfs:comment "Measures the catalysis of the hydrolysis of ATP+ H2O = ADP + phosphate." ;
rdfs:subClassOf obo:MI_0879 .
obo:MI_0097 a rdfs:Class ;
rdfs:label "reverse ras recruitment system" ;
rdfs:comment "In this complementation approach the bait can be any membrane protein (for example a receptor or a channel protein), the prey is cloned as a fusion protein of any cDNA from a library and the coding sequence of cytoplasmic RAS (cdc25 in yeast). If the bait and the prey interact, RAS is recruited close to the membrane and can activate cell growth. This procedure must take place in cells having a mutated RAS (Cdc25-2 yeast strain having a temperature sensitive mutation of RAS) to avoid constitutive growth activation." ;
rdfs:subClassOf obo:MI_0090 .
obo:MI_0652 a rdfs:Class ;
rdfs:label "nanomolar" ;
rdfs:comment """10E-9 moles per liter of solution.
OBSOLETE: term redundant with the schema exponent attribute of the parameter.""" .
obo:MI_2133 a rdfs:Class ;
rdfs:label "neutralization by glucuronidation or sulfatation" ;
rdfs:comment "Neutralization of a compound occuring via its glucuronidation or sulfatation." ;
rdfs:subClassOf obo:MI_2048 .
obo:MI_1281 a rdfs:Class ;
rdfs:label "mutual genetic suppression (complete)" ;
rdfs:comment """An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting combination is wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* <= b < ab = wt
OR
wt = ab < b <= a*
OR
a < wt = ab < b
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1290 , obo:MI_2389 .
obo:MI_0840 a rdfs:Class ;
rdfs:label "stimulator" ;
rdfs:comment "Molecule stimulating an interaction by interacting with one or more of the participants." ;
rdfs:subClassOf obo:MI_2274 .
obo:MI_0597 a rdfs:Class ;
rdfs:label "feature description" ;
rdfs:comment "The feature text description may include information about the feature detection method." ;
rdfs:subClassOf obo:MI_0668 .
obo:MI_0018 a rdfs:Class ;
rdfs:label "two hybrid" ;
rdfs:comment "The classical two-hybrid system is a method that uses transcriptional activity as a measure of protein-protein interaction. It relies on the modular nature of many site-specific transcriptional activators (GAL 4) , which consist of a DNA-binding domain and a transcriptional activation domain. The DNA-binding domain serves to target the activator to the specific genes that will be expressed, and the activation domain contacts other proteins of the transcriptional machinery to enable transcription to occur. The two-hybrid system is based on the observation that the two domains of the activator need to be non-covalently brought together by the interaction of any two proteins. The application of this system requires the expression of two hybrid. Generally this assay is performed in yeast cell, but it can also be carried out in other organism. The bait protein is fused to the DNA binding molecule, the prey to the transcriptional activator." ;
rdfs:subClassOf obo:MI_0232 .
obo:MI_1073 a rdfs:Class ;
rdfs:label "statistical-based confidence" ;
rdfs:comment "Confidence in an interaction is based on a measure of the probability of these molecules interacting." ;
rdfs:subClassOf obo:MI_1064 .
obo:MI_1093 a rdfs:Class ;
rdfs:label "bibliographic attribute name" ;
rdfs:comment "Attributes specific to the publication." ;
rdfs:subClassOf obo:MI_0665 .
obo:MI_2182 a rdfs:Class ;
rdfs:label "dflat" ;
rdfs:comment """Database dedicated to annotating gene function related to human fetal development using the Gene Ontology for functional annotation.
http://bcb.cs.tufts.edu/dflat/""" ;
rdfs:subClassOf obo:MI_0473 .
obo:MI_2372 a rdfs:Class ;
rdfs:label "synthetic haploinsufficiency (sensu BioGRID)" ;
rdfs:comment "Genetic perturbations of multiple genes in combination that results in a more severe growth defect than each individual perturbation, when one mutation is hemizygous." ;
rdfs:subClassOf obo:MI_2402 .
obo:MI_0255 a rdfs:Class ;
rdfs:label "post transcriptional interference" ;
rdfs:comment "This term refers to methods designed to interfere with gene expression at post-transcriptional level rather than with the gene itself." ;
rdfs:subClassOf obo:MI_0045 .
obo:MI_1317 a rdfs:Class ;
rdfs:label "eukaryotic linear motif resource" ;
rdfs:comment "The ELM resource provides a database of curated short linear motif classes and instances, as well as a sequence analysis tool to detect putative short linear motif instances in query sequences. http://elm.eu.org/" ;
rdfs:subClassOf obo:MI_0447 .
obo:MI_0208 a rdfs:Class ;
rdfs:label "genetic interaction (sensu unexpected)" ;
rdfs:comment """An effect in which two genetic perturbations, when combined, result in a phenotype that does not appear to be merely explained by the superimposition or addition of effects of the original perturbations.
ab (not=) E""" ;
rdfs:subClassOf obo:MI_2402 .
obo:MI_0926 a rdfs:Class ;
rdfs:label "fiash label" ;
rdfs:comment "This fluorescent label is a small ligand membrane-permeant and nonfluorescent until it binds with high affinity and specificity to the tetracysteine domain. Such in situ labeling adds much less mass than does green fluorescent protein and offers greater versatility in attachment sites as well as potential spectroscopic and chemical properties." ;
rdfs:subClassOf obo:MI_0857 .
obo:MI_0641 a rdfs:Class ;
rdfs:label "ic50" ;
rdfs:comment "Molar concentration of an antagonist which produces 50% of the maximum possible inhibitory response for that antagonist. Note this measure depends on the specific antagonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ic50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_2197 a rdfs:Class ;
rdfs:label "probe interaction assay" ;
rdfs:comment "An assay that uses molecular probes, such as ions, small molecules or antibodies to monitor interactions between biomolecules under study." ;
rdfs:subClassOf obo:MI_0401 .
obo:MI_2397 a rdfs:Class ;
rdfs:label "cisphenotypic co-suppressing genetic interaction" ;
rdfs:comment """An effect in which individual perturbations of different genes result in the same mutant phenotype but to varying degrees of severity/penetrance and the resulting phenotype of their combination is less severe/penetrant than both of the phenotypes resulting from the individual perturabtions. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* < b < ab < wt [E = a*]
OR
wt < ab < b < a* [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1282 .
obo:MI_1109 a rdfs:Class ;
rdfs:label "gene database" ;
rdfs:comment "Primarily nomenclature/cross-reference databases, used by curators to establish a link between a gene and protein ID. In some cases, database records do not contain actual sequence but point to loci on specific reference genomes." ;
rdfs:subClassOf obo:MI_0473 .
obo:MI_1065 a rdfs:Class ;
rdfs:label "replication-based confidence" ;
rdfs:comment "Methods based on counting the number of replicates in which an interaction has been observed." ;
rdfs:subClassOf obo:MI_1064 .
obo:MI_0692 a rdfs:Class ;
rdfs:label "b42 activation domain" ;
rdfs:comment "B42 is an acidic sequence of 89 residues derived from Escherichia coli acting as weak transcription activation domain. When use in two hybrid experiments, the weakness of B42 as activator increases the sensitivity of the interaction detection." ;
rdfs:subClassOf obo:MI_0689 .
obo:MI_0630 a rdfs:Class ;
rdfs:label "3d-structure" ;
rdfs:comment "Comments on the 3D structure. This attribute is generally associated to an interaction." ;
rdfs:subClassOf obo:MI_0664 .
obo:MI_0984 a rdfs:Class ;
rdfs:label "deamination assay" ;
rdfs:comment "The measurement of the removal of an amine group from a molecule." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_2415 a rdfs:Class ;
rdfs:label "cell line ontology" ;
rdfs:comment "The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns." ;
rdfs:subClassOf obo:MI_0473 .
obo:MI_0904 a rdfs:Class ;
rdfs:label "polysaccharide" ;
rdfs:comment "A polysaccharide is a complex polymer of carbohydrate monormers. They are polymers made up of many monosaccharides joined together by glycosidic bonds. They are therefore very large, often branched, macromolecules." ;
rdfs:subClassOf obo:MI_1100 .
obo:MI_1166 a rdfs:Class ;
rdfs:label "allosteric change in dynamics" ;
rdfs:comment "The allosteric mechanism where changes in the local dynamics of an allosteric molecule result in altered binding or catalytic properties." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_1164 .
obo:MI_2307 a rdfs:Class ;
rdfs:label "carbohydrate chemical modification increasing interaction rate" ;
rdfs:comment "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate." ;
rdfs:subClassOf obo:MI_2305 .
obo:MI_0946 a rdfs:Class ;
rdfs:label "miniaturized immunoprecipitation" ;
rdfs:comment "Combines on-chip in-vitro protein synthesis with an in situ microfluidic affinity assay. Co-spotted DNA microarray containing a linear template encoding the proteins is aligned and bonded with a microfluidic device that creates chambers in the array chip. The experiment consists of three main stages: (i) an antibody that recognizes the bait protein or a specific tag is deposited on a circular area inside each individual chamber; (ii) proteins are expressed in vitro by transcription and translation of DNA spotted on the chip; (iii) the bait is immobilized on the chamber surface by the antibody and the chamber is washed, retaining only interacting bait-prey pairs." ;
rdfs:subClassOf obo:MI_0019 , obo:MI_0092 .
obo:MI_1209 a rdfs:Class ;
rdfs:label "firefly-c" ;
rdfs:comment "The c-terminus of the firefly luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay." ;
rdfs:subClassOf obo:MI_1208 , obo:MI_1215 .
obo:MI_2172 a rdfs:Class ;
rdfs:label "aspgd" ;
rdfs:comment """AspGD is an organized collection of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). AspGD contains information about genes and proteins of multiple Aspergillus species; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Aspergillus species.
www.aspergillusgenome.org/""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0995 a rdfs:Class ;
rdfs:label "depalmitoylase assay" ;
rdfs:comment "Measures the removal of S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine, which are cleaved and return C,K,T or S residues." ;
rdfs:subClassOf obo:MI_0991 .
obo:MI_0367 a rdfs:Class ;
rdfs:label "green fluorescent protein tag" ;
rdfs:comment "The green fluorescent protein of organisms such as the bioluminescent jellyfish Aequorea victoria can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native." ;
rdfs:subClassOf obo:MI_0687 .
obo:MI_0624 a rdfs:Class ;
rdfs:label "stimulant" ;
rdfs:comment "Reaction occurs at a faster rate in the presence of this compound or molecule i.e. the molecule directly physically co-operates with the interaction. Reaction may not occur at all in the absence of this molecule." ;
rdfs:subClassOf obo:MI_0664 .
obo:MI_0171 a rdfs:Class ;
rdfs:label "omega-n-phospho-arginine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00227.""" .
obo:MI_2138 a rdfs:Class ;
rdfs:label "mutagenicity" ;
rdfs:comment "Tendency of a bioactive entity to induce genetic mutations at the nucleotide level e.g. substitution of nucleotide base-pairs and insertions and deletions of one or more nucleotides in DNA sequences." ;
rdfs:subClassOf obo:MI_2135 .
obo:MI_0616 a rdfs:Class ;
rdfs:label "example" ;
rdfs:comment "Example generally associated to Cv terms. Test." ;
rdfs:subClassOf obo:MI_0667 , obo:MI_1041 .
obo:MI_2430 a rdfs:Class ;
rdfs:label "MuSIC" ;
rdfs:comment "MuSIC (multi-scale integrated cell ) is a machine learning framework to identify protein complexes from mass spectrometry and other large-scale interaction experiments" ;
rdfs:subClassOf obo:MI_0489 .
obo:MI_1174 a rdfs:Class ;
rdfs:label "configurational pre-organization" ;
rdfs:comment "Multivalent ligands form multiple discrete interactions with one or more binding partners. In some cases, An initial binding event can pre-organize other sites for binding. This reduces the degrees of freedom of these sites, thus reducing the entropic costs of their interactions. In addition, the combined strength of multiple interactions increases the enthalpic stability of each interaction (avidity effect). As a result of such effects, interactions of this kind can have a cooperative effect on subsequent interactions." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_1170 .
obo:MI_1177 a rdfs:Class ;
rdfs:label "phylogenetic profiling of predicted gene regulatory region binding sites" ;
rdfs:comment "Sequence analysis based on multiple homologous alignments of the regulatory region of a gene used to predict specific elements, transcription factor binding sites (TFBS), where binding of specific transcription factors can occur. These methods often also use transcription factor binding motif models." ;
rdfs:subClassOf obo:MI_0100 , obo:MI_1176 .
obo:MI_0915 a rdfs:Class ;
rdfs:label "physical association" ;
rdfs:comment "Interaction between molecules within the same physical complex. Often identified under conditions which suggest that the molecules are in close proximity but not necessarily in direct contact with each other." ;
rdfs:subClassOf obo:MI_0914 .
obo:MI_1332 a rdfs:Class ;
rdfs:label "bhf-ucl" ;
rdfs:comment "The Cardiovascular Gene Annotation Initiative represents a collaboration between University College London and the European Bioinformatics Institute (EBI), funded by the British Heart Foundation. This annotation group is a member of the IMEx Consortium." ;
rdfs:subClassOf obo:MI_0461 , obo:MI_0973 .
obo:MI_1115 a rdfs:Class ;
rdfs:label "spike" ;
rdfs:comment "SPIKE" ;
rdfs:subClassOf obo:MI_1106 .
obo:MI_0593 a rdfs:Class ;
rdfs:label "translocation" ;
rdfs:comment "Xref pointing to a GO process term describing the start and end location of a migrating molecule, for instance see GO:0006611, 'protein-nucleus export'." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_1155 a rdfs:Class ;
rdfs:label "negative cooperative effect" ;
rdfs:comment "This term specifies that an interaction diminishes a subsequent interaction." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_1153 .
obo:MI_0068 a rdfs:Class ;
rdfs:label "mass detection of residue modification" ;
rdfs:comment "Mass spectrometry can be used to characterise chemical modifications within peptides. One approach consists in the observation of a mass difference when a sample is treated with an enzyme that can specifically remove a peptide modification, for instance a phosphatase. The mass difference corresponds to the mass of the chemical group covalently linked to a residue. Such experiments carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) do not allow the mapping of the modification site within the sequence, whereas any tandem mass spectrometer (LC MS/MS Liquid Chromatography Tandem Mass Spectrometry, nanoESI MS/MS nanoElectrospray Ionisation tandem mass spectrometry, FTMS Fourier Transform mass spectrometry) provide such information. A second approach consists of the direct mass measurement of the ionized chemical group dissociated from the residue within a tandem mass spectrometer. Both approaches need a prior enrichment of the modified peptide population in the samples with IMAC (Immobilized Metal Affinity Chromatography)or specific anti-modification antibodies." ;
rdfs:subClassOf obo:MI_0659 .
obo:MI_0433 a rdfs:Class ;
rdfs:label "partial identification of protein sequence" ;
rdfs:comment "partial protein sequence identification." ;
rdfs:subClassOf obo:MI_0093 , obo:MI_0659 .
obo:MI_2281 a rdfs:Class ;
rdfs:label "deamidation assay" ;
rdfs:comment "Assay to measure the catalysis of the reaction: a monocarboxylic acid amide + H2O = a monocarboxylate + NH3." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0267 a rdfs:Class ;
rdfs:label "suppression scalable" ;
rdfs:comment """Level of over/underexpression scales the 'extend' of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803. """ .
obo:MI_2252 a rdfs:Class ;
rdfs:label "guanine nucleotide exchange factor reaction" ;
rdfs:comment "The process mediated by guanine nucleotide exchange factors (GEFs) that catalyze the exchange of bound GDP with cytosolic GTP." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_1062 a rdfs:Class ;
rdfs:label "bipartite expansion" ;
rdfs:comment "Complex n-ary data has been expanded to binary using the bipartite model. This assumes that all molecules in the complex interact with a single externally designated entity." ;
rdfs:subClassOf obo:MI_1059 .
obo:MI_0894 a rdfs:Class ;
rdfs:label "electron diffraction" ;
rdfs:comment "Analysis of diffraction pattern using electron beam." ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_0485 a rdfs:Class ;
rdfs:label "uniparc" ;
rdfs:comment """UniProt Archive (UniParc) is part of UniProt project. It is a non-redundant archive of protein sequences derived from many sources.
http://www.ebi.ac.uk/uniparc/""" ;
rdfs:subClassOf obo:MI_1097 .
obo:MI_2241 a rdfs:Class ;
rdfs:label "down-regulates activity" ;
rdfs:comment "The effect of a modulator entity A on a modulated entity B that decreases the frequency, rate or extent of the molecular function of B, an elemental biological activity occurring at the molecular level, such as catalysis or binding (GO:0044093)." ;
rdfs:subClassOf obo:MI_2240 .
obo:MI_1126 a rdfs:Class ;
rdfs:label "self interaction" ;
rdfs:comment "Intra-molecular interaction between two or more regions of the same molecule." ;
rdfs:subClassOf obo:MI_0407 .
obo:MI_1314 a rdfs:Class ;
rdfs:label "proximity-dependent biotin identification" ;
rdfs:comment "A promiscuous biotin protein ligase is fused to the bait protein, neighbouring prey are then biotinylated. The biotin tag may be used for isolation and/or identification." ;
rdfs:subClassOf obo:MI_1313 .
obo:MI_2404 a rdfs:Class ;
rdfs:label "oxidase assay" ;
rdfs:comment "Enzymatic oxido-reductions where only O2 is an acceptor of hydrogen or electrons" ;
rdfs:subClassOf obo:MI_0979 .
obo:MI_0422 a rdfs:Class ;
rdfs:label "immunostaining" ;
rdfs:comment "Method using an antibody coupled with some colouring agent to detect a specific protein within a cell or tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody." ;
rdfs:subClassOf obo:MI_0421 .
obo:MI_2171 a rdfs:Class ;
rdfs:label "complemented donor-acceptor resonance energy transfer" ;
rdfs:comment "This technology is based on quantifying the BRET between a pair of participants bearing complementation tags and a participant tagged with a bioluminescent enzyme or a fluorescent tag. The tags held by the pair of participants are complementary halves of either a fluorescent tag (N- and C- fragments of the Venus fluorescent protein, for example) or a bioluminescent enzyme (N- and C- fragments of Renilla luciferase, for example). Interaction between the pair of participants leads to reconstruction of the bioluminescent enzyme/fluorescent protein, which can then emit/accept photons that are accepted/emitted by the tag in the third participant, generating the signal used to detect the interaction. The signals emitted by the bioluminescent enzyme and the fluorescent tag have different wavelengths, so they can be distinguished." ;
rdfs:subClassOf obo:MI_0051 , obo:MI_2169 .
obo:MI_2290 a rdfs:Class ;
rdfs:label "optical tweezers" ;
rdfs:comment "Optical tweezers are instruments that use a focused laser beam to apply force to particles suspended in a liquid medium. This allows to measure forces generated between interacting molecules - either at the level of just single interacting pair of molecules or at the level of larger molecular assemblies." ;
rdfs:subClassOf obo:MI_0859 .
obo:MI_0814 a rdfs:Class ;
rdfs:label "protease accessibility laddering" ;
rdfs:comment "In protease accessibility laddering (PAL) tagged proteins are purified on magnetic beads in their natively folded state. While attached to the beads, proteins are probed with proteases. Proteolytic fragments are eluted and detected by immunoblotting with antibodies against the tag (e.g., Protein A, GFP, and 6xHis)." ;
rdfs:subClassOf obo:MI_0605 .
obo:MI_0407 a rdfs:Class ;
rdfs:label "direct interaction" ;
rdfs:comment "Interaction between molecules that are in direct contact with each other." ;
rdfs:subClassOf obo:MI_0915 .
obo:MI_1149 a rdfs:Class ;
rdfs:label "cooperative interaction" ;
rdfs:comment "A set of molecular binding events that influence each other either positively or negatively through allostery or pre-assembly. In this context, covalent post-translational modifications are considered as binding events. CV terms that are part of this term allow the description of cooperative interactions using the current PSI-MI schema." ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_0111 a rdfs:Class ;
rdfs:label "dihydrofolate reductase reconstruction" ;
rdfs:comment "The gene for DHFR is rationally dissected into two fragments called F[1,2] and F[3]. Two proteins or protein domains that are thought to bind to each other can then be fused to either of the two DHFR fragments. Reconstitution of enzyme activity can be monitored in vivo by cell survival in DHFR-negative cells grown in the absence of nucleotides. A fluorescence assay can also be carried out taking advantage of fMTX binding to reconstituted DHFR. The basis of this assay is that complementary fragments of DHFR, when expressed and reassembled in cells, will bind with high affinity (Kd 5 540 pM) to fMTX in a 1:1 complex. fMTX is retained in cells by this complex, whereas the unbound fMTX is actively and rapidly transported out of the cells. Survival depends only on the number of molecules of DHFR reassembled." ;
rdfs:subClassOf obo:MI_0090 .
obo:MI_1275 a rdfs:Class ;
rdfs:label "obsolete neutral epistasis" ;
rdfs:comment """OBSOLETE: An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are EITHER traits measured on the same quantitative scale but each significantly deviating, in opposite directions, from wild type, OR completely (qualitatively) different phenotypes), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a < wt < b) AND (ab = a OR ab = b)
OR
(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value, and 'a != b' indicates qualitatively different phenotypes.""" .
obo:MI_0527 a rdfs:Class ;
rdfs:label "adp ribosylated residue" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00752.""" .
obo:MI_2211 a rdfs:Class ;
rdfs:label "nucleic acid chemical modification increasing an interaction" ;
rdfs:comment "Chemical modification observed on a nucleic acid molecule observed to increase the strength or rate of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition." ;
rdfs:subClassOf obo:MI_2206 .
obo:MI_0369 a rdfs:Class ;
rdfs:label "lex-a dimerization assay" ;
rdfs:comment "The method is based on the repression of a reporter gene activity by two LexA DNA binding domains with different binding specificities. LexA is a transcription factor with an N-terminal DNA binding/activation domain (DBAct) and a C-terminal dimerization domain. LexA dimerization is required to repress transcription efficiently. The discovery of LexA DNA binding domains that bind to different DNA sequence enabled the development of this system." ;
rdfs:subClassOf obo:MI_0232 .
obo:MI_2151 a rdfs:Class ;
rdfs:label "other drug interaction" ;
rdfs:comment "Effect of additional drug treatments on a given drug action." ;
rdfs:subClassOf obo:MI_2089 .
obo:MI_0213 a rdfs:Class ;
rdfs:label "methylation reaction" ;
rdfs:comment "The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Irreversible reaction that can affect A,G,M,F,P,C,R,N,Q,E,H,or K residues." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0202 a rdfs:Class ;
rdfs:label "depalmitoylation reaction" ;
rdfs:comment "S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine are cleaved and return C,K,T or S residues." ;
rdfs:subClassOf obo:MI_0212 .
obo:MI_2278 a rdfs:Class ;
rdfs:label "polymer chain length" ;
rdfs:comment "Length of a repetitive polymer chain. Applicable to carbohydrates and other non-protein, non-nucleic acid polymers." ;
rdfs:subClassOf obo:MI_0666 .
obo:MI_0582 a rdfs:Class ;
rdfs:label "suppressed gene" ;
rdfs:comment "A gene whose genetic perturbation phenotype is suppressed by a different genetic perturbation." ;
rdfs:subClassOf obo:MI_0495 .
obo:MI_1220 a rdfs:Class ;
rdfs:label "tag visualisation by luciferase assay" ;
rdfs:comment "The protein is expressed as a hybrid protein fused to a tag containing a luciferase activity. Subsequence observation or measurement of luciferase activity is used to identify the presence of the molecule in an interaction." ;
rdfs:subClassOf obo:MI_0980 .
obo:MI_0187 a rdfs:Class ;
rdfs:label "n6-(4-amino-2-hydroxybutyl)-lysine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00125.""" .
obo:MI_2330 a rdfs:Class ;
rdfs:label "sumo tag" ;
rdfs:comment "Covalent attachment of the small ubiquitin-like modifier (SUMO) protein as a fusion protein." ;
rdfs:subClassOf obo:MI_0240 .
obo:MI_0075 a rdfs:Class ;
rdfs:label "myc tag coimmunoprecipitation" ;
rdfs:comment """The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.
OBSOLETE redundant term. Map to feature type: myc-tagged (MI:0522) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).""" .
obo:MI_0868 a rdfs:Class ;
rdfs:label "author identifier" ;
rdfs:comment "Author published identifier." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_0512 a rdfs:Class ;
rdfs:label "zymography" ;
rdfs:comment "Samples run on a gelatine containing gels under non-reducing condition, gels then incubated under conditions in which the enzyme is active. Gels are stained with coomasie and gelatine-free regions of the gel taken as a measure of enzyme activity." ;
rdfs:subClassOf obo:MI_0435 .
obo:MI_1006 a rdfs:Class ;
rdfs:label "deglycosylase assay" ;
rdfs:comment "Measurement of the removal of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0429 a rdfs:Class ;
rdfs:label "necessary binding region" ;
rdfs:comment "A sequence range within a molecule identified as being absolutely required for an interaction. The sequence may or may not be in direct physical contact with the interaction partner." ;
rdfs:subClassOf obo:MI_0117 , obo:MI_0573 , obo:MI_1128 , obo:MI_1129 .
obo:MI_1286 a rdfs:Class ;
rdfs:label "surpassing genetic interaction" ;
rdfs:comment """An effect in which the observed phenotype of a double perturbation is opposite (relative to the wild type phenotype) to that which is expected upon the double perturbation. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab < wt < E
OR
E < wt < ab
where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0208 .
obo:MI_1303 a rdfs:Class ;
rdfs:label "transient complex" ;
rdfs:comment "A macromolecular complex of which the participants associate and dissociate in vivo. Weak transient complexes feature a dynamic oligomeric equilibrium in solution where the interaction is broken and formed continuously. Strong transient associations that require a molecular trigger to shift the oligomeric equilibrium." ;
rdfs:subClassOf obo:MI_1298 .
obo:MI_0569 a rdfs:Class ;
rdfs:label "deneddylation reaction" ;
rdfs:comment "Cleavage of the G-K bond and release of the NEDD8 ubiquitin like proteins. Deneddylation, which removes the NEDD8 moiety, requires the isopeptidase activity of the COP9 signalosome." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0501 a rdfs:Class ;
rdfs:label "enzyme" ;
rdfs:comment "Molecule catalyzing a modification on its interacting partner." ;
rdfs:subClassOf obo:MI_0500 .
obo:MI_1138 a rdfs:Class ;
rdfs:label "decarboxylation assay" ;
rdfs:comment "The measurement of a the introduction of a carboxylic acid group into a substrate." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_1270 a rdfs:Class ;
rdfs:label "xpress tag" ;
rdfs:comment "Contains a polyhistidine sequence, the Xpress epitope (part of bacteriophage T7 gene 10 protein) and an enterokinase cleavage site. Anti-Xpress antibodies recognise the Xpress epitope sequence found in this leader peptide. Asp-Leu-Tyr-Asp-Asp-Asp-Asp-Lys." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_1245 a rdfs:Class ;
rdfs:label "mkate" ;
rdfs:comment "Monomeric far-red fluorescent protein generated from the wild-type RFP from sea anemone Entacmaea quadricolor. It possesses bright fluorescence with excitation/emission maxima at 588 and 635 nm, respectively." ;
rdfs:subClassOf obo:MI_0732 .
obo:MI_1013 a rdfs:Class ;
rdfs:label "ensemblgenomes" ;
rdfs:comment """Genome browser complementary to Ensembl which extends the search space across a broader taxonomic range.
http://www.ensemblgenomes.org""" ;
rdfs:subClassOf obo:MI_1094 .
obo:MI_0064 a rdfs:Class ;
rdfs:label "interologs mapping" ;
rdfs:comment "Protein interactions, experimentally detected in an organism, are extended to a second organism assuming that homologue proteins, in different organisms, maintain their interaction properties." ;
rdfs:subClassOf obo:MI_0046 , obo:MI_0101 .
obo:MI_0160 a rdfs:Class ;
rdfs:label "omega-n,omega-n-dimethyl-arginine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00077.""" .
obo:MI_1343 a rdfs:Class ;
rdfs:label "enzyme regulator" ;
rdfs:comment "Regulatory subunits of enzyme complexes can determine the activity level or specificity of catalytic subunits." ;
rdfs:subClassOf obo:MI_2274 .
obo:MI_0538 a rdfs:Class ;
rdfs:label "n4-glycosyl-asparagine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00160.""" .
obo:MI_2200 a rdfs:Class ;
rdfs:label "primesdb" ;
rdfs:comment """PRIMESDB is a systems biology platform that is developed to enable the collection, integration and analysis of state-of-the-art genomics, proteomics and mathematical modelling data being generated by the PRIMES project. PRIMES iinvestigates the role of protein interaction machines in oncogenic signalling with a particular focus on the EGFR network. PRIMESDB provides a centralised knowledgebase and analysis platform for cancer protein interaction networks.
http://primesdb.eu/""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0321 a rdfs:Class ;
rdfs:label "catalytic rna" ;
rdfs:comment "Species of RNA that catalyses cleavage or trans-esterification of the phosphodiester link." ;
rdfs:subClassOf obo:MI_0320 .
obo:MI_0244 a rdfs:Class ;
rdfs:label "reactome complex" ;
rdfs:comment """Collection of functional complexes within Reactome - a knowledgebase of biological processes.
http://www.reactome.org/. OSOLETE - this concept no longer exists within Reactome.""" .
obo:MI_0100 a rdfs:Class ;
rdfs:label "sequence based phylogenetic profile" ;
rdfs:comment "Multiple alignments of orthologous sequences in the same species and their corresponding phylogenetic trees are built. Every phylogenetic tree is computed as a matrix of distances between all possible interacting pairs. The covariation of the distance matrices reveals interacting pairs." ;
rdfs:subClassOf obo:MI_0058 , obo:MI_0101 .
obo:MI_0029 a rdfs:Class ;
rdfs:label "cosedimentation through density gradient" ;
rdfs:comment "Sedimentation through a density gradient measures the sedimentation rate of a mixture of proteins through either a glycerol or sucrose gradient. Two interacting proteins will sediment mostly as a complex at concentrations above the binding constant. By varying the concentration of one or both of the complex constituents and taking into account the dilution of the species during sedimentation, one can reasonably accurately estimate the binding constant." ;
rdfs:subClassOf obo:MI_0027 .
obo:MI_1020 a rdfs:Class ;
rdfs:label "hilyte fluor 488" ;
rdfs:comment "A carbonyl-reactive fluorescent labelling dye." ;
rdfs:subClassOf obo:MI_0857 .
obo:MI_2271 a rdfs:Class ;
rdfs:label "edam" ;
rdfs:comment """EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats.
http://edamontology.org/""" ;
rdfs:subClassOf obo:MI_1336 .
obo:MI_1234 a rdfs:Class ;
rdfs:label "silac" ;
rdfs:comment "SILAC (Stable Isotope Labeling by Amino acids in Cell culture) can be used to detect features (typically PTMs) required for a given interaction." ;
rdfs:subClassOf obo:MI_0659 .
obo:MI_0851 a rdfs:Class ;
rdfs:label "protein genbank identifier" ;
rdfs:comment "GenBank Identifier or GI numbers for proteins." ;
rdfs:subClassOf obo:MI_0860 .
obo:MI_0605 a rdfs:Class ;
rdfs:label "enzymatic footprinting" ;
rdfs:comment "Binding sites are identified by altered reactivity of a complex to an enzymatic probe compared to the unbound molecules. Residues in close contact with the binding partner are protected from cleavage by the enzyme. When these enzymes are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein or protein-protein interactions in vivo." ;
rdfs:subClassOf obo:MI_0417 .
obo:MI_0351 a rdfs:Class ;
rdfs:label "homogeneous" ;
rdfs:comment "The author states a molecule is completely pure, i.e. no other molecular species are present." ;
rdfs:subClassOf obo:MI_0350 .
obo:MI_0681 a rdfs:Class ;
rdfs:label "double stranded deoxyribonucleic acid" ;
rdfs:comment """DNA that consists of two base pairing strands. The 2 nucleotide chains are held together by hydrogen bonds between base pairs of nucleotides.
""" ;
rdfs:subClassOf obo:MI_0319 .
obo:MI_0356 a rdfs:Class ;
rdfs:label "identical object in an external resource" ;
rdfs:comment "Reference to the corresponding object in another database. Correspondence may be complete or partial." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_0910 a rdfs:Class ;
rdfs:label "nucleic acid cleavage" ;
rdfs:comment "Covalent bond breakage of a nucleic acid molecule leading to the formation of smaller fragments." ;
rdfs:subClassOf obo:MI_0194 .
obo:MI_1151 a rdfs:Class ;
rdfs:label "participant-ref" ;
rdfs:comment "Referring to a previously described interaction as a participant allows the description of ordered assembly of molecular complexes in PSI-MI2.5. When one of the components of the preformed complex has a feature, the participant-ref term indicates on which component this feature is located. The component is identified by referring to its participant id in the previous interaction." ;
rdfs:subClassOf obo:MI_0668 .
obo:MI_2429 a rdfs:Class ;
rdfs:label "Number of molecules" ;
rdfs:comment "Relative or absolute number of molecules in a sample. Used in the context of quantatative proteomics" ;
rdfs:subClassOf obo:MI_0647 .
obo:MI_1328 a rdfs:Class ;
rdfs:label "coumarin label" ;
rdfs:comment "A class of labels derived from the benzopyrone coumarin." ;
rdfs:subClassOf obo:MI_0857 .
obo:MI_0345 a rdfs:Class ;
rdfs:label "author assigned name" ;
rdfs:comment "Name assigned to a molecule by the authors within a paper that may differ from the reference database." ;
rdfs:subClassOf obo:MI_1041 .
obo:MI_0957 a rdfs:Class ;
rdfs:label "full coverage" ;
rdfs:comment "All interactions which can be ascribed to an unambiguous identified in this paper have been captured." ;
rdfs:subClassOf obo:MI_0956 .
obo:MI_0909 a rdfs:Class ;
rdfs:label "native" ;
rdfs:comment "State of the protein without interference i.e. the natural form." ;
rdfs:subClassOf obo:MI_0907 .
obo:MI_2105 a rdfs:Class ;
rdfs:label "pka" ;
rdfs:comment "Negative decimal logarithm of Ka, acid dissociation equilibrium constant for the dissociation of a weak acid." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_1205 a rdfs:Class ;
rdfs:label "luciferase tag" ;
rdfs:comment "Luciferase is a generic term for the class of oxidative enzymes used in bioluminescence and is distinct from a photoprotein. Luciferase catalyzes a bioluminescent reaction which requires the substrate luciferin as well as Mg2+ and ATP, produces green light with a wavelength of 562 nm." ;
rdfs:subClassOf obo:MI_0240 .
obo:MI_0424 a rdfs:Class ;
rdfs:label "protein kinase assay" ;
rdfs:comment "Catalysis of the transfer of a phosphate group, usually from ATP, to a protein substrate." ;
rdfs:subClassOf obo:MI_0841 .
obo:MI_0879 a rdfs:Class ;
rdfs:label "nucleoside triphosphatase assay" ;
rdfs:comment "Measures the catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate." ;
rdfs:subClassOf obo:MI_0415 , obo:MI_0434 .
obo:MI_2122 a rdfs:Class ;
rdfs:label "clearance" ;
rdfs:comment "The ratio of excretion is or measure of the speed at which a constituent is lost from the body." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_2004 a rdfs:Class ;
rdfs:label "drug brand name" ;
rdfs:comment "Alternate names of the drug, brand names from different manufacturers." ;
rdfs:subClassOf obo:MI_1041 .
obo:MI_0332 a rdfs:Class ;
rdfs:label "naturally occurring" ;
rdfs:comment "Unaltered endogenous molecule in its naturally occurring state." ;
rdfs:subClassOf obo:MI_0330 .
obo:MI_2186 a rdfs:Class ;
rdfs:label "alut" ;
rdfs:comment """The Alzheimers-University of Toronto project adds functional annotation to Alzheimer's related gene products using the Gene Ontology.
http://www.ims.utoronto.ca/""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_1133 a rdfs:Class ;
rdfs:label "mutation decreasing interaction strength" ;
rdfs:comment "Region of a molecule whose mutation or deletion decreases significantly interaction strength." ;
rdfs:subClassOf obo:MI_0119 .
obo:MI_1128 a rdfs:Class ;
rdfs:label "mutation disrupting interaction strength" ;
rdfs:comment "Region of a molecule whose mutation or deletion totally disrupts an interaction strength." ;
rdfs:subClassOf obo:MI_0573 .
obo:MI_0891 a rdfs:Class ;
rdfs:label "neutron fiber diffraction" ;
rdfs:comment "Analysis of diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using neutron beam." ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_1196 a rdfs:Class ;
rdfs:label "quantitative reverse transcription pcr" ;
rdfs:comment "Technique used to measure the quantity of DNA amplified from RNA." ;
rdfs:subClassOf obo:MI_1194 .
obo:MI_0635 a rdfs:Class ;
rdfs:label "contact-comment" ;
rdfs:comment "Free text notes on how to contact the author or organisation which has produced the data This attribute is generally associated to an experiment." ;
rdfs:subClassOf obo:MI_1093 .
obo:MI_0198 a rdfs:Class ;
rdfs:label "defarnesylation reaction" ;
rdfs:comment "S-farnesyl-L-cysteined is cleaved and returns a C residue." ;
rdfs:subClassOf obo:MI_0212 .
obo:MI_2418 a rdfs:Class ;
rdfs:label "ensemblmetazoa" ;
rdfs:comment "Ensembl Metazoa is a is a browser for genomes of metazoan species of scientific interest. https://metazoa.ensembl.org/" ;
rdfs:subClassOf obo:MI_1013 .
obo:MI_1086 a rdfs:Class ;
rdfs:label "equilibrium dialysis" ;
rdfs:comment "Two chambers are separated by a dialysis membrane. The molecular weight cut off (MWCO) of this membrane is chosen such that it will retain the receptor component of the sample (the element which will bind the ligand). A known concentration and volume of ligand is placed into one of the chambers. The ligand is small enough to pass freely through the membrane. A known concentration of receptor is then placed in the remaining chamber in an equivalent volume to that placed in the first chamber. As the ligand diffuses across the membrane some of it will bind to the receptor and some will remain free in solution. The higher the affinity of the interaction, the higher the concentration of ligand that will be bound at any time." ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_0722 a rdfs:Class ;
rdfs:label "protein electroporation" ;
rdfs:comment "Method for temporarily permeabilising cell membranes in order to facilitate the entry of a protein." ;
rdfs:subClassOf obo:MI_0308 , obo:MI_0721 .
obo:MI_1039 a rdfs:Class ;
rdfs:label "c-terminal range" ;
rdfs:comment "The C-terminal region of a sequence, exact coordinates not available." ;
rdfs:subClassOf obo:MI_0333 .
obo:MI_1325 a rdfs:Class ;
rdfs:label "sulfurtransferase assay" ;
rdfs:comment "Measures the rate of a sulphate molecule transfer between two molecules." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_2288 a rdfs:Class ;
rdfs:label "DAP-seq" ;
rdfs:comment "DAP-seq is an in vitro TF-DNA binding assay in which a DAP-seq gDNA library is prepared by attaching a short DNA sequencing adaptor onto purified and fragmented gDNA. In a separate reaction, an affinity-purified TF is prepared by in vitro expression, bound to ligand-coupled beads, and washed to remove non-specific cellular components. The gDNA library is added to the affinity-bound TF and the unbound DNA is washed away. The bound fraction is eluted, amplified with PCR primers to introduce an indexed adaptor, and the DNA is sequenced." ;
rdfs:subClassOf obo:MI_0004 .
obo:MI_0662 a rdfs:Class ;
rdfs:label "imex-primary" ;
rdfs:comment """IMEx primary identifier that is assigned to an experiment record by the database that created the record in the context of IMEx consortium. The identifiers are unique across all member database as they are all generated by a centralized key-assigner.
http://imex.sourceforge.net/""" ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_1239 a rdfs:Class ;
rdfs:label "amino-acid variant" ;
rdfs:comment "A naturally-occuring amino-acid variation to the reference sequence, including polymorphisms, variations between strains, isolates or cultivars, disease-associated mutations and RNA editing events." ;
rdfs:subClassOf obo:MI_1241 .
obo:MI_0170 a rdfs:Class ;
rdfs:label "phosphorylated residue" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00696.""" .
obo:MI_2334 a rdfs:Class ;
rdfs:label "luminescence donor" ;
rdfs:comment "Fluorophore or luminiscence source which emits electromagnetic radiation of given wavelength." ;
rdfs:subClassOf obo:MI_0495 .
obo:MI_0673 a rdfs:Class ;
rdfs:label "complex synonym" ;
rdfs:comment "Alternative names to describe a complex." ;
rdfs:subClassOf obo:MI_1041 .
obo:MI_0550 a rdfs:Class ;
rdfs:label "gamma-carboxyglutamic acid" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00041.""" .
obo:MI_0273 a rdfs:Class ;
rdfs:label "synthetic growth effect" ;
rdfs:comment """Two silent mutations show altered growth effect when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')""" .
obo:MI_0313 a rdfs:Class ;
rdfs:label "interactor type" ;
rdfs:comment "Molecular species involved in the interaction." ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_1097 a rdfs:Class ;
rdfs:label "uniprot" ;
rdfs:comment "UniProt is a centralized repository of protein sequences with comprehensive coverage and a systematic approach to protein annotation, incorporating, interpreting, integrating and standardizing data from numerous sources and is the most comprehensive catalog of protein sequences and functional annotation." ;
rdfs:subClassOf obo:MI_1096 .
obo:MI_0565 a rdfs:Class ;
rdfs:label "neddylated lysine" ;
rdfs:comment """Residue modification due to a cross-link between a lysine and a glycine from the Nedd8 protein family.
OBSOLETE remap to MOD:01150.""" .
obo:MI_1111 a rdfs:Class ;
rdfs:label "two hybrid bait or prey pooling approach" ;
rdfs:comment "Individual baits are mated against pools of preys, or pools of baits are mated against individual preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners." ;
rdfs:subClassOf obo:MI_0398 .
obo:MI_0628 a rdfs:Class ;
rdfs:label "validation regular expression" ;
rdfs:comment "Regular Expression used to check the validity of cross references' identifier. Attribute generally associated to terms in Cv Database." ;
rdfs:subClassOf obo:MI_0667 .
obo:MI_1306 a rdfs:Class ;
rdfs:label "open set" ;
rdfs:comment "A group of interactors that can be counted in principle but not in practice, such as mRNA or long-chain fatty acid. Examples - ceruloplasmin mRNA, palmitic acid." ;
rdfs:subClassOf obo:MI_1304 .
obo:MI_2161 a rdfs:Class ;
rdfs:label "experimental logs" ;
rdfs:comment "Experimental derived value for the solubility of a molecule in a given solvant." ;
rdfs:subClassOf obo:MI_2160 .
obo:MI_1346 a rdfs:Class ;
rdfs:label "bmrb" ;
rdfs:comment "Database for NMR spectroscopy information on biomolecules hosted at the University of Wisconsin, Madison, US." ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_1267 a rdfs:Class ;
rdfs:label "nub" ;
rdfs:comment "N-terminal ubiquitin moiety (nub, residues 1-34)." ;
rdfs:subClassOf obo:MI_1265 .
obo:MI_0216 a rdfs:Class ;
rdfs:label "palmitoylation reaction" ;
rdfs:comment "Covalent attachment of palmitic acid to the cysteine residues of membrane proteins. Reversible reaction that can affect C,K,T or S residues." ;
rdfs:subClassOf obo:MI_0211 .
obo:MI_0543 a rdfs:Class ;
rdfs:label "gpi-anchor amidated cysteine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00169.""" .
obo:MI_0644 a rdfs:Class ;
rdfs:label "km" ;
rdfs:comment "Michaelis-Menten constant: concentration of substrate at which the reaction rate is equal to half the maximal rate (i.e. Km={s} when Vo=1/2Vmax). Unit Molar." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0249 a rdfs:Class ;
rdfs:label "huge" ;
rdfs:comment """A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project.
http://www.kazusa.or.jp/huge/""" ;
rdfs:subClassOf obo:MI_0683 .
obo:MI_0110 a rdfs:Class ;
rdfs:label "text mining" ;
rdfs:comment "Text mining methods can be used to predict or confirm interactions by automated processing of scientific literature. Co-occurrence in the same sentence of an abstract of gene products labels are analysed to evaluate whether it represents a valid evidence of an interaction." ;
rdfs:subClassOf obo:MI_0046 .
obo:MI_1139 a rdfs:Class ;
rdfs:label "carboxylation reaction" ;
rdfs:comment "Carboxylation is a posttranslational modification of glutamate residues, to gamma-carboxyglutamate, in proteins." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_2294 a rdfs:Class ;
rdfs:label "5' range" ;
rdfs:comment "Term describing the upstream region of a nucleotide sequence, exact coordinates not available." ;
rdfs:subClassOf obo:MI_0333 .
obo:MI_0633 a rdfs:Class ;
rdfs:label "data-processing" ;
rdfs:comment "Information about how the data was processed. This attribute is used mainly for large scale experiment." ;
rdfs:subClassOf obo:MI_0665 .
obo:MI_0942 a rdfs:Class ;
rdfs:label "uniprot taxonomy" ;
rdfs:comment """Based on NCBO Taxonomy but adapted for UniProt
http://www.uniprot.org/taxonomy/""" ;
rdfs:subClassOf obo:MI_0473 .
obo:MI_0931 a rdfs:Class ;
rdfs:label "genetic interaction defined by inequality" ;
rdfs:comment "Two genes A and B present an genetic interaction defined by inequality if the phenotypes of the two single mutants a and b, the double mutant ab and the wild-type WT can be measured quantitatively and described relative to each other by an inequality relationship." .
obo:MI_0970 a rdfs:Class ;
rdfs:label "inchi key" ;
rdfs:comment "InChIKeys consist of 14 characters resulting from a hash of the connectivity information of the InChI, followed by a hyphen, followed by 9 characters resulting from a hash of the remaining layers of the InChI, followed by a single character indication the version of InChI used, another hyphen, followed by single checksum character" ;
rdfs:subClassOf obo:MI_1212 , obo:MI_2091 .
obo:MI_2116 a rdfs:Class ;
rdfs:label "cell permeability" ;
rdfs:comment "The permitting or activating of the passage of substances into, out of, or through cells." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0903 a rdfs:Class ;
rdfs:label "mpidb" ;
rdfs:comment "The microbial protein-protein interactions database (MPDIB) aims to collect and provide all known physical prokaryotic interactions. Note as of 2013, this database is no longer active, but all IMEx curation was imported and is now maintained by the IntAct database (www.ebi.ac.uk/intact)." ;
rdfs:subClassOf obo:MI_0461 , obo:MI_0973 .
obo:MI_1296 a rdfs:Class ;
rdfs:label "amino acid analysis" ;
rdfs:comment "The presence of particular residues,for example those altered through post-translational modification, can be identified by amino acid analysis. Popular techniques for this include mass spectrometry or residue-specific antibodies." ;
rdfs:subClassOf obo:MI_0659 .
obo:MI_2440 a rdfs:Class ;
rdfs:label "antibody" ;
rdfs:comment """An immunoglobulin molecule having a specific amino acid sequence that gives each antibody the ability to adhere to and interact with the antigen that induced its synthesis and with molecules containing structures similar to that antigen.
http://purl.obolibrary.org/obo/XCO_0000194""" ;
rdfs:subClassOf obo:MI_0315 , obo:MI_0326 .
obo:MI_0155 a rdfs:Class ;
rdfs:label "n-myristoyl-glycine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00068.""" .
obo:MI_0404 a rdfs:Class ;
rdfs:label "comigration in non denaturing gel electrophoresis" ;
rdfs:comment "A method allowing the detection of strong interactions between two or more molecules as running, all of them, within a single band in a non-denaturing gel." ;
rdfs:subClassOf obo:MI_0807 .
obo:MI_1335 a rdfs:Class ;
rdfs:label "hpidb" ;
rdfs:comment """Host-pathogen database. HPIDB integrates experimental PPIs from several public databases into a single, non-redundant web accessible resource. Manual curation is performed via the IntAct (ww.ebi.ac.uk/intact) curation interface.
http://www.agbase.msstate.edu/hpi/main.html""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0491 a rdfs:Class ;
rdfs:label "in silico" ;
rdfs:comment """Results generated by predictive bioinformatics approaches rather than experimental data.
OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.""" .
obo:MI_0738 a rdfs:Class ;
rdfs:label "pride" ;
rdfs:comment """PRIDE is a public repository of protein and peptide identifications for the proteomics community.
http://www.ebi.ac.uk/pride/""" ;
rdfs:subClassOf obo:MI_0737 .
obo:MI_0036 a rdfs:Class ;
rdfs:label "domain fusion" ;
rdfs:comment "The rosetta stone, or domain fusion procedure, is based on the assumption that proteins whose homologues in other organisms happen to be fused into a single protein chain are likely to interact or to be functionally related." ;
rdfs:subClassOf obo:MI_0058 , obo:MI_0101 .
obo:MI_0126 a rdfs:Class ;
rdfs:label "n-acetyl-cysteine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00052.""" .
obo:MI_0496 a rdfs:Class ;
rdfs:label "bait" ;
rdfs:comment "Molecule experimentally treated to capture its interacting partners." ;
rdfs:subClassOf obo:MI_0495 .
obo:MI_0883 a rdfs:Class ;
rdfs:label "gtpase reaction" ;
rdfs:comment "Catalysis of the hydrolisis of GTP+ H2O = GDP + phosphate." ;
rdfs:subClassOf obo:MI_0881 .
obo:MI_0469 a rdfs:Class ;
rdfs:label "intact" ;
rdfs:comment """INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions.
http://www.ebi.ac.uk/intact""" ;
rdfs:subClassOf obo:MI_0461 , obo:MI_0973 .
obo:MI_0864 a rdfs:Class ;
rdfs:label "brenda" ;
rdfs:comment """A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.
http://www.brenda-enzymes.info""" ;
rdfs:subClassOf obo:MI_0473 .
obo:MI_1002 a rdfs:Class ;
rdfs:label "myristoylase assay" ;
rdfs:comment "Measurement of the irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid." ;
rdfs:subClassOf obo:MI_1001 .
obo:MI_0115 a rdfs:Class ;
rdfs:label "yeast display" ;
rdfs:comment "The proteins are displayed on the surface of the yeast S. cerevisiae by fusion to signal sequences for protein secretion. This method is limited by the low efficiency of the yeast display system but can take full advantage of exploiting cell sorting methods (FACS) to isolate cells that display molecules with desired binding properties." ;
rdfs:subClassOf obo:MI_0034 , obo:MI_0054 .
obo:MI_0262 a rdfs:Class ;
rdfs:label "suppression mutation" ;
rdfs:comment """A given (suppressed) mutation phenotype is reverted by a supressor gene mutation.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'mutated gene' MI:0804. """ .
obo:MI_0803 a rdfs:Class ;
rdfs:label "expression level alteration" ;
rdfs:comment "Synthesis rate of a molecule under investigation differs from its naturally occurring expression level in a cell." ;
rdfs:subClassOf obo:MI_0787 .
obo:MI_0436 a rdfs:Class ;
rdfs:label "protein footprinting" ;
rdfs:comment "Protein footprinting is a technique for identifying structural changes modulated by protein-ligand binding, and mapping protein-ligand interfaces This technique involves attaching cutting reagents randomly to amino acid residue (e.g. lysine or cysteine) on the proteins surface and then using this lysine-labelled protein to cleave polypeptide backbone of the other protein at exposed residues adjacent to its binding site." ;
rdfs:subClassOf obo:MI_0659 .
obo:MI_0166 a rdfs:Class ;
rdfs:label "n6,n6-dimethyl-lysine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00084.""" .
obo:MI_2130 a rdfs:Class ;
rdfs:label "cyp-450 inhibition" ;
rdfs:comment "Inhibitor of one or more of the family of cytochrome p450 enzymes, probably the most important elements of oxidative metabolism of exogenous compounds." ;
rdfs:subClassOf obo:MI_2135 .
obo:MI_0302 a rdfs:Class ;
rdfs:label "gene name synonym" ;
rdfs:comment "Gene name synonym." ;
rdfs:subClassOf obo:MI_1041 .
obo:MI_2374 a rdfs:Class ;
rdfs:label "phenotypic suppression (sensu BioGRID)" ;
rdfs:comment "Genetic perturbation of one gene suppresses a phenotype (other than lethality or growth defect) associated with perturbation of another gene." ;
rdfs:subClassOf obo:MI_2379 .
obo:MI_1122 a rdfs:Class ;
rdfs:label "neYFP" ;
rdfs:comment "n-terminal fragment of enhanced yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC)." ;
rdfs:subClassOf obo:MI_1118 .
obo:MI_0823 a rdfs:Class ;
rdfs:label "predetermined feature" ;
rdfs:comment "Feature detection not verified in the context of an experiment but assumed from external or previous experimental evidence(s)." ;
rdfs:subClassOf obo:MI_0093 , obo:MI_0427 , obo:MI_0659 .
obo:MI_0707 a rdfs:Class ;
rdfs:label "anti tag immunostaining" ;
rdfs:comment "Immunostaining assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient antibodies are available. The anti tag antibody may be either monoclonal or polyclonal." ;
rdfs:subClassOf obo:MI_0422 .
obo:MI_0916 a rdfs:Class ;
rdfs:label "lexa vp16 complementation" ;
rdfs:comment "Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) that can specifically activate transcription of a reporter gene located downstream." ;
rdfs:subClassOf obo:MI_0018 .
obo:MI_0340 a rdfs:Class ;
rdfs:label "n-terminal position" ;
rdfs:comment "Term describing the first amino acid of a peptide chain." ;
rdfs:subClassOf obo:MI_0333 .
obo:MI_0104 a rdfs:Class ;
rdfs:label "static light scattering" ;
rdfs:comment "In static light scattering, the average intensity of scattered light at multiple angles is measured. The data yield information on particle molecular weight, particle size and shape, and particle-particle interactions." ;
rdfs:subClassOf obo:MI_0067 .
obo:MI_2363 a rdfs:Class ;
rdfs:label "in tag" ;
rdfs:comment "Intein N-terminal fragment tag, commonly used in SIMPL and related methods." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_1058 a rdfs:Class ;
rdfs:label "imported" ;
rdfs:comment "The data has been imported into the database form an external resource." ;
rdfs:subClassOf obo:MI_1053 .
obo:MI_1024 a rdfs:Class ;
rdfs:label "scanning electron microscopy" ;
rdfs:comment "A type of electron microscope that images the sample surface by scanning it with a high-energy beam of electrons in a raster scan pattern. The electrons interact with the atoms that make up the sample producing signals that contain information about the sample's surface topography, composition and other properties such as electrical conductivity." ;
rdfs:subClassOf obo:MI_0040 .
obo:MI_1278 a rdfs:Class ;
rdfs:label "mutual genetic enhancement (sensu unexpected)" ;
rdfs:comment """An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is more severe/penetrant (further from wild type) than expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab < a* <= b < wt [E = a*]
OR
wt < b <= a* < ab [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1271 , obo:MI_2401 .
obo:MI_0177 a rdfs:Class ;
rdfs:label "o-phospho-threonine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00047.""" .
obo:MI_0137 a rdfs:Class ;
rdfs:label "n-acetyl-proline" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00059.""" .
obo:MI_1354 a rdfs:Class ;
rdfs:label "lipase assay" ;
rdfs:comment "Cleavage (hydrolysis) of a lipid molecule." ;
rdfs:subClassOf obo:MI_0990 .
obo:MI_0609 a rdfs:Class ;
rdfs:label "small nucleolar rna" ;
rdfs:comment "The small nucleolar RNAs, are stable RNA contained in the nucleoli and these RNAs exist as snoRNA: protein complexes called snoRNPs (also called 'snorps'). The snoRNPs function is in the maturation of ribosomal RNA and other RNAs, by: creating two types of modified nucleotides, (2'-O-methylated nucleotides and pseudouridine), and mediating endonucleolytic cleavages of pre-rRNA." ;
rdfs:subClassOf obo:MI_0320 .
obo:MI_0622 a rdfs:Class ;
rdfs:label "confidence-mapping" ;
rdfs:comment "Description of confidence assessment method generally associated to the experiment." ;
rdfs:subClassOf obo:MI_0665 .
obo:MI_0936 a rdfs:Class ;
rdfs:label "emdb" ;
rdfs:comment """The Electron Microscopy Data Bank (EMDB) contains experimentally determined three-dimensional maps and associated experimental data and files.
https://www.ebi.ac.uk/emdb""" ;
rdfs:subClassOf obo:MI_0472 .
obo:MI_0025 a rdfs:Class ;
rdfs:label "copurification" ;
rdfs:comment """Approaches designed to separate cell components on the basis of their physicochemical properties. The observation that two or more proteins copurify in one or several conditions is taken as an indication that they form a molecular complex.
OBSOLETE since too non-specific. Consider use of cosedimentation (MI:0027) or comigration in non denaturing gel electrophoresis (MI:0404) or affinity chromatography technologies (MI:0004) or molecular sieving (MI:0071) or for unspecific cases biochemical (MI:0401).""" .
obo:MI_2323 a rdfs:Class ;
rdfs:label "kiss" ;
rdfs:comment "KISS (KInase Substrate Sensor) is a protein complementation technology that allows in situ analysis of protein-protein interactions in intact mammalian cells. In this method, which is derived from MAPPIT (mammalian protein-protein interaction trap), the bait protein is coupled to the kinase domain of TYK2, while the prey protein is fused to a fragment of the gp130 cytokine receptor chain. Bait and prey interaction leads to phosphorylation of the gp130 anchor by TYK2, followed by recruitment and activation of STAT3, resulting in transcription of a STAT3-dependent reporter system. This approach enables the identification of interactions between proteins, including transmembrane and cytosolic proteins, and their modulation in response to physiological or pharmacological challenges." ;
rdfs:subClassOf obo:MI_0090 .
obo:MI_1082 a rdfs:Class ;
rdfs:label "zfin" ;
rdfs:comment "Extensive information on Danio rerio, including genomics databases, developmental stages, publications and molecular tools." ;
rdfs:subClassOf obo:MI_1094 .
obo:MI_1228 a rdfs:Class ;
rdfs:label "pyo tag" ;
rdfs:comment "A polyoma virus-derived (Pyo) epitope tag (amino acids MEYMPME)." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_0655 a rdfs:Class ;
rdfs:label "lambda repressor two hybrid" ;
rdfs:comment "A protein of interest (the bait) is fused to the full-length bacteriophage lambda repressor protein (lambdacI, 237 amino acids), containing the amino terminal DNA-binding domain and the carboxylterminal dimerization domain. The corresponding target (prey) protein is fused to the N-terminal domain of the alfa-subunit of RNA polymerase (248 amino acids). The bait is tethered to the lambda operator sequence upstream of the reporter promoter through the DNA-binding domain of lambdacI. When the bait and prey interact, they recruit and stabilize the binding of RNA polymerase at the promoter and activate the transcription of the HIS3 reporter gene. Due to the tendency of both the lambda repressor protein and the N-terminal domain of the alfa-subunit of RNA polymerase to dimerize, this system might not be optimal for the analysis of proteins that self-associate unless their interaction with other protein partners depends on the oligomerization." ;
rdfs:subClassOf obo:MI_0232 .
obo:MI_0425 a rdfs:Class ;
rdfs:label "kinase scintillation proximity assay" ;
rdfs:comment "Relies on the radiolabelling of a peptide substrate immobilized on a scintillant coated SPA-bead. The kinase transfers a phosphate isotope from the nucleotide to the substrate." ;
rdfs:subClassOf obo:MI_0099 , obo:MI_0424 .
obo:MI_0920 a rdfs:Class ;
rdfs:label "ribonuclease assay" ;
rdfs:comment "Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of RNA." ;
rdfs:subClassOf obo:MI_1034 .
obo:MI_0953 a rdfs:Class ;
rdfs:label "polymerization" ;
rdfs:comment "Interaction inferred by monitoring polymerization/depolymerization of an interactor" ;
rdfs:subClassOf obo:MI_0401 .
obo:MI_0914 a rdfs:Class ;
rdfs:label "association" ;
rdfs:comment "Interaction between molecules that may participate in formation of one, but possibly more, physical complexes. Often describes a set of molecules that are co-purified in a single pull-down or coimmunoprecipitation but might participate in formation of distinct physical complexes sharing a common bait." ;
rdfs:subClassOf obo:MI_2232 .
obo:MI_2339 a rdfs:Class ;
rdfs:label "electron microscopy 3D single particle reconstruction" ;
rdfs:comment "Three-dimensional (3D) reconstruction of single, transparent objects from a collection of images of randomly oriented particles recorded with a transmission electron microscope." ;
rdfs:subClassOf obo:MI_0410 .
obo:MI_0415 a rdfs:Class ;
rdfs:label "enzymatic study" ;
rdfs:comment "Participants are enzyme or substrate in a biochemical reaction." ;
rdfs:subClassOf obo:MI_0401 .
obo:MI_0576 a rdfs:Class ;
rdfs:label "structural proximity" ;
rdfs:comment "Method to identify domain-domain interactions within the same resolved structure. Domains are first projected onto a pdb structure and then the distance between all pairs of residues in different domains are calculated. When the distance between 2 residues is below the non covalent bond threshold, the corresponding pair of domains is predicted to interact." ;
rdfs:subClassOf obo:MI_0577 .
obo:MI_0905 a rdfs:Class ;
rdfs:label "amplified luminescent proximity homogeneous assay" ;
rdfs:comment "AlphaScreen relies on the use of Donor and Acceptor beads that are coated with a layer of hydrogel providing functional groups for bioconjugation. When a biological interaction between molecules brings the beads into proximity, a cascade of chemical reactions is initiated to produce a greatly amplified signal. Upon laser excitation, a photosensitizer in the Donor bead converts ambient oxygen to a more excited singlet state. The singlet state oxygen molecules diffuse across to react with a chemiluminescer in the Acceptor bead that further activates fluorophores contained within the same bead. The fluorophores subsequently emit light at 520-620 nm. In the absence of a specific biological interaction, the singlet state oxygen molecules produced by the Donor bead go undetected without the close proximity of the Acceptor bead. AlphaScreen has successfully been developed for enzyme assays (kinase, helicase, protease, ...), interaction assays (ligand/receptor, protein/protein, protein/DNA), immunoassays, and GPCR functional assays (cAMP, IP3)." ;
rdfs:subClassOf obo:MI_0051 .
obo:MI_0615 a rdfs:Class ;
rdfs:label "search-url" ;
rdfs:comment "Search engine URL associated to Cv Database terms." ;
rdfs:subClassOf obo:MI_0667 .
obo:MI_1289 a rdfs:Class ;
rdfs:label "obsolete phenotype bias" ;
rdfs:comment """OBSOLETE: An effect when two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is intermediate to the individual mutant phenotypes, but greater or less than wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a < wt < b) AND (a < ab < b) AND (ab != wt)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" .
obo:MI_0420 a rdfs:Class ;
rdfs:label "kinase homogeneous time resolved fluorescence" ;
rdfs:comment "Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being added from close proximity on the phosphorylated substrate due to the action of the kinase." ;
rdfs:subClassOf obo:MI_0424 , obo:MI_0510 .
obo:MI_0793 a rdfs:Class ;
rdfs:label "amorph" ;
rdfs:comment "The gene function has been abolished by mutation, though the type of mutation is not known." ;
rdfs:subClassOf obo:MI_0787 .
obo:MI_1162 a rdfs:Class ;
rdfs:label "allosteric k-type response" ;
rdfs:comment "An allosteric response in which the affinity of a molecule is altered." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_1161 .
obo:MI_0412 a rdfs:Class ;
rdfs:label "electrophoretic mobility supershift assay" ;
rdfs:comment "The EMSA supershift is a EMSA experiment carried out using a third lane loaded with the radiolabeled nucleic acid, a protein mixture and an antibody for a specific protein. If an extra retardation is observed, this is due to the formation of a larger complex including the antibody. By this approach, at least one protein of the complex is directly identified." ;
rdfs:subClassOf obo:MI_0413 .
obo:MI_1197 a rdfs:Class ;
rdfs:label "radioimmunoassay" ;
rdfs:comment "To perform a radioimmunoassay, a known quantity of an antigen is made radioactive, frequently by labeling it with gamma-radioactive isotopes of iodine attached to tyrosine. This radiolabeled antigen is then mixed with a known amount of antibody for that antigen, and as a result, the two chemically bind to one another. Then, a sample containing an unknown quantity of that same antigen is added. This causes the unlabeled (or \"cold\") antigen from the serum to compete with the radiolabeled antigen (\"hot\") for antibody binding sites. As the concentration of \"cold\" antigen is increased, more of it binds to the antibody, displacing the radiolabeled variant, and reducing the ratio of antibody-bound radiolabeled antigen to free radiolabeled antigen. The bound antigens are then separated from the unbound ones, and the radioactivity of the free antigen remaining in the supernatant is measured." ;
rdfs:subClassOf obo:MI_0421 .
obo:MI_0875 a rdfs:Class ;
rdfs:label "dataset" ;
rdfs:comment "Targeted curation dataset grouping experiments by topic or dataset origin." ;
rdfs:subClassOf obo:MI_1093 .
obo:MI_2165 a rdfs:Class ;
rdfs:label "bar" ;
rdfs:comment "The Arabidopsis Interactions Viewer of BAR (the Bio-Array Resource for plant biology) queries a database of 70944 predicted and 28556 confirmed Arabidopsis interacting proteins. The predicted interactions (interologs) were generated by Drs Matt Geisler and Jane Geisler-Lee at the Southern Illinois University. Their current version is Interactome 2.0. The confirmed Arabidopsis interacting proteins come from BIND, the Biomolecular Interaction Network Database, from high-density Arabidopsis protein microarrays, from Braun et al.'s Arabidopsis Interactome 2011 , from Wolf Frommer's Membrane protein INteractome Database MIND, from Etsuko Moryiama's Arabidopsis G-signaling Interactome Database, and over 1190 other literature sources. The interactions in BIND were identified using several different methods, such as yeast two hybrid screens, but also via traditional biochemical methods. http://bar.utoronto.ca/interactions/cgi-bin/arabidopsis_interactions_viewer.cgi\" [PMID:15960624]" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0834 a rdfs:Class ;
rdfs:label "ka" ;
rdfs:comment "Association rate constant or rate of complex formation. Unit MOLE per SECOND (M-1 s-1)" ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0695 a rdfs:Class ;
rdfs:label "sandwich immunoassay" ;
rdfs:comment "Antibody array where proteins retained by the arrayed antibodies are identified using a detector antibody. The detector antibody is either modified with a directly detectable label (enzyme, fluorescent molecule, isotope, etc.), or it is biotinylated for detection after subsequent probing with labeled streptavidin." ;
rdfs:subClassOf obo:MI_0678 .
obo:MI_1017 a rdfs:Class ;
rdfs:label "rna immunoprecipitation" ;
rdfs:comment "Proteins are crosslinked to nucleic acids, for example by the addition of formaldehyde. RNA sequences that cross-link with a given protein are isolated by immunoprecipitation of the protein, and reversal of the cross-linking permits recovery and quantitative analysis of the immunoprecipitated RNA by reverse transcription PCR." ;
rdfs:subClassOf obo:MI_0019 .
obo:MI_2149 a rdfs:Class ;
rdfs:label "withdrawn drug" ;
rdfs:comment "A drug for which the licencing for prescriptive use has been withdrawn." ;
rdfs:subClassOf obo:MI_2040 .
obo:MI_0205 a rdfs:Class ;
rdfs:label "disaggregation" ;
rdfs:comment """Dissociation of partners interacting via non-covalent bond.
OBSOLETE because considered misleading.""" .
obo:MI_0733 a rdfs:Class ;
rdfs:label "cyan fluorescent protein tag" ;
rdfs:comment "The cyan fluorescent protein derived from Anthozoa reef coral can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native." ;
rdfs:subClassOf obo:MI_0687 .
obo:MI_2230 a rdfs:Class ;
rdfs:label "nucleicacid-nucleicacid" ;
rdfs:comment "Interaction between a nucleic acid and a corresponding nucleic acid." ;
rdfs:subClassOf obo:MI_1046 .
obo:MI_0925 a rdfs:Class ;
rdfs:label "observed-ptm" ;
rdfs:comment "Post translational modification observed on a protein in the context of an interaction." ;
rdfs:subClassOf obo:MI_0668 .
obo:MI_0639 a rdfs:Class ;
rdfs:label "resulting-ptm" ;
rdfs:comment "Post translational modification occurs subsequently to an interaction." ;
rdfs:subClassOf obo:MI_0925 .
obo:MI_1137 a rdfs:Class ;
rdfs:label "carboxylation assay" ;
rdfs:comment "The measurement of a the introduction of a carboxylic acid group into a substrate." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0401 a rdfs:Class ;
rdfs:label "biochemical" ;
rdfs:comment "The application of chemical principles and methods to biological experiments to demonstrate an interaction." ;
rdfs:subClassOf obo:MI_0045 .
obo:MI_1192 a rdfs:Class ;
rdfs:label "antisense oligonucleotides" ;
rdfs:comment "This approach is based on the observation that a synthesized nucleic acid that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation." ;
rdfs:subClassOf obo:MI_0255 .
obo:MI_0554 a rdfs:Class ;
rdfs:label "sumoylated lysine" ;
rdfs:comment """Residue modification due to a cross-link between a lysine and a glycine from the sumo (Small Ubiquitin-related MOdifier) protein.
OBSOLETE remap to MOD:01149.""" .
obo:MI_0390 a rdfs:Class ;
rdfs:label "alexa 568 label" ;
rdfs:comment "Alexa fluorescent dye analogue to Rhodamine Red-X with an approximate excitation wavelength maximum of 568nm." ;
rdfs:subClassOf obo:MI_0384 .
obo:MI_2390 a rdfs:Class ;
rdfs:label "transphenotypic genetic suppression" ;
rdfs:comment "A genetic mutual suppression in which each genetic perturbation results in opposite phenotypes (for example, one genetic perturbation results in an increased quality phenotype and the second genetic perturbation results in a decreased quality phenotype), and their combination (the double genetic perturbation) results in an intermediate phenotype that is at least closer to wild type than the most severe phenotype of the individual genetic perturbations. Note that the double genetic perturbation phenotype may be expected according to some chosen neutrality function." ;
rdfs:subClassOf obo:MI_2387 , obo:MI_2389 .
obo:MI_2284 a rdfs:Class ;
rdfs:label "complex component" ;
rdfs:comment "Indicates that the cross-referenced molecule is a component of a containing complex." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_2187 a rdfs:Class ;
rdfs:label "ri" ;
rdfs:comment """The Roslin Institute uses the Gene Ontology to add functional annotation to different gene products.
http://www.roslin.ac.uk/""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0339 a rdfs:Class ;
rdfs:label "undetermined sequence position" ;
rdfs:comment "Term describing a completely unknown or unspecified sequence position." ;
rdfs:subClassOf obo:MI_0333 .
obo:MI_2379 a rdfs:Class ;
rdfs:label "genetic suppression" ;
rdfs:comment "A genetic phenotype modification whereby one genetic perturbation suppresses, or alleviates, the phenotype of another genetic perturbation. Note that if the individual genetic perturbations have opposite phenotypes, this may be an expected result." ;
rdfs:subClassOf obo:MI_2367 .
obo:MI_0711 a rdfs:Class ;
rdfs:label "nucleic acid electroporation" ;
rdfs:comment "Electroporation, or electropermeabilization, is a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance inside the cell, such as loading it with a molecular probe, a drug that can change cell's function, or a piece of coding DNA." ;
rdfs:subClassOf obo:MI_0308 , obo:MI_0704 .
obo:MI_2431 a rdfs:Class ;
rdfs:label "biotin ligase tag" ;
rdfs:comment "Biotin ligase tags that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_1256 a rdfs:Class ;
rdfs:label "luminscent dye label" ;
rdfs:comment "Luminescent dyes such as cyanines,commonly used for DNA labelling." ;
rdfs:subClassOf obo:MI_0373 .
obo:MI_0975 a rdfs:Class ;
rdfs:label "fc-igg tag" ;
rdfs:comment "A fusion protein tag consisting of a portion of the constant region of IgG." ;
rdfs:subClassOf obo:MI_0240 .
obo:MI_0463 a rdfs:Class ;
rdfs:label "biogrid" ;
rdfs:comment """The General Repository for Interaction Datasets (BioGRID) is a database of genetic and physical interactions.
http://thebiogrid.org""" ;
rdfs:subClassOf obo:MI_0461 , obo:MI_0489 .
obo:MI_0927 a rdfs:Class ;
rdfs:label "iaedans label" ;
rdfs:comment "IAEDANS is fluorescent tag that bind to cysteines. IAEDANS is the acronyme of (5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid) with free SH groups." ;
rdfs:subClassOf obo:MI_0857 .
obo:MI_1035 a rdfs:Class ;
rdfs:label "deoxyribonuclease assay" ;
rdfs:comment "Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of DNA." ;
rdfs:subClassOf obo:MI_1034 .
obo:MI_2299 a rdfs:Class ;
rdfs:label "carbohydrate chemical modification decreasing interaction" ;
rdfs:comment "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate." ;
rdfs:subClassOf obo:MI_2276 .
obo:MI_2350 a rdfs:Class ;
rdfs:label "empiar" ;
rdfs:comment """EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. The purpose of EMPIAR is to provide easy access to state-of-the-art raw data to facilitate methods development and validation, which will lead to better 3D structures. It complements the Electron Microscopy Data Bank (EMDB), where 3D volumes are stored, and uses the fault-tolerant Aspera platform for data transfers.
https://www.ebi.ac.uk/empiar""" ;
rdfs:subClassOf obo:MI_0936 .
obo:MI_2223 a rdfs:Class ;
rdfs:label "inference by quantitative co-purification" ;
rdfs:comment "This method measures co-purification of proteins through several orthogonal purification steps, deriving a set of correlation measures that are then computationally weighted and combined to infer interacting pairs." ;
rdfs:subClassOf obo:MI_0363 .
obo:MI_2420 a rdfs:Class ;
rdfs:label "ensemblprotists" ;
rdfs:comment "Ensembl Protists is a browser for protist genomes. https://protists.ensembl.org/" ;
rdfs:subClassOf obo:MI_1013 .
obo:MI_2445 a rdfs:Class ;
rdfs:label "alphafold" ;
rdfs:comment """AlphaFold DB is an open-access database of more than 200 million predicted protein structures. The predictions are generated by AlphaFold, system that estimates a protein's 3D structure from its amino acid sequence. In many cases, its predictions are comparable in accuracy to experimentally determined structures.
https://alphafold.ebi.ac.uk/""" ;
rdfs:subClassOf obo:MI_0489 .
obo:MI_0442 a rdfs:Class ;
rdfs:label "sufficient binding region" ;
rdfs:comment "Binding will occur when this sequence range is present within a molecule or part of a molecule. This region will contain the direct binding region but may be longer." ;
rdfs:subClassOf obo:MI_0117 .
obo:MI_0808 a rdfs:Class ;
rdfs:label "comigration in sds page" ;
rdfs:comment "A method allowing the detection of strong interactions between two or more molecules as running, all of them, within a single band in a denaturing gel." ;
rdfs:subClassOf obo:MI_0807 .
obo:MI_2300 a rdfs:Class ;
rdfs:label "carbohydrate chemical modification decreasing interaction rate" ;
rdfs:comment "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate." ;
rdfs:subClassOf obo:MI_2299 .
obo:MI_0306 a rdfs:Class ;
rdfs:label "open reading frame name" ;
rdfs:comment "A name temporarily attributed by a sequencing project to an open reading frame. This name is generally based on a cosmid numbering system." ;
rdfs:subClassOf obo:MI_1041 .
obo:MI_1280 a rdfs:Class ;
rdfs:label "cisphenotypic genetic suppression" ;
rdfs:comment """An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a* <= b < wt) AND (a* < ab <= wt) [E = a*]
OR
(wt < b <= a*) AND (wt <= ab < a*) [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0796 , obo:MI_2385 , obo:MI_2389 .
obo:MI_0362 a rdfs:Class ;
rdfs:label "inference" ;
rdfs:comment "Evidence based on human assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences." ;
rdfs:subClassOf obo:MI_0001 , obo:MI_0002 , obo:MI_0003 .
obo:MI_1223 a rdfs:Class ;
rdfs:label "ptm decreasing an interaction" ;
rdfs:comment "Post translational modification on a protein observed to decrease the strength or rate of an interaction." ;
rdfs:subClassOf obo:MI_0925 .
obo:MI_2306 a rdfs:Class ;
rdfs:label "carbohydrate chemical modification increasing interaction strength" ;
rdfs:comment "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction strength when compared with the unaltered carbohydrate." ;
rdfs:subClassOf obo:MI_2305 .
obo:MI_1181 a rdfs:Class ;
rdfs:label "paired end tags sequence identification" ;
rdfs:comment "Paired-end tags (PET) are the short sequences at the 5 prime and 3 prime ends of the DNA fragment of interest, which can be a piece of genomic DNA or cDNA." ;
rdfs:subClassOf obo:MI_1180 .
obo:MI_2438 a rdfs:Class ;
rdfs:label "iedb" ;
rdfs:comment """The Immune Epitope Database (IEDB) catalogs experimental data on antibody and T cell epitopes studied in humans and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation.
https://www.iedb.org""" ;
rdfs:subClassOf obo:MI_0447 .
obo:MI_0623 a rdfs:Class ;
rdfs:label "inhibition" ;
rdfs:comment "The interaction between the proteins or the formation of a complex is disrupted by a biological molecule or by a modification of the interactors." ;
rdfs:subClassOf obo:MI_0664 .
obo:MI_0260 a rdfs:Class ;
rdfs:label "inhibitor small molecules" ;
rdfs:comment """Protein activity is inhibited by small inorganic molecules (drugs) that specifically bind to their targets. Recently this classical pharmacological approach is sometime referred to as 'chemical genetics'.
OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).""" .
obo:MI_0032 a rdfs:Class ;
rdfs:label "de novo protein sequencing by mass spectrometry" ;
rdfs:comment "The strategy to determine the complete amino acid sequence of a protein by mass spectrometry relies on the generation of a nested set of fragments differing by one amino acid. This reveals the identity of the residue that has been removed at each degradation step by measuring the mass difference of fragments differing of one residue. Peptide fragments can be obtained by protease treatment combined with the fragmentation promoted by collision (or other methods) within a tandem mass spectrometer. This approach can be carried out with LC MS/MS (Liquid Chromatography Tandem Mass Spectrometry), nanoESI MS/MS (nanoElectrospray Ionisation tandem mass spectrometry), or FTMS (Fourier Transform mass spectrometry) instruments." ;
rdfs:subClassOf obo:MI_0093 , obo:MI_0427 , obo:MI_0659 .
obo:MI_0093 a rdfs:Class ;
rdfs:label "protein sequence identification" ;
rdfs:comment "Single amino acid identification along a protein sequence." ;
rdfs:subClassOf obo:MI_0661 .
obo:MI_0992 a rdfs:Class ;
rdfs:label "defarnesylase assay" ;
rdfs:comment "Measures the removal of S-farnesyl-L-cysteined, which is cleaved and returns a C residue." ;
rdfs:subClassOf obo:MI_0991 .
obo:MI_2141 a rdfs:Class ;
rdfs:label "hepatotoxicity" ;
rdfs:comment "Tendency of a bioactive entity to affect liver function." ;
rdfs:subClassOf obo:MI_2135 .
obo:MI_2368 a rdfs:Class ;
rdfs:label "phenotypic enhancement (sensu BioGRID)" ;
rdfs:comment "Genetic perturbation of multiple genes in combination that results in a more severe phenotype (except lethality or growth defect) than individual genetic perturbations." ;
rdfs:subClassOf obo:MI_2380 .
obo:MI_2345 a rdfs:Class ;
rdfs:label "pa tag" ;
rdfs:comment "The protein is fused to a 12-residue peptide segment (GVAMPGAEDDVV) derived from human podoplanin PLAG domain for which antibodies are available." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_2209 a rdfs:Class ;
rdfs:label "nucleic acid chemical modification decreasing an interaction" ;
rdfs:comment "Chemical modification observed on a nucleic acid molecule observed to decrease the strength or rate of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition." ;
rdfs:subClassOf obo:MI_2206 .
obo:MI_0159 a rdfs:Class ;
rdfs:label "n,n,n-trimethyl-alanine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00071.""" .
obo:MI_0003 a rdfs:Class ;
rdfs:label "feature detection method" ;
rdfs:comment "Method to determine the features of the proteins involved in the interaction." ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_2385 a rdfs:Class ;
rdfs:label "cisphenotypic phenotype result" ;
rdfs:comment "A phenotype result in which both of two perturbations result in the phenotype in question and do so in the same manner compared to wild type. For example, both perturbations result in an increased quality phenotype, or both perturbations result in a decreased quality phenotype." ;
rdfs:subClassOf obo:MI_2384 .
obo:MI_2311 a rdfs:Class ;
rdfs:label "attached carbohydrate decreasing interaction" ;
rdfs:comment "Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule." ;
rdfs:subClassOf obo:MI_2308 .
obo:MI_0480 a rdfs:Class ;
rdfs:label "omim" ;
rdfs:comment """Online Mendelian Inheritance in Man (OMIM) is a catalogue of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM""" ;
rdfs:subClassOf obo:MI_0683 .
obo:MI_0119 a rdfs:Class ;
rdfs:label "mutation decreasing interaction" ;
rdfs:comment "Region of a molecule whose mutation or deletion decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction)." ;
rdfs:subClassOf obo:MI_0118 .
obo:MI_0802 a rdfs:Class ;
rdfs:label "enhancement interaction" ;
rdfs:comment """The A genetic perturbation enhances the phenotype of the B perturbation, or vice versa (e.g. WT = A < B < AB or WT = B < A < AB). This could be conditional or additive by the above scheme.
OBSOLETE: remap to MI:0933 'negative genetic interaction'""" .
obo:MI_1046 a rdfs:Class ;
rdfs:label "interacting molecules" ;
rdfs:comment "Defines an interaction by the type of binary molecule pairs it can generates." ;
rdfs:subClassOf obo:MI_1045 .
obo:MI_0559 a rdfs:Class ;
rdfs:label "glycosylation reaction" ;
rdfs:comment "The covalent attachment of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Reaction that can affect Ser, Thr, Cys, Arg, and Asn residues. This reaction is known to be reversible in the case of Asn substrate." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0987 a rdfs:Class ;
rdfs:label "rna strand elongation" ;
rdfs:comment "The process by which an RNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent RNA strand." ;
rdfs:subClassOf obo:MI_0986 .
obo:MI_0856 a rdfs:Class ;
rdfs:label "fluorophore" ;
rdfs:comment "A fluorophore is a component of a molecule which causes a molecule to be fluorescent. It is a functional group in a molecule which will absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength. The amount and wavelength of the emitted energy depend on both the fluorophore and the chemical environment of the fluorophore." ;
rdfs:subClassOf obo:MI_0505 .
obo:MI_0043 a rdfs:Class ;
rdfs:label "electron resonance" ;
rdfs:comment "A form of spectroscopy in which the absorption of microwave by a sample in a strong magnetic field is used to study atoms or molecules with unpaired electrons." ;
rdfs:subClassOf obo:MI_0013 , obo:MI_0659 .
obo:MI_0727 a rdfs:Class ;
rdfs:label "lexa b52 complementation" ;
rdfs:comment "Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), E. coli B42 acidic sequence as the activation domain (AD), and two reporters, lacZ and LEU2, each containing upstream LexA binding elements." ;
rdfs:subClassOf obo:MI_0018 .
obo:MI_2317 a rdfs:Class ;
rdfs:label "attached carbohydrate disrupting interaction" ;
rdfs:comment "Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule." ;
rdfs:subClassOf obo:MI_2311 .
obo:MI_0813 a rdfs:Class ;
rdfs:label "proximity ligation assay" ;
rdfs:comment "Upon binding of two proximity probes (usually antibodies conjugated to DNA) to the same target protein complex, the oligonucleotides on the proximity probes are brought close together. These antibody-conjugated oligonucleotides hybridize to two connector oligonucleotides that are ligated to form a circular DNA molecule. This newly formed DNA-molecule can be amplified by rolling circle amplification. The resulting single-stranded DNA-molecule collapses into a bundle, which is detectable through hybridization of fluorescently labeled complementary oligonucleotides." ;
rdfs:subClassOf obo:MI_0400 , obo:MI_0421 .
obo:MI_1217 a rdfs:Class ;
rdfs:label "nGFP" ;
rdfs:comment "n-terminal fragment of green fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC)." ;
rdfs:subClassOf obo:MI_0367 , obo:MI_1215 .
obo:MI_0964 a rdfs:Class ;
rdfs:label "infrared spectroscopy" ;
rdfs:comment "Subset of spectroscopy that deals with the infrared region of the electromagnetic spectrum." ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_1009 a rdfs:Class ;
rdfs:label "desumoylase assay" ;
rdfs:comment "Measurement of the reaction that breaks a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0998 a rdfs:Class ;
rdfs:label "deubiquitinase assay" ;
rdfs:comment "Measures the cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0699 a rdfs:Class ;
rdfs:label "rna directed dna polymerase assay" ;
rdfs:comment "Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time." ;
rdfs:subClassOf obo:MI_0696 .
obo:MI_0561 a rdfs:Class ;
rdfs:label "palmitoylated residue" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00440.""" .
obo:MI_0132 a rdfs:Class ;
rdfs:label "n-acetyl-leucine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00782.""" .
obo:MI_0700 a rdfs:Class ;
rdfs:label "rna directed rna polymerase assay" ;
rdfs:comment "Measures the catalysis of the reaction: nucleoside triphosphate + RNA (n) = diphosphate + RNA (n+1); uses an RNA template." ;
rdfs:subClassOf obo:MI_0696 .
obo:MI_0684 a rdfs:Class ;
rdfs:label "ancillary" ;
rdfs:comment "Molecule required for an observed binary interaction to occur. This molecule may act as stabilizer of any of the interaction partners or may act as a bridge molecule between them but the method does not provide resolution or evidence to demonstrate its actual molecular function (i.e.Mudpit, tri hybrid etc)." ;
rdfs:subClassOf obo:MI_0495 , obo:MI_0500 .
obo:MI_0121 a rdfs:Class ;
rdfs:label "acetylated residue" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00394.""" .
obo:MI_0108 a rdfs:Class ;
rdfs:label "t7 phage display" ;
rdfs:comment "T7 is a double stranded DNA bacteriophage with a thin-walled icosahedral capsid, ~550 Angstrom in diameter, which is decorated by 415 copies of the capsid protein, the product of gene 10. gp10 can tolerate insertions at the carboxyterminus without loosing its ability to be inserted into functional phage capsids. Both low density and high density display (albeit only with short peptides) can be achieved." ;
rdfs:subClassOf obo:MI_0084 .
obo:MI_0796 a rdfs:Class ;
rdfs:label "genetic suppression (sensu unexpected)" ;
rdfs:comment """An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than the most severe phenotype of the original perturbations, in effect making the organism more \"wild type\" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* < ab <= wt [E = a*]
OR
wt <= ab < a* [E = a*]
where 'a*' is the most severe observed phenotype value of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0935 , obo:MI_2379 .
obo:MI_2176 a rdfs:Class ;
rdfs:label "gramene" ;
rdfs:comment """Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species. Gramene currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations.
http://www.gramene.org""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0054 a rdfs:Class ;
rdfs:label "fluorescence-activated cell sorting" ;
rdfs:comment "Cells in suspension flow through a laser beam, the scattered light or emitted fluorescence is measured, filtered and converted to digital values. Cells can be sorted according to their properties. Using flow cytometry, any fluorescent or light scattering experiment can be carried out on entire cells. With this instrument, interactions occurring either on cell surfaces or in any other subcellular location can be studied by using suitable fluorescent labels." ;
rdfs:subClassOf obo:MI_0051 .
obo:MI_2108 a rdfs:Class ;
rdfs:label "solubility ph 7.4" ;
rdfs:comment "Solubility pH 7.4" ;
rdfs:subClassOf obo:MI_2064 .
obo:MI_0431 a rdfs:Class ;
rdfs:label "obsolete" ;
rdfs:comment """Deprecated terms.
OBSOLETE term replaced by the default OBO class 'Obsolete'.""" .
obo:MI_0071 a rdfs:Class ;
rdfs:label "molecular sieving" ;
rdfs:comment "In sizing columns (gel filtration), the elution position of a protein or of a complex depends on its Stokes radius. Molecules with a radius that is smaller than the bead size are retained and retarded by the interaction with the matrix. The observation that two proteins, loaded on a sieving column, elute in a fraction(s) corresponding to a MW that is larger than the MW of either protein may be taken as an indication that the two proteins interact. Furthermore this technique provides a conceptually simple method for evaluating the affinity of the interaction." ;
rdfs:subClassOf obo:MI_0013 , obo:MI_0091 .
obo:MI_0716 a rdfs:Class ;
rdfs:label "passive uptake" ;
rdfs:comment "Entrance of molecules into cells that does not involved specific treatments but relies on natural cellular processes." ;
rdfs:subClassOf obo:MI_0307 .
obo:MI_0845 a rdfs:Class ;
rdfs:label "spin label" ;
rdfs:comment "Paramagnetic fragment, most often a cyclic nitroxide derivative, covalently attached to a molecule of interest." ;
rdfs:subClassOf obo:MI_0505 .
obo:MI_0396 a rdfs:Class ;
rdfs:label "predetermined participant" ;
rdfs:comment "Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s)." ;
rdfs:subClassOf obo:MI_0661 .
obo:MI_0548 a rdfs:Class ;
rdfs:label "methylated-lysine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00663.""" .
obo:MI_0373 a rdfs:Class ;
rdfs:label "dye label" ;
rdfs:comment "Dye coupled to a molecule allowing its identification isolation and monitoring." ;
rdfs:subClassOf obo:MI_0505 .
obo:MI_0530 a rdfs:Class ;
rdfs:label "glutamyl-5-poly(adp-ribose)" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00300.""" .
obo:MI_2169 a rdfs:Class ;
rdfs:label "luminiscence technology" ;
rdfs:comment "Techniques based upon the measurement of the emission of one or more photons in a bioluminescent reaction. Such reactions are typically catalyzed by two groups of enzymes: photoproteins and luciferases. Photoproteins emit light in proportion to the concentration of the protein itself, while in a luciferin-luciferase reaction, photon emission is directly proportional to the amount of luciferin." ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_0238 a rdfs:Class ;
rdfs:label "3h radiolabel" ;
rdfs:comment "Molecules labelled with isotope 3 of hydrogen atoms." ;
rdfs:subClassOf obo:MI_0517 .
obo:MI_0938 a rdfs:Class ;
rdfs:label "rheology measurement" ;
rdfs:comment "Characterization of viscoelastic properties of biomolecule solution is used to infer interactions between molecules." ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_0014 a rdfs:Class ;
rdfs:label "adenylate cyclase complementation" ;
rdfs:comment "Adenylate cyclase is encoded by the cyaA gene and contains a catalytic domain which can be proteolytically cleaved into two complementary fragments, T25 and T18, which remain associated in the presence of calmodulin in a fully active ternary complex. In the absence of calmodulin, the mixture of the two fragments does not exhibit detectable activity, suggesting that the two fragments do not associate. When expressed in an adenylate cyclase-deficient E. coli strain (E. coli lacks calmodulin or calmodulin-related proteins), the T25 and T18 fragments fused to putative interacting proteins are brought into close association which result in cAMP synthesis. The level of reconstructed adenylate cyclase can be estimated by monitoring the expression of a cAMP dependent reporter gene. The T25 tagged protein is generally regarded as the bait, the T18 as the prey." ;
rdfs:subClassOf obo:MI_0090 .
obo:MI_1100 a rdfs:Class ;
rdfs:label "bioactive entity" ;
rdfs:comment "Molecules showing activity in a living system but not encoded by a genomic sequence." ;
rdfs:subClassOf obo:MI_0313 .
obo:MI_0453 a rdfs:Class ;
rdfs:label "prints" ;
rdfs:comment """PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family.
http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/""" ;
rdfs:subClassOf obo:MI_0449 .
obo:MI_0021 a rdfs:Class ;
rdfs:label "colocalization by fluorescent probes cloning" ;
rdfs:comment """Two proteins can be localised to cell compartments, in the same experiment, if they are expressed as chimeric proteins fused to distinct proteins fluorescing at different wavelengths (Green Fluorescent Protein and Red Fluorescent Protein for example). Using a confocal microscope the two proteins can be visualized in living cells and it can be determined whether they have the same subcellular location. Fluorescence microscopy of cells expressing a GFP fusion protein can also demonstrate dynamic processes such as its translocation from one subcellular compartment to another.
OBSOLETE: use imaging technique (MI:0428) and specific probe as feature of each interacting protein.""" .
obo:MI_0729 a rdfs:Class ;
rdfs:label "luminescence based mammalian interactome mapping" ;
rdfs:comment "This strategy uses a luciferase enzyme fused to proteins of interest, which are then coexpressed with individual epitope-tagged partners in mammalian cells. Their interactions are determined by performing an enzymatic assay on anti-tag immunoprecipitates." ;
rdfs:subClassOf obo:MI_0004 .
obo:MI_0572 a rdfs:Class ;
rdfs:label "dna cleavage" ;
rdfs:comment "Covalent bond breakage of a DNA molecule leading to the formation of smaller fragments." ;
rdfs:subClassOf obo:MI_0910 .
obo:MI_0937 a rdfs:Class ;
rdfs:label "glu tag" ;
rdfs:comment "This peptide is a 314 to 319 amino acids fragment of the middle T antigen of mouse polymavirus. Glu-Glu epitope peptide." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_0819 a rdfs:Class ;
rdfs:label "molecular weight estimation by bromide staining" ;
rdfs:comment "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with bromide dyes." ;
rdfs:subClassOf obo:MI_0816 .
obo:MI_2396 a rdfs:Class ;
rdfs:label "cisphenotypic genetic suppression (complete)" ;
rdfs:comment """An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is equivalent to the wild type phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a* <= b < wt) AND (ab = wt) [E = a*]
OR
(wt < b <= a*) AND (ab = wt) [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1280 , obo:MI_1281 .
obo:MI_0082 a rdfs:Class ;
rdfs:label "peptide massfingerprinting" ;
rdfs:comment "This approach leads to protein identification by matching peptide masses, as measured by mass spectrometry, to the ones calculated from in silico fragmentation of a protein sequence database. A peptide mixture from a tryptic digest is analysed by MALDI-MS (Matrix-assisted laser desorption ionization mass spectrometry). The list of peptide masses obtained by MALDI MS is automatically compared to the calculated masses of the predicted peptide fragments for each entry in the database. High mass accuracy is very important in order to obtain a statistically significant and unambiguous match This method is best applied to completely sequenced genomes and well characterised proteomes. However, depending on the data quality, proteins that are highly homologous to already characterised proteins (greater than 80 to 90% sequence identity) can also be identified. The retrieved sequence are evaluated by mass accuracy of the peptides, matching of additional peptide masses in the MALDI spectrum after accounting for common modifications such as oxidation, acrylamidation of cysteine and missed cleavages and the use of secondary information (apparent isoelectric point and molecular weight). If any ambiguity about the identification by MALDI-MS still exists, the results must verified by an other identification method. Peptide mass fingerprint is generally carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) instrument but can also be achieved ESI-TOF (Electrospray Ionisation time-of-flight) or LC-MS (Liquid Chromatography-Mass Spectrometry) mass spectrometer." ;
rdfs:subClassOf obo:MI_0427 , obo:MI_0433 .
obo:MI_0705 a rdfs:Class ;
rdfs:label "anti tag western blot" ;
rdfs:comment "Western blot assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag for which efficient antibodies are available. The antibody may be either monoclonal or polyclonal." ;
rdfs:subClassOf obo:MI_0113 , obo:MI_0866 .
obo:MI_2198 a rdfs:Class ;
rdfs:label "labelling assay" ;
rdfs:comment "The interaction is inferred from the effect it exerts on specific chemical labelling of one of the interacting partners." ;
rdfs:subClassOf obo:MI_2197 .
obo:MI_0148 a rdfs:Class ;
rdfs:label "hydroxylated residue" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00428.""" .
obo:MI_1028 a rdfs:Class ;
rdfs:label "modified chromatin immunoprecipitation" ;
rdfs:comment "Chromatin-bound protein networks isolated using magnetic beads coated with antibodies." ;
rdfs:subClassOf obo:MI_0402 .
obo:MI_2356 a rdfs:Class ;
rdfs:label "adp deribosylation reaction" ;
rdfs:comment "Involves the substraction of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0670 a rdfs:Class ;
rdfs:label "imex" ;
rdfs:comment "International Molecular Interaction Exchange." ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0219 a rdfs:Class ;
rdfs:label "synthetic lethal" ;
rdfs:comment """Death phenotype observed on cells carrying combination of two independently silent mutations.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)""" .
obo:MI_0474 a rdfs:Class ;
rdfs:label "chebi" ;
rdfs:comment """A definitive, freely available database of Chemical compounds of Biological Interest (ChEBI).
http://www.ebi.ac.uk/chebi/""" ;
rdfs:subClassOf obo:MI_2054 .
obo:MI_2427 a rdfs:Class ;
rdfs:label "complex-cluster" ;
rdfs:comment "Used to link large ML assemblies to smaller curated complexes which are a subset of this. Added as qualifier to all entries linked by a common cross reference to an entry which represents a superset." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_0335 a rdfs:Class ;
rdfs:label "certain sequence position" ;
rdfs:comment "Position within the sequence clearly defined." ;
rdfs:subClassOf obo:MI_0333 .
obo:MI_2328 a rdfs:Class ;
rdfs:label "snap tag" ;
rdfs:comment "The SNAP-tag protein is an engineered version of the ubiquitous mammalian enzyme AGT, encoded in humans by the O-6-methylguanine-DNA methyltransferase (MGMT) gene. The tag is a 182 residues polypeptide with self-labeling activity that accepts O6-benzylguanine derivatives." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_0328 a rdfs:Class ;
rdfs:label "small molecule" ;
rdfs:comment "Molecule not part of or directly encoded by the genome, encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity." ;
rdfs:subClassOf obo:MI_1100 .
obo:MI_2026 a rdfs:Class ;
rdfs:label "melting point" ;
rdfs:comment "The melting point of a solid is the temperature range at which it changes state from solid to liquid." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0227 a rdfs:Class ;
rdfs:label "reverse phase chromatography" ;
rdfs:comment "Reverse phase chromatography operates on the basis of hydrophilicity and lipophilicity. The stationary phase consists of silica based packings with n-alkyl chains covalently bound. For example, C-8 signifies an octyl chain and C-18 an octadecyl ligand in the matrix. The more hydrophobic the matrix on each ligand, the greater is the tendency of the column to retain hydrophobic moieties. Thus hydrophilic compounds elute more quickly than do hydrophobic compounds." ;
rdfs:subClassOf obo:MI_0091 .
obo:MI_0385 a rdfs:Class ;
rdfs:label "alexa 350 label" ;
rdfs:comment "Alexa fluorescent dye analogue to AMCA (7-amino-4-methylcoumarin-3-acetic acid) with an approximate excitation wavelength maximum of 350 nm." ;
rdfs:subClassOf obo:MI_0384 .
obo:MI_1069 a rdfs:Class ;
rdfs:label "network-based confidence" ;
rdfs:comment """Network-based confidence scoring systems assign confidence based on multiple parameters, potentially shared by interacting proteins e.g. interaction partners, topological parameters, comparison
with genetic interactions.""" ;
rdfs:subClassOf obo:MI_1064 .
obo:MI_0981 a rdfs:Class ;
rdfs:label "tag visualisation by peroxidase activity" ;
rdfs:comment "The protein is expressed as a hybrid protein fused to a tag containing a peroxidase activity. Subsequent observation or measurement of peroxidase activity is used to identify the presence of the molecule in an interaction." ;
rdfs:subClassOf obo:MI_0980 .
obo:MI_0317 a rdfs:Class ;
rdfs:label "interaction" ;
rdfs:comment "Previously described interaction now being used as an interactor to describe hierarchical build-up of complexes." ;
rdfs:subClassOf obo:MI_0313 .
obo:MI_0604 a rdfs:Class ;
rdfs:label "potassium permanganate footprinting" ;
rdfs:comment "Potassium permanganate bind to single-stranded pyrimidine residues, it is commonly used to detect promoters opening regions in vivo. KMnO4 treatment of cells, followed by treatment with piperidine, followed by either PCR and/or acrylamide gel electrophoresis allows detection of interaction between transcription factor and the DNA sequence under their control." ;
rdfs:subClassOf obo:MI_0602 .
obo:MI_0490 a rdfs:Class ;
rdfs:label "experiment condition" ;
rdfs:comment """Describes the location of the experiment.
OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.""" .
obo:MI_0256 a rdfs:Class ;
rdfs:label "rna interference" ;
rdfs:comment "RNA interference (RNAi) is a post-transcriptional gene silencing method reproducing a naturally occurring phenomena. RNAi is the process whereby double-stranded RNA (dsRNA) induces the sequence-specific degradation of homologous mRNA. RNAi or dsRNA-induced silencing phenomena are present in evolutionarily diverse organisms, e.g., nematodes, plants, fungi, and trypanosomes. The mechanisms by which RNAi works is initiated by a progressive cleavage of dsRNA into 21 to 23 nucleotide (nt) short interfering RNAs (siRNAs). These native siRNA duplexes are then incorporated into a protein complex called RNA-induced silencing complex (RISC). ATP-dependent unwinding of the siRNA duplex generates an active RISC complex. Guided by the antisense strand of siRNA, the active RISC complex recognizes and cleaves the corresponding mRNA." ;
rdfs:subClassOf obo:MI_0255 .
obo:MI_0084 a rdfs:Class ;
rdfs:label "phage display" ;
rdfs:comment "Peptide sequences or entire proteins can be displayed on phage capsids by fusion to coat proteins to generate a library of fusion phages each displaying a different peptide. Such a library can then be exploited to identify specific phages that display peptides that bind to any given bait molecule for instance an antibody. The selection is performed by a series of cycles of affinity purification known as panning. The bait protein, immobilized on a solid support (plastic, agarose, sepharose, magnetic beads and others) is soaked in the phage mixture and that phage that remains attached to the bait is amplified and carried through a further affinity purification step. Each cycle results in an approximately 1,000-fold enrichment of specific phage and after a few selection rounds (2-4), DNA sequencing of the tight-binding phage reveals only a small number of sequences. Phage display panning experiments can be carried out either on libraries of peptides of random amino acid sequence or on libraries of displaying natural peptides obtained by inserting cDNA fragments into the phage vector (cDNA libraries). Libraries have been assembled on several different phages (Fd, Lambda or T7)." ;
rdfs:subClassOf obo:MI_0034 .
obo:MI_0583 a rdfs:Class ;
rdfs:label "fluorescence donor" ;
rdfs:comment "Fluorophore which emits electromagnetic radiation of given wavelength." ;
rdfs:subClassOf obo:MI_2334 .
obo:MI_0980 a rdfs:Class ;
rdfs:label "tag visualisation by enzyme assay" ;
rdfs:comment "The protein is expressed as a hybrid protein fused to a tag containing an enzyme activity e.g. peroxidase. Subsequence observation or measurement of enzyme activity is used to identify the presence of the molecule in an interaction." ;
rdfs:subClassOf obo:MI_0866 .
obo:MI_1108 a rdfs:Class ;
rdfs:label "biocarta" ;
rdfs:comment "BioCarta, whose core business is in assays and reagents, has also developed a collection of diagrams representing molecular and cellular signal transduction pathways." ;
rdfs:subClassOf obo:MI_1106 .
obo:MI_2154 a rdfs:Class ;
rdfs:label "wikipedia" ;
rdfs:comment "Hyperlink to wikipedia entry for the given drug (if it exists)" ;
rdfs:subClassOf obo:MI_2054 .
obo:MI_0812 a rdfs:Class ;
rdfs:label "calmodulin binding protein tag" ;
rdfs:comment "The protein is expressed and purified as a fusion to the calmoduling-binding protein. The fusion protein can be purified by affinity chromatography using a calmodulin resin." ;
rdfs:subClassOf obo:MI_0240 .
obo:MI_0658 a rdfs:Class ;
rdfs:label "multidimensional protein identification technology" ;
rdfs:comment "MudPIT is a method for rapid and large-scale protein identification by multidimensional liquid chromatography associated with tandem mass spectrometry. The chromatography step consists of strong cation exchange material back-to-back with reversed phase material inside fused silica capillaries. The peptides bound to the cation-exchange resin are freed by the gradually increasing salt concentration of the buffer and are subsequently retained by the reversed phase resin. Increasing buffers hydrophobicity progressively elute peptides from the reversed phase packing directly into the mass spectrometer. Typically this mass spectrometer will be a tandem electrospray, so peptides undergo ionization in the liquid phase, are separated in a primary mass spectrometer, analysed in the second mass spectrometer and identified." ;
rdfs:subClassOf obo:MI_0093 , obo:MI_0427 , obo:MI_0815 .
obo:MI_1145 a rdfs:Class ;
rdfs:label "phospholipase assay" ;
rdfs:comment "A phospholipase is an enzyme that hydrolyzes phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_1105 a rdfs:Class ;
rdfs:label "biocyc" ;
rdfs:comment "BioCyc is a collection of Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism. (http://biocyc.org/)." ;
rdfs:subClassOf obo:MI_1106 .
obo:MI_1224 a rdfs:Class ;
rdfs:label "ptm increasing an interaction" ;
rdfs:comment "Post translational modification on a protein observed to increase the strength or rate of an interaction." ;
rdfs:subClassOf obo:MI_0925 .
obo:MI_2384 a rdfs:Class ;
rdfs:label "multiple perturbation phenotype result" ;
rdfs:comment "A phenotype result in which multiple perturbations affect an organism individually and in combination." ;
rdfs:subClassOf obo:MI_2383 .
obo:MI_2344 a rdfs:Class ;
rdfs:label "rhea" ;
rdfs:comment "Rhea is an expert curated resource of biochemical reactions designed for the annotation of enzymes and genome-scale metabolic networks and models. Rhea uses the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules to precisely describe reactions participants and their chemical structures. All reactions are balanced for mass and charge and are linked to source literature, metabolic resources and other functional vocabularies such as the enzyme classification of the NC-IUBMB." ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_2132 a rdfs:Class ;
rdfs:label "gsh adducts" ;
rdfs:comment "Derivative molecule which has formed from a reaction with glutathione." ;
rdfs:subClassOf obo:MI_2115 .
obo:MI_0186 a rdfs:Class ;
rdfs:label "n6-biotinyl-lysine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00126.""" .
obo:MI_0991 a rdfs:Class ;
rdfs:label "lipoprotein cleavage assay" ;
rdfs:comment "The cleavage of a lipid molecule from a larger biomolecule." ;
rdfs:subClassOf obo:MI_0990 .
obo:MI_1142 a rdfs:Class ;
rdfs:label "aminoacylation assay" ;
rdfs:comment "The measurement of the addition of an aminoacyl group to a compound." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0603 a rdfs:Class ;
rdfs:label "dimethylsulphate footprinting" ;
rdfs:comment "Dimethylsulphate (DMS) is the most commonly used chemical to study DNA-protein interactions. DMS induces methylation of guanine residues so DNA interaction with protein binding to AT rich sequences or to the phosphate backbone may be not detected by DMS footprinting. However as DMS diffuses across membrane it can also be used for in vivo footprinting. The experiment involves the treatment with DMS of two DNA samples with identical sequence, one protein bound and the other naked. The two samples are treated with piperidine to induce chemical cleavage of the DMS modified guanine residues followed by digestion with restriction enzymes. Once labelled the samples are run in parallel on a gel to visualize the pattern of nested fragments sharing a common end generated by restriction enzyme(or PCR primer extension) and a variable end guanine dependent. The missing bands of the protein bound sample correspond to the guanine residues protected from modification by an interaction." ;
rdfs:subClassOf obo:MI_0602 .
obo:MI_2025 a rdfs:Class ;
rdfs:label "molecular weight" ;
rdfs:comment "Molecular weight in g/mol, determined from molecular formula or sequence." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0118 a rdfs:Class ;
rdfs:label "mutation" ;
rdfs:comment "A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event." ;
rdfs:subClassOf obo:MI_0252 .
obo:MI_2196 a rdfs:Class ;
rdfs:label "quartz crystal microbalance" ;
rdfs:comment "A method that monitors ligand binding by measuring the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator." ;
rdfs:subClassOf obo:MI_0968 .
obo:MI_2434 a rdfs:Class ;
rdfs:label "molecule cleavage site" ;
rdfs:comment "The location on a molecule where the molecule is broken down by enzymatic or chemical activity." ;
rdfs:subClassOf obo:MI_0252 .
obo:MI_1351 a rdfs:Class ;
rdfs:label "inferred-from" ;
rdfs:comment "Refers to the original experimentally verified object from which the described object has been derived." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_2137 a rdfs:Class ;
rdfs:label "genotoxicity" ;
rdfs:comment "Tendency of a bioactive entity to induce damage at the level of the gene." ;
rdfs:subClassOf obo:MI_2135 .
obo:MI_2158 a rdfs:Class ;
rdfs:label "predicted water solubility" ;
rdfs:comment "Water solubility in mg/mL or g/L" ;
rdfs:subClassOf obo:MI_2027 .
obo:MI_0928 a rdfs:Class ;
rdfs:label "filter trap assay" ;
rdfs:comment "Biomolecules are mixed in a buffer and the resulting mixture is passed through a filter. Large aggregates are retained on the filter and the pariticipants may then be identified." ;
rdfs:subClassOf obo:MI_0013 , obo:MI_0091 .
obo:MI_2205 a rdfs:Class ;
rdfs:label "pir" ;
rdfs:comment """The PIR-International Protein Sequence Database (PIR-PSD) was the world's first database of classified and functionally annotated protein sequences that grew out of the Atlas of Protein Sequence and Structure (1965-1978) edited by Margaret Dayhoff. Produced and distributed by the Protein Information Resource in collaboration with MIPS (Munich Information Center for Protein Sequences) and JIPID (Japan International Protein Information Database), PIR-PSD has been the most comprehensive and expertly-curated protein sequence database in the public domain for over 20 years. In 2002, PIR joined EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics) to form the UniProt consortium. PIR-PSD sequences and annotations have been integrated into UniProt Knowledgebase. Bi-directional cross-references between UniProt (UniProt Knowledgebase and/or UniParc) and PIR-PSD are established to allow easy tracking of former PIR-PSD entries. PIR-PSD unique sequences, reference citations, and experimentally-verified data can now be found in the relevant UniProt records.
Legacy data can be found at
http://pir.georgetown.edu/pirwww/dbinfo/pir_psd.shtml""" ;
rdfs:subClassOf obo:MI_1096 .
obo:MI_0341 a rdfs:Class ;
rdfs:label "ragged n-terminus" ;
rdfs:comment "Mixture of protein forms where N-terminus has been progressively truncated." ;
rdfs:subClassOf obo:MI_0340 .
obo:MI_0672 a rdfs:Class ;
rdfs:label "library-used" ;
rdfs:comment "This annotation topic will be used to store information about the cDNA library. If a name is available this should be reported along with a short description of the library." ;
rdfs:subClassOf obo:MI_0665 .
obo:MI_0978 a rdfs:Class ;
rdfs:label "author-name" ;
rdfs:comment "Author given name for a participant, not commonly found in source databases." ;
rdfs:subClassOf obo:MI_0666 .
obo:MI_2301 a rdfs:Class ;
rdfs:label "carbohydrate chemical modification decreasing interaction strength" ;
rdfs:comment "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction strength when compared with the unaltered carbohydrate." ;
rdfs:subClassOf obo:MI_2299 .
obo:MI_0447 a rdfs:Class ;
rdfs:label "feature database" ;
rdfs:comment "A database describing a feature on a molecule." ;
rdfs:subClassOf obo:MI_0444 .
obo:MI_0441 a rdfs:Class ;
rdfs:label "synthetic genetic analysis" ;
rdfs:comment "Identification of genetic interactions by generation of an organism harbouring mutations in 2 or more genes and scoring for a phenotype, such as loss of viability, that is not observed for any of the mutations in isolation." ;
rdfs:subClassOf obo:MI_0254 .
obo:MI_1052 a rdfs:Class ;
rdfs:label "clustered" ;
rdfs:comment "Binary pair is defined by multiple pieces of experimental evidence which have been clustered together." ;
rdfs:subClassOf obo:MI_1050 .
obo:MI_0030 a rdfs:Class ;
rdfs:label "cross-linking study" ;
rdfs:comment "Analysis of complexes obtained by input of energy or chemical treatments, or by introducing cysteines followed by oxidation to promote the formation of covalent bonds among molecules in close proximity." ;
rdfs:subClassOf obo:MI_0401 .
obo:MI_1287 a rdfs:Class ;
rdfs:label "mutual genetic over-suppression" ;
rdfs:comment """An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is opposite (relative to wild type) to that expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* <= b < wt < ab [E = a*]
OR
ab < wt < b <= a* [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1286 , obo:MI_2385 , obo:MI_2388 .
obo:MI_1150 a rdfs:Class ;
rdfs:label "affected interaction" ;
rdfs:comment "For an interaction that has a cooperative effect on a subsequent interaction, this term indicates which subsequent interaction is affected. The affected interaction is identified by referring to its interaction id." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_1149 .
obo:MI_0178 a rdfs:Class ;
rdfs:label "o4'-phospho-tyrosine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00048.""" .
obo:MI_0939 a rdfs:Class ;
rdfs:label "fluorescein label" ;
rdfs:comment "Fluorescence label used to monitor the presence of a protein." ;
rdfs:subClassOf obo:MI_0857 .
obo:MI_2188 a rdfs:Class ;
rdfs:label "par-clip" ;
rdfs:comment """Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) is a biochemical method used for identifying the binding sites of cellular RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs). The method relies on the incorporation of photoreactive ribonucleoside analogs, such as 4-thiouridine (4-SU) and 6-thioguanosine (6-SG) into nascent RNA transcripts by living cells. Irradiation of the cells by UV light of 365 nm induces efficient crosslinking of photoreactive nucleoside-labeled cellular RNAs to interacting RBPs. Immunoprecipitation of the RBP of interest is followed by isolation of the crosslinked and coimmunoprecipitated RNA. The isolated RNA is converted into a cDNA library and deep sequenced using next-generation sequencing technology.
http://en.wikipedia.org/wiki/PAR-CLIP""" ;
rdfs:subClassOf obo:MI_2191 .
obo:MI_0852 a rdfs:Class ;
rdfs:label "nucleotide genbank identifier" ;
rdfs:comment "GenBank Identifier or GI numbers for nucleotide." ;
rdfs:subClassOf obo:MI_0860 .
obo:MI_2395 a rdfs:Class ;
rdfs:label "positive genetic interaction" ;
rdfs:comment "An effect in which two genetic perturbations, when combined, result in a fitness that is greater than expected given the fitness resulting from the individual perturbations." ;
rdfs:subClassOf obo:MI_0935 .
obo:MI_2355 a rdfs:Class ;
rdfs:label "adp deribosylase assay" ;
rdfs:comment "Measurement of the substraction of one or more ADP-ribose moieties to molecules." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_2255 a rdfs:Class ;
rdfs:label "chemical inhibition reaction" ;
rdfs:comment "The effect of a chemical compound that stops, prevents, or reduces the activity of a target molecule." .
obo:MI_1131 a rdfs:Class ;
rdfs:label "mutation increasing interaction rate" ;
rdfs:comment "Region of a molecule whose mutation or deletion increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction)." ;
rdfs:subClassOf obo:MI_0382 .
obo:MI_1182 a rdfs:Class ;
rdfs:label "full identification by RNA sequencing" ;
rdfs:comment "Sequencing occurs during the course of the experiment. To sequence RNA, the usual method is first to reverse transcribe the sample to generate cDNA fragments." ;
rdfs:subClassOf obo:MI_0078 .
obo:MI_0006 a rdfs:Class ;
rdfs:label "anti bait coimmunoprecipitation" ;
rdfs:comment "A specific antibody for the molecule of interest (bait) is available, this is used to generate a high affinity resin to capture the endogenous bait present in a sample." ;
rdfs:subClassOf obo:MI_0019 .
obo:MI_0614 a rdfs:Class ;
rdfs:label "url" ;
rdfs:comment "URL/Web address describing an experiment, an interaction, a Cv term or an organism." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_0665 , obo:MI_0667 , obo:MI_0669 .
obo:MI_0194 a rdfs:Class ;
rdfs:label "cleavage reaction" ;
rdfs:comment "Covalent bond breakage in a molecule leading to the formation of smaller molecules." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0841 a rdfs:Class ;
rdfs:label "phosphotransferase assay" ;
rdfs:comment "Measures the rate of a phosphate transfer between two molecules." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_2102 a rdfs:Class ;
rdfs:label "nutraceutical drug" ;
rdfs:comment "A drug which may also be regarded as a foodstuff." ;
rdfs:subClassOf obo:MI_2040 .
obo:MI_2312 a rdfs:Class ;
rdfs:label "attached carbohydrate increasing interaction" ;
rdfs:comment "Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule." ;
rdfs:subClassOf obo:MI_2308 .
obo:MI_0458 a rdfs:Class ;
rdfs:label "tigrfams" ;
rdfs:comment """TIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, Hidden Markov Models (HMMs) and annotation.
http://www.tigr.org/TIGRFAMs""" ;
rdfs:subClassOf obo:MI_0449 .
obo:MI_1340 a rdfs:Class ;
rdfs:label "human orfeome collection" ;
rdfs:comment "A central resource of single-colony, fully-sequenced cloned human ORFs which can be readily transferred to Gateway compatible destination vectors for various functional proteomics studies. This set of ORFs ranges in size from 75 to more than 10,000 base pairs, and contains over 1,000 ORFs from genes with multiple splice variants." ;
rdfs:subClassOf obo:MI_1096 .
obo:MI_0855 a rdfs:Class ;
rdfs:label "5 prime overhang" ;
rdfs:comment "An overhang is a stretch of unpaired nucleotides in the end of a 5' strand of a DNA molecule." ;
rdfs:subClassOf obo:MI_0853 .
obo:MI_2362 a rdfs:Class ;
rdfs:label "ic tag" ;
rdfs:comment "Intein C-terminal fragment tag, commonly used in SIMPL and related methods." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_0352 a rdfs:Class ;
rdfs:label "partially purified" ;
rdfs:comment "The author states a molecule is only partially purified, i.e. other molecular species also known to be present." ;
rdfs:subClassOf obo:MI_0350 .
obo:MI_0506 a rdfs:Class ;
rdfs:label "over expressed level" ;
rdfs:comment "A molecule is estimated to be expressed at higher levels than in physiological condition." ;
rdfs:subClassOf obo:MI_0221 , obo:MI_0803 .
obo:MI_0240 a rdfs:Class ;
rdfs:label "fusion protein" ;
rdfs:comment "The protein under study is expressed as a fusion with a labelling protein, having either fluorescence properties or an enzymatic activity that facilitates its purification, identification, localisation or quantification." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_1161 a rdfs:Class ;
rdfs:label "allosteric response" ;
rdfs:comment "This term describes the effect of an allosteric binding event. It specifies which properties of the allosteric molecule are altered, i.e. whether the interaction alters either (a) binding or (b) catalytic properties of the allosteric molecule at a site distinct from the allosteric site." ;
rdfs:subClassOf obo:MI_1149 .
obo:MI_1029 a rdfs:Class ;
rdfs:label "proteomics of isolated chromatin segments" ;
rdfs:comment "Specific nucleic acid probes are fixed to solid supports (e.g. beads) and act as affinity probes. The molecules associated with the nucleic acid probes can then be isolated and identified." ;
rdfs:subClassOf obo:MI_0402 .
obo:MI_0475 a rdfs:Class ;
rdfs:label "ddbj/embl/genbank" ;
rdfs:comment """DDBJ EMBL GenBank Nucleotide Sequence Database Collaboration exchange new and updated data on a daily basis to achieve optimal synchronisation.
http://www.ebi.ac.uk/embl/Contact/collaboration""" ;
rdfs:subClassOf obo:MI_0683 .
obo:MI_2244 a rdfs:Class ;
rdfs:label "down-regulates quantity by destabilization" ;
rdfs:comment "The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B by promoting its degradation." ;
rdfs:subClassOf obo:MI_2242 .
obo:MI_2412 a rdfs:Class ;
rdfs:label "membrane two hybrid" ;
rdfs:comment "Protein complementation methods specifically developed to assay for interactions of membrane proteins with both cytosolic or membrane-bound partners." ;
rdfs:subClassOf obo:MI_0232 .
obo:MI_2227 a rdfs:Class ;
rdfs:label "mutation causing an interaction" ;
rdfs:comment "A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that enables an interaction when compared with the wild-type, which does not interact." ;
rdfs:subClassOf obo:MI_0118 .
obo:MI_0052 a rdfs:Class ;
rdfs:label "fluorescence correlation spectroscopy" ;
rdfs:comment "FCS monitors the random motion of fluorescently labelled molecules inside a defined volume irradiated by a focused laser beam. These fluctuations provide information on the rate of diffusion or diffusion time of a particle and this is directly dependent on the particle mass. As a consequence, any increase in the mass of a biomolecule, e.g. as a result of an interaction with a second molecule, is readily detected as an increase in the diffusion time of the particle. From these results the concentration of the different molecules can be calculated as well as their binding constant." ;
rdfs:subClassOf obo:MI_0051 .
obo:MI_0789 a rdfs:Class ;
rdfs:label "knock down" ;
rdfs:comment "The gene expression has been significantly reduced compared to wild-type by introduction of an external substance, e.g. by RNA interference." ;
rdfs:subClassOf obo:MI_0804 .
obo:MI_0000 a rdfs:Class ;
rdfs:label "molecular interaction" ;
rdfs:comment "Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions." .
obo:MI_0017 a rdfs:Class ;
rdfs:label "classical fluorescence spectroscopy" ;
rdfs:comment "Proteins contain endogenous fluorophores such as tryptophan residue and heme or flavins groups. Protein folding and protein-protein interaction can be studied by monitoring changes in the tryptophan environment detected by changes in its intrinsic fluorescence. Changes in the fluorescence emission spectrum on complex formation can occur either due to a shift in the wavelength of maximum fluorescence emission or by a shift in fluorescence intensity caused by the mixing of two proteins. The interaction of two proteins causes a shift in the fluorescence emission spectrum relative to the sum of the individual fluorescence spectra, resulting in a difference spectrum [F (complex)-2 F (sum)], which is a measurable effect of the interaction. Loss of fluorescence signal from a substrate can be used to measure protein cleavage." ;
rdfs:subClassOf obo:MI_0051 .
obo:MI_1119 a rdfs:Class ;
rdfs:label "nYFP" ;
rdfs:comment "n-terminal fragment of yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC)." ;
rdfs:subClassOf obo:MI_0368 , obo:MI_1215 .
obo:MI_1213 a rdfs:Class ;
rdfs:label "n-venus" ;
rdfs:comment "N-terminal region of the Venus fusion protein, created by the introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L). This tag is used for split flurescence complementation assays." ;
rdfs:subClassOf obo:MI_1135 , obo:MI_1215 .
obo:MI_0801 a rdfs:Class ;
rdfs:label "double nonmonotonic genetic interaction defined by inequality" ;
rdfs:comment "The phenotype resulting from genetic perturbation of both A and B show opposing effects in the WT background and the background with the other mutant gene. E.g., WT >= ab > a >= b" .
obo:MI_1201 a rdfs:Class ;
rdfs:label "anti-tag immunocytochemistry" ;
rdfs:comment "Method using an antibody coupled with some colouring agent to detect a specific tag fused to a protein within a cell. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody." ;
rdfs:subClassOf obo:MI_1200 .
obo:MI_2250 a rdfs:Class ;
rdfs:label "direct causal regulation" ;
rdfs:comment "The effect of a modulator entity A on a modulated entity B that occurs when A is immediately upstream of B." .
obo:MI_1221 a rdfs:Class ;
rdfs:label "author-based confidence" ;
rdfs:comment "A score generated by an author, usually only relevant for that particular dataset." ;
rdfs:subClassOf obo:MI_1064 .
obo:MI_1134 a rdfs:Class ;
rdfs:label "mcherry fluorescent protein tag" ;
rdfs:comment "mCherry is a red monomer which matures extremely rapidly, making it possible to see results very soon after activating transcription. It is highly photostable and resistant to photobleaching. Excitation maximum: 587 nm. Emission maximum: 610 nm." ;
rdfs:subClassOf obo:MI_0732 .
obo:MI_2181 a rdfs:Class ;
rdfs:label "cacao" ;
rdfs:comment """The Community Assessment of Community Annotation with Ontologies (CACAO) is a project to do large-scale manual community annotation of gene function using the Gene Ontology as a multi-institution student competition.
http://gowiki.tamu.edu/wiki/index.php/Category:CACAO""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_2042 a rdfs:Class ;
rdfs:label "disease indication" ;
rdfs:comment "Description or common names of diseases that the drug is used to treat." ;
rdfs:subClassOf obo:MI_2089 .
obo:MI_2266 a rdfs:Class ;
rdfs:label "de-phosphorylated residue" ;
rdfs:comment "A protein modification that effectively remove a phosphate group from a protein by hydrolysis." ;
rdfs:subClassOf obo:MI_2262 .
obo:MI_2152 a rdfs:Class ;
rdfs:label "food interaction" ;
rdfs:comment "Effect of food ingestion on a given drug treatment." ;
rdfs:subClassOf obo:MI_2089 .
obo:MI_0513 a rdfs:Class ;
rdfs:label "collagen film assay" ;
rdfs:comment "Measures the amount of radiolabel released into the medium when enzyme is added onto a film of isotope-labelled collagen." ;
rdfs:subClassOf obo:MI_0435 .
obo:MI_1083 a rdfs:Class ;
rdfs:label "cog" ;
rdfs:comment "Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain." ;
rdfs:subClassOf obo:MI_0447 .
obo:MI_0324 a rdfs:Class ;
rdfs:label "messenger rna" ;
rdfs:comment "Single-stranded RNA molecule that specifies the amino acid sequence of one or more polypeptide chains." ;
rdfs:subClassOf obo:MI_0320 .
obo:MI_1210 a rdfs:Class ;
rdfs:label "firefly-n" ;
rdfs:comment "The n-terminus of the firefly luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay." ;
rdfs:subClassOf obo:MI_1208 , obo:MI_1215 .
obo:MI_0245 a rdfs:Class ;
rdfs:label "reactome protein" ;
rdfs:comment """Collection of protein within the Reactome database - a knowledgebase of biological processes.
http://www.reactome.org/. OBSOLETE - this concept no longer exists within Reactome.""" .
obo:MI_2239 a rdfs:Class ;
rdfs:label "up-regulates quantity by stabilization" ;
rdfs:comment "The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B by preventing its degradation." ;
rdfs:subClassOf obo:MI_2237 .
obo:MI_2322 a rdfs:Class ;
rdfs:label "Illumina dye sequencing" ;
rdfs:comment "This method generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence." ;
rdfs:subClassOf obo:MI_2321 .
obo:MI_0688 a rdfs:Class ;
rdfs:label "dna binding domain tag" ;
rdfs:comment "Part of a transcription factor responsible for the binding of gene regulatory region prior to their transcription. Such tags are generally used in two hybrid experiments where they are fused to a bait polypeptide tested for its ability to interact with a prey fused to an activation domain tag." ;
rdfs:subClassOf obo:MI_0240 .
obo:MI_2423 a rdfs:Class ;
rdfs:label "gene reference" ;
rdfs:comment "Reference to the gene encoding for the observed nucleic acid or protein" ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_0460 a rdfs:Class ;
rdfs:label "rcsb pdb" ;
rdfs:comment """The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease.
http://www.pdb.org/""" ;
rdfs:subClassOf obo:MI_0805 .
obo:MI_1262 a rdfs:Class ;
rdfs:label "iid" ;
rdfs:comment "Interologous Interaction Database is an on-line database of known and predicted mammalian and eukaryotic protein-protein interactions." ;
rdfs:subClassOf obo:MI_0461 , obo:MI_0973 .
obo:MI_1164 a rdfs:Class ;
rdfs:label "allosteric mechanism" ;
rdfs:comment "The process that mediates the allosteric response of a molecule upon allosteric post-translational modification or binding of an allosteric effector." ;
rdfs:subClassOf obo:MI_1149 .
obo:MI_2442 a rdfs:Class ;
rdfs:label "lipid bilayer" ;
rdfs:comment "A structural arrangement consisting predominantly of lipid molecules organized into one or more continuous layers." ;
rdfs:subClassOf obo:MI_2441 .
obo:MI_0095 a rdfs:Class ;
rdfs:label "proteinchip(r) on a surface-enhanced laser desorption/ionization" ;
rdfs:comment "ProteinChip(r) Array technology is a surface-enhanced laser desorption/ionization (SELDI) approach (Ciphergen Biosystems Inc. Fremont, CA, USA) for sample fractionation accomplished by retentate chromatography. Retentate chromatography is performed on ProteinChip Arrays with varying chromatographic properties (e.g. anion exchange, cation exchange, metal affinity and reverse phase). By utilising arrays with differing surface chemistries in parallel and in series, a complex mixture of proteins, as from cells or body fluids, can be resolved into subsets of proteins with common properties. Specific analytes can also be examined by using preactivated arrays to which a bait molecule (such as an antibody or biotinylated DNA) is immobilized and a solution containing the binding partner(s) is presented to the array. This array-based immunoprecipitation or protein-binding experiment has been used with good success to study DNA-binding proteins, receptor-ligand interactions, and protein complexes. Any ligand retained on a SELDI chip can directly be identified by mass spectrometry." ;
rdfs:subClassOf obo:MI_0089 .
obo:MI_0028 a rdfs:Class ;
rdfs:label "cosedimentation in solution" ;
rdfs:comment "The ultracentrifuge can be used to characterise and/or purify macromolecules in solution according to their mass and hydrodynamic properties. Sedimentation studies provide information about the molecular weight and shape of a molecule. It is also possible to measure the association state of the sample. Both the mass of a molecule and its shape, that influences the friction forces and diffusion that counterbalances gravity, determine the sedimentation speed." ;
rdfs:subClassOf obo:MI_0027 .
obo:MI_0430 a rdfs:Class ;
rdfs:label "nucleic acid uv cross-linking assay" ;
rdfs:comment "Nucleic acids are incubated with purified proteins or a protein mixture and then exposed to a chemical cross-linking agent that may be activated by UV light exposure. The eventual complexes can be identified by sequencing or autoradiography if the nucleic acid is radio-labelled and the sequence is known. The proteins involved in the complex can be recognized by specific antibodies or by retrieving the original protein mixture and carrying further analysis on it." ;
rdfs:subClassOf obo:MI_0030 .
obo:MI_0055 a rdfs:Class ;
rdfs:label "fluorescent resonance energy transfer" ;
rdfs:comment "FRET is a quantum mechanical process involving the radiationless transfer of energy from a donor fluorophore to an appropriately positioned acceptor fluorophore. The fluorophores are genetically fused to the protein in analysis and cotransfected. Three basic conditions must be fulfilled for FRET to occur between a donor molecule and acceptor molecule. First, the donor emission spectrum must significantly overlap the absorption spectrum of the acceptor. Second, the distance between the donor and acceptor fluorophores must fall within the range 20 to 100 Angstrom. Third, the donor and acceptor fluorophores must be in favourable orientations." ;
rdfs:subClassOf obo:MI_0051 .
obo:MI_0223 a rdfs:Class ;
rdfs:label "under expressed level" ;
rdfs:comment "A molecule is estimated to be expressed at lower levels than in physiological condition." ;
rdfs:subClassOf obo:MI_0221 , obo:MI_0803 .
obo:MI_0234 a rdfs:Class ;
rdfs:label "131i radiolabel" ;
rdfs:comment "Molecule labelled with 131 radio isotope of iodine atoms." ;
rdfs:subClassOf obo:MI_0517 .
obo:MI_2174 a rdfs:Class ;
rdfs:label "ecoliwiki" ;
rdfs:comment """Community annotation portal associated with PortEco (formerly EcoliHub, http://porteco.org/). It aims to generate community-based pages about
everything related to non-pathogenic E. coli, its phages, plasmids, and
mobile genetic elements.
http://ecoliwiki.net/colipedia/""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_2401 a rdfs:Class ;
rdfs:label "mutual genetic enhancement" ;
rdfs:comment "A phenotype result in which both of two genetic perturbations result in the phenotype in question and do so in the same manner compared to wild type (for example, both genetic perturbations result in an increased quality phenotype, or both genetic perturbations result in a decreased quality phenotype) and the resulting double genetic perturbation results in a phenotype that is more severe than the most severe single genetic perturbation phenotype. Note that this may be an expected result." ;
rdfs:subClassOf obo:MI_2380 , obo:MI_2385 .
obo:MI_1063 a rdfs:Class ;
rdfs:label "consensuspathdb" ;
rdfs:comment "ConsensusPathDB-human integrates functional interaction networks including complex protein-protein, metabolic, signaling and gene regulatory interaction networks in Homo sapiens. Data originate from currently 20 public resources for functional interactions (listed below), as well as interactions that we have curated from literature. Data are integrated in a complementary manner and redundancies are avoided." ;
rdfs:subClassOf obo:MI_1106 .
obo:MI_0661 a rdfs:Class ;
rdfs:label "experimental participant identification" ;
rdfs:comment "experimental participant identification." ;
rdfs:subClassOf obo:MI_0002 .
obo:MI_1012 a rdfs:Class ;
rdfs:label "sbp" ;
rdfs:comment "38 amino acid (MDEKTTGWRGGHWEGLAGELEQLRARLEHHPQGQREP) Streptavidin binding peptide." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_0571 a rdfs:Class ;
rdfs:label "mrna cleavage" ;
rdfs:comment "Any process by which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner." ;
rdfs:subClassOf obo:MI_0902 .
obo:MI_0594 a rdfs:Class ;
rdfs:label "translocation start" ;
rdfs:comment "Xref pointing to a GO compartment term describing the start location of a migrating molecule." ;
rdfs:subClassOf obo:MI_0593 .
obo:MI_0535 a rdfs:Class ;
rdfs:label "glycosyl-serine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00163.""" .
obo:MI_0060 a rdfs:Class ;
rdfs:label "ha tag coimmunoprecipitation" ;
rdfs:comment """The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemaglutinin protein) for which antibodies are commercially available.
OBSOLETE redundant term. Map to feature type : ha-tagged (MI:0520) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).""" .
obo:MI_2029 a rdfs:Class ;
rdfs:label "logp" ;
rdfs:comment "Water/octanol partition coefficient of a small molecule." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0022 a rdfs:Class ;
rdfs:label "colocalization by immunostaining" ;
rdfs:comment """The subcellular location of a protein can be demonstrated by treating cells fixed on a microscope slide with an antibody specific for the protein of interest. A secondary antibody conjugated with a reactive enzyme (e.g. horseradish peroxidase) is then added. Following a washing step to remove the unbound secondary ligand, a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme and can then be visualised by standard microscopic techniques.
OBSOLETE since combination of Interaction Detection Method and Interaction Type.Consider using the Interaction Detection Method imaging techniques (MI:0428) coupled with Interaction Type colocalisation (MI:0403) and Participant detection immunostaining (MI:0422) instead.""" .
obo:MI_0073 a rdfs:Class ;
rdfs:label "mrna display" ;
rdfs:comment "This method relies on the covalent coupling of mRNA to the nascent polypeptide. The mRNA (natural or artificial) is first covalently linked to a short DNA linker carrying a puromycin moiety. The mRNA mixture is then translated in vitro. When the ribosome reaches the RNA-DNA junction the ribosome stalls and the puromycin moiety enters the peptidyltransferase site of the ribosome and forms a covalent linkage to the nascent polypeptide. As a result the protein and the mRNA are covalently joined and can be isolated from the ribosome and purified. In the current protocol, a cDNA strand is then synthesised to form a less sticky RNA-DNA hybrid and these complexes are finally used for affinity selection. As in most display approaches, several selections cycles (3-6) are sufficient to enrich for mRNAs encoding ligand proteins." ;
rdfs:subClassOf obo:MI_0034 .
obo:MI_0482 a rdfs:Class ;
rdfs:label "rfam" ;
rdfs:comment """Rfam is a large collection of multiple sequence alignments and covariance models covering many common non-coding RNA families.
http://www.sanger.ac.uk/Software/Rfam/""" ;
rdfs:subClassOf obo:MI_0683 .
obo:MI_0346 a rdfs:Class ;
rdfs:label "experimental preparation" ;
rdfs:comment "Set of terms to describe the participant experimental treatment and status. This term groups a number of orthologous short controlled vocabularies delivery method, expression level, molecular source, and sample process. Each participant can then be annotated with a maximum of 4 terms selected from each short list." ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_0532 a rdfs:Class ;
rdfs:label "n4-(adp-ribosyl)-asparagine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00236.""" .
obo:MI_2405 a rdfs:Class ;
rdfs:label "circular RNA" ;
rdfs:comment "Circular RNAs are stable circular transcripts generated when a pre-mRNA undergoes “backsplicing” to join a splice donor to an upstream splice acceptor. They can originate from exons, introns or lncRNAs." ;
rdfs:subClassOf obo:MI_0320 .
obo:MI_0452 a rdfs:Class ;
rdfs:label "pirsf" ;
rdfs:comment """PIRSF is a classification system based on evolutionary relationship of whole proteins.
http://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml""" ;
rdfs:subClassOf obo:MI_0449 .
obo:MI_0033 a rdfs:Class ;
rdfs:label "deletion analysis" ;
rdfs:comment "In this approach, once a molecule is demonstrated to participate in an interaction, several deletion derivatives are produced and tested in the binding assay to identify the minimal fragment (domain) that can still support the interaction." ;
rdfs:subClassOf obo:MI_0074 .
obo:MI_0833 a rdfs:Class ;
rdfs:label "autoradiography" ;
rdfs:comment "Experimental method by which radiolabel is detected by exposure to a photographic emulsion forming a pattern on the film." ;
rdfs:subClassOf obo:MI_0659 , obo:MI_0866 .
obo:MI_2121 a rdfs:Class ;
rdfs:label "transporter binding" ;
rdfs:comment "Substrate of a carrier system allowing the intake of an agent into an organ or part of body." ;
rdfs:subClassOf obo:MI_2115 .
obo:MI_0398 a rdfs:Class ;
rdfs:label "two hybrid pooling approach" ;
rdfs:comment "In the pooling strategy sets of either both bait and prey hybrid vectors are mated or, more commonly, individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners. The pooling of both baits and prey molecules is now a rarely used technique as the pooling of baits often leads to misleading results." ;
rdfs:subClassOf obo:MI_0018 .
obo:MI_2261 a rdfs:Class ;
rdfs:label "phenotype" ;
rdfs:comment "Cellular phenotype is the conglomerate of multiple cellular processes involving gene and protein expression that result in the elaboration of a cell's particular morphology and function." ;
rdfs:subClassOf obo:MI_2259 .
obo:MI_0271 a rdfs:Class ;
rdfs:label "conditional synthetic lethal temperature-sensitivity" ;
rdfs:comment """Two silent mutations show a temperature sensitive lethal phenotype when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (FBcv:0000310 'temperature conditional')""" .
obo:MI_0212 a rdfs:Class ;
rdfs:label "lipoprotein cleavage reaction" ;
rdfs:comment "Cleavage of a lipid group covalently bound to a protein residue." ;
rdfs:subClassOf obo:MI_0194 .
obo:MI_0718 a rdfs:Class ;
rdfs:label "nucleic acid transfection by treatment" ;
rdfs:comment "Transient introduction and expression of nucleic acid carried out by treatment with chemicals." ;
rdfs:subClassOf obo:MI_0312 .
obo:MI_1193 a rdfs:Class ;
rdfs:label "partial RNA sequence identification" ;
rdfs:comment "Identification of a part of a RNA sequence, usually then related to the full length sequence by alignment." ;
rdfs:subClassOf obo:MI_1179 .
obo:MI_1018 a rdfs:Class ;
rdfs:label "deltamass" ;
rdfs:comment "A database of protein post translational modifications. www.abrf.org/index.cfm/dm.home" ;
rdfs:subClassOf obo:MI_0447 .
obo:MI_0197 a rdfs:Class ;
rdfs:label "deacetylation reaction" ;
rdfs:comment "N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_2210 a rdfs:Class ;
rdfs:label "nucleic acid chemical modification disrupting an interaction" ;
rdfs:comment "Chemical modification observed on a nucleic acid molecule observed to disrupt an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition." ;
rdfs:subClassOf obo:MI_2206 .
obo:MI_0374 a rdfs:Class ;
rdfs:label "cyanine label" ;
rdfs:comment "The organic polymethine cyanine dyes which, depending on structure, cover the spectrum from IR to UV.s. Their emission range is such that background fluorescence is often reduced. In addition these molecules can be linked directly to specific locations in synthetically produced nucleic acids." ;
rdfs:subClassOf obo:MI_0373 , obo:MI_0857 .
obo:MI_1276 a rdfs:Class ;
rdfs:label "opposing genetic epistasis" ;
rdfs:comment """An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a < wt < b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1284 , obo:MI_2387 .
obo:MI_0408 a rdfs:Class ;
rdfs:label "disulfide bond" ;
rdfs:comment "Covalent bond mediated by 2 sulfur atoms." ;
rdfs:subClassOf obo:MI_0195 .
obo:MI_0640 a rdfs:Class ;
rdfs:label "parameter type" ;
rdfs:comment "Parameter for enzymatic or binding kinetic studies." ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_0379 a rdfs:Class ;
rdfs:label "13c label" ;
rdfs:comment "Molecules labelled with isotope 13 of carbon atoms." ;
rdfs:subClassOf obo:MI_0378 .
obo:MI_2216 a rdfs:Class ;
rdfs:label "deampylation assay" ;
rdfs:comment """Measurement of de-AMPylation, the removal of a phosphodiester or phosphoramide ester of AMP from Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino
acids.""" ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0666 a rdfs:Class ;
rdfs:label "participant attribute name" ;
rdfs:comment "Attribute name of annotation associated to a participant element." ;
rdfs:subClassOf obo:MI_0590 .
obo:MI_1251 a rdfs:Class ;
rdfs:label "methylmalonyl-CoA isomerase reaction" ;
rdfs:comment "The catalysis of the conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2." ;
rdfs:subClassOf obo:MI_1250 .
obo:MI_0677 a rdfs:Class ;
rdfs:label "tandem tag" ;
rdfs:comment "A tandem tag consists of the concatenation of simple distinct tags that is engineered to be cloned as a unique element onto a sequence of interest. Note that when a protein is fused to many simple tags that are inserted individually and possibly in different sequence positions these should be reported as independent features." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_0587 a rdfs:Class ;
rdfs:label "inhibited" ;
rdfs:comment """Molecule being identified as target of an inhibitor.
OBSOLETE as term is deprecated to describe the target of an inhibitor that can have any other biological role.""" .
obo:MI_0822 a rdfs:Class ;
rdfs:label "molecular weight estimation by hoechst staining" ;
rdfs:comment "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with Hoechst dyes." ;
rdfs:subClassOf obo:MI_0816 .
obo:MI_1329 a rdfs:Class ;
rdfs:label "cpm" ;
rdfs:comment "The thiol-reactive coumarin, CPM is very weakly fluorescent until reacted with thiols producing a conjugate with excitation/emission maxima of ~384/470 nm." ;
rdfs:subClassOf obo:MI_1328 .
obo:MI_1355 a rdfs:Class ;
rdfs:label "lipid cleavage" ;
rdfs:comment "Reaction monitoring the cleavage (hydrolysis) or a lipid molecule." ;
rdfs:subClassOf obo:MI_0194 .
obo:MI_1005 a rdfs:Class ;
rdfs:label "adp ribosylase assay" ;
rdfs:comment "Measurement of the addition of one or more ADP-ribose moieties to molecules." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0683 a rdfs:Class ;
rdfs:label "sequence database" ;
rdfs:comment "Database collecting nucleic or amino acid sequences mainly derived from genomic or mRNA sequencing." ;
rdfs:subClassOf obo:MI_0473 .
obo:MI_1116 a rdfs:Class ;
rdfs:label "genemania" ;
rdfs:comment "GeneMANIA predicts interactions based on multiple evidences including physical and genetic interactions, pathways, co-localisation, co-expression and protein domain similarity." ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_1057 a rdfs:Class ;
rdfs:label "predicted" ;
rdfs:comment "The interaction has been predicted using a specific algorithm." ;
rdfs:subClassOf obo:MI_1053 .
obo:MI_1156 a rdfs:Class ;
rdfs:label "cooperative mechanism" ;
rdfs:comment "For an interaction that has a cooperative effect on a subsequent interaction, this term indicates the process that mediates this effect." ;
rdfs:subClassOf obo:MI_1149 .
obo:MI_0041 a rdfs:Class ;
rdfs:label "electron nuclear double resonance" ;
rdfs:comment "A combination of NMR and EPR. The lines in the EPR spectrum that are caused by coupling of an unpaired electron nearby nuclei change in intensity when these nuclei are excited at their NMR frequency." ;
rdfs:subClassOf obo:MI_0043 .
obo:MI_1235 a rdfs:Class ;
rdfs:label "thermal shift binding" ;
rdfs:comment "Ligand binding to a target protein can stabilize a protein's native state, as shown in the increase of the bound protein's melting temperature. The midpoint of the melting curve of a protein will increase in the presence of ligands that bind more tightly to the native state than the unfolded state." ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_1243 a rdfs:Class ;
rdfs:label "fc-igg2" ;
rdfs:comment "A fusion protein tag consisting of a portion of the constant region of IgG2." ;
rdfs:subClassOf obo:MI_0975 .
obo:MI_0524 a rdfs:Class ;
rdfs:label "calmodulin binding peptide plus protein a tag" ;
rdfs:comment "Tag encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A fused to a target protein. The tag allows two purification steps ensuring a highly selective purification of the tagged protein." ;
rdfs:subClassOf obo:MI_0677 .
obo:MI_2272 a rdfs:Class ;
rdfs:label "tyrosinylation" ;
rdfs:comment "Reversible reaction that add a tyrosine residue to an amino-acid." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0382 a rdfs:Class ;
rdfs:label "mutation increasing interaction" ;
rdfs:comment "Region of a molecule whose mutation or deletion increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction)." ;
rdfs:subClassOf obo:MI_0118 .
obo:MI_1088 a rdfs:Class ;
rdfs:label "phenotype-based detection assay" ;
rdfs:comment "Assays that are used to determine interactions by monitoring, for example activation of a certain pathway when screening for inhibitors of a given receptor." ;
rdfs:subClassOf obo:MI_0045 .
obo:MI_0129 a rdfs:Class ;
rdfs:label "n-acetylglycine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00055.""" .
obo:MI_2333 a rdfs:Class ;
rdfs:label "mutation with complex effect" ;
rdfs:comment "A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that has a complex effect over the interaction when compared with the wild-type. A complex effect is such that cannot be described in increasing, decreasing, causing, disrupting or no effect terms." ;
rdfs:subClassOf obo:MI_0118 .
obo:MI_1068 a rdfs:Class ;
rdfs:label "location-based confidence" ;
rdfs:comment "Confidence in an interaction is based on shared functionality of interacting molecules e.g. co-occurrence of GO component terms or co-occurrence in the same tissues." ;
rdfs:subClassOf obo:MI_1064 .
obo:MI_0721 a rdfs:Class ;
rdfs:label "protein delivery" ;
rdfs:comment "Method by which proteins are delivered into a cell." ;
rdfs:subClassOf obo:MI_0307 .
obo:MI_0691 a rdfs:Class ;
rdfs:label "vp16 activation domain" ;
rdfs:comment "Full viral protein vp16 exclusively responsible for preferential transcriptional activation of viral genes. Activation requires the formation of a complex with the host cell transcription factor." ;
rdfs:subClassOf obo:MI_0689 .
obo:MI_0732 a rdfs:Class ;
rdfs:label "red fluorescent protein tag" ;
rdfs:comment "The red fluorescent protein derived from, for example, marine anemone Discosoma striata and reef corals belonging to the class Anthozoacan can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native." ;
rdfs:subClassOf obo:MI_0687 .
obo:MI_0405 a rdfs:Class ;
rdfs:label "competition binding" ;
rdfs:comment "Competitive binding experiments measure equilibrium binding of a single concentration of ligand at various concentrations of an unlabeled competitor. Analysis of these data gives the affinity of the receptor for the competitor." ;
rdfs:subClassOf obo:MI_0400 .
obo:MI_2051 a rdfs:Class ;
rdfs:label "patient information" ;
rdfs:comment "Information on the disease indications and treatment regime for the drug. May also include contra-indications." ;
rdfs:subClassOf obo:MI_2089 .
obo:MI_2232 a rdfs:Class ;
rdfs:label "molecular association" ;
rdfs:comment "A particular way two or more molecules influence one another." ;
rdfs:subClassOf obo:MI_0190 .
obo:MI_1246 a rdfs:Class ;
rdfs:label "ion mobility mass spectrometry of complexes" ;
rdfs:comment "IM-MS analysis is performed by first ionizing the protein complex of interest followed by ion mobility separation according to their cross-section-to-charge (Q/z) ratio. After separation, ions are sampled by a mass spectrometer and analyzed according to their mass-to-charge (m/z) ratio. Combined knowledge of both Q/z and m/z can be used to infer the size and shape of the complex." ;
rdfs:subClassOf obo:MI_0069 .
obo:MI_1313 a rdfs:Class ;
rdfs:label "proximity labelling technology" ;
rdfs:comment "Methods depend on a modification that only takes place with the close proximity of two molecules - a protein fused to the bait can then modify any neighbouring prey proteins, for example. The resulting tag can be used for isolation and/or identification." ;
rdfs:subClassOf obo:MI_2198 .
obo:MI_2221 a rdfs:Class ;
rdfs:label "gaussia-n" ;
rdfs:comment "The n-terminus of the gaussia luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay." ;
rdfs:subClassOf obo:MI_2219 .
obo:MI_2170 a rdfs:Class ;
rdfs:label "bimolecular luminiscence complementation" ;
rdfs:comment "The bimolecular luminescence complementation (BiLC) is an assay for determination of protein interactions and/or their location in living cells. This approach is based on complementation between two fragments of a bioluminescent enzyme such as luciferin or aequorin. Interactions between proteins fused to each fragment bring the fragments together resulting in the reconstitution of a fully functional bioluminescent enzyme that can be identified through microscopy or luminescence detection." ;
rdfs:subClassOf obo:MI_2169 .
obo:MI_1127 a rdfs:Class ;
rdfs:label "putative self interaction" ;
rdfs:comment "Interaction between two or more regions of possibly the same molecule but it is also possible that the observation is due to an interaction between two identical molecules." ;
rdfs:subClassOf obo:MI_0407 .
obo:MI_0275 a rdfs:Class ;
rdfs:label "synthetic growth increase" ;
rdfs:comment """Two silent mutations show growth increase when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')""" .
obo:MI_0651 a rdfs:Class ;
rdfs:label "micromolar" ;
rdfs:comment """10E-6 moles per liter of solution.
OBSOLETE: term redundant with the schema exponent attribute of the parameter.""" .
obo:MI_0471 a rdfs:Class ;
rdfs:label "mint" ;
rdfs:comment """The Molecular INTeraction database (MINT) is a relational database designed to store interactions between biological molecules.
http://mint.bio.uniroma2.it""" ;
rdfs:subClassOf obo:MI_0461 , obo:MI_0973 .
obo:MI_1265 a rdfs:Class ;
rdfs:label "ubiquitin reconstruction tag" ;
rdfs:comment "In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety (residues 35-76) and an N-terminal ubiquitin moiety (residues 1-34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor that can be cleaved off by ubiquitin specific proteases." ;
rdfs:subClassOf obo:MI_0240 .
obo:MI_0694 a rdfs:Class ;
rdfs:label "lexa dna binding domain" ;
rdfs:comment "Amino terminal (1-220) part of the Escherichia coli lexA repressor, binding to 16 base pair palindromic DNA sequences." ;
rdfs:subClassOf obo:MI_0688 .
obo:MI_2007 a rdfs:Class ;
rdfs:label "iupac name" ;
rdfs:comment "IUPAC or standard chemical name for a drug, or a chemical." ;
rdfs:subClassOf obo:MI_1041 .
obo:MI_1074 a rdfs:Class ;
rdfs:label "rgs-his tag" ;
rdfs:comment "The protein of interest is expressed as a fusion to a RGS(His)n tag." ;
rdfs:subClassOf obo:MI_0521 .
obo:MI_1077 a rdfs:Class ;
rdfs:label "merck index" ;
rdfs:comment "Comprehensive information on chemicals, drugs, and biologicals." ;
rdfs:subClassOf obo:MI_2054 .
obo:MI_2185 a rdfs:Class ;
rdfs:label "parkinsonsuk-ucl" ;
rdfs:comment """The Parkinson's UK Gene Ontology Project represents a collaboration between University College London and the European Bioinformatics Institute (EBI), funded by Parkinson's UK. This annotation group is a member of the IMEx Consortium.
http://www.ucl.ac.uk/functional-gene-annotation/neurological""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0830 a rdfs:Class ;
rdfs:label "tissue list" ;
rdfs:comment """List of tissue used as topic in UniProt RC line.
http://www.expasy.org/cgi-bin/lists?tisslist.txt""" ;
rdfs:subClassOf obo:MI_0473 .
obo:MI_2126 a rdfs:Class ;
rdfs:label "paracellular absorption" ;
rdfs:comment "Water soluble compounds are absorbed in the small intestine mainly via two pathways, the transcellular and the paracellular pathways. The paracellular absorption involves movement of solutes through a restrictive aqueous channel in the tight junctions of adjoining cells by diffusion." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_1167 a rdfs:Class ;
rdfs:label "allostery type" ;
rdfs:comment "This term indicates the chemical relationship between the two ligands whose binding is allosterically coupled." ;
rdfs:subClassOf obo:MI_1149 .
obo:MI_0502 a rdfs:Class ;
rdfs:label "enzyme target" ;
rdfs:comment "Molecule that is the target of its binding partner catalytic activity." ;
rdfs:subClassOf obo:MI_0500 .
obo:MI_1318 a rdfs:Class ;
rdfs:label "sulfate donor" ;
rdfs:comment "Any molecule that is able to transfer a sulphate group to another chemical species." ;
rdfs:subClassOf obo:MI_0918 .
obo:MI_1153 a rdfs:Class ;
rdfs:label "cooperative effect outcome" ;
rdfs:comment "For an interaction that has a cooperative effect on a subsequent interaction, this term indicates whether this effect is positive or negative, i.e. whether the subsequent interaction is augmented or diminished." ;
rdfs:subClassOf obo:MI_1149 .
obo:MI_0890 a rdfs:Class ;
rdfs:label "qdot" ;
rdfs:comment "Qdot are nanocrystals fluorophores . Nanocrystals a are extremely efficient materials for generating and they have a highly customizable surface for directing their bioactivity, producing a fluorescent probe that outperforms traditional dyes in many fluorescence applications." ;
rdfs:subClassOf obo:MI_0857 .
obo:MI_0493 a rdfs:Class ;
rdfs:label "in vivo" ;
rdfs:comment """Experiment undertaken within a cellular environment, although this may not be the natural host of the proteins in the study.
OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.""" .
obo:MI_0560 a rdfs:Class ;
rdfs:label "myristoylated residue" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00438.""" .
obo:MI_1206 a rdfs:Class ;
rdfs:label "renilla-n" ;
rdfs:comment "The n-terminus of the renilla luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay." ;
rdfs:subClassOf obo:MI_0896 , obo:MI_1215 .
obo:MI_0180 a rdfs:Class ;
rdfs:label "selenocysteine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00031.""" .
obo:MI_0419 a rdfs:Class ;
rdfs:label "gtpase assay" ;
rdfs:comment "Measures the catalysis of the reaction: GTP + H2O = GDP + phosphate." ;
rdfs:subClassOf obo:MI_0879 .
obo:MI_0039 a rdfs:Class ;
rdfs:label "edman degradation" ;
rdfs:comment "In this procedure the N-terminus amino acid is cleaved from a polypeptide and identified by high-pressure liquid chromatography. The cycle is repeated on the ever-shortening polypeptide until all the residues are identified. On average only 20-30 consecutive cycles can be performed and lead to amino acid identification. Longer polypeptides or full length proteins must be cleaved by specific protease before Edman degradation and their sequences built by fragment overlapping." ;
rdfs:subClassOf obo:MI_0433 .
obo:MI_2277 a rdfs:Class ;
rdfs:label "Cr-two hybrid" ;
rdfs:comment "This method uses Cre recombinase as a two-hybrid protein-protein interaction reporter that functions intracellularly to covalently and unidirectionally link interacting bait and prey plasmids via specialized loxP sites that flank the protein-coding sequences. The linked protein-coding sequences serve as interaction-identifying DNA molecules that enable massively multiplexed screening coupled with next-generation DNA sequencing to detect protein-protein interactions." ;
rdfs:subClassOf obo:MI_1113 .
obo:MI_0521 a rdfs:Class ;
rdfs:label "his tag" ;
rdfs:comment "The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_0917 a rdfs:Class ;
rdfs:label "matrixdb" ;
rdfs:comment """Knowledgebase of the extracellular matrix storing experimentally determined interactions involving extracellular biomolecules. It includes protein-protein, protein-polysaccharide, and protein-lipid interactions.
https://matrixdb.univ-lyon1.fr""" ;
rdfs:subClassOf obo:MI_0461 , obo:MI_0973 .
obo:MI_2373 a rdfs:Class ;
rdfs:label "negative genetic interaction (sensu BioGRID)" ;
rdfs:comment "Genetic perturbation of multiple genes in combination that results in a more severe phenotypic defect (or lethality) than from individual viable perturbations. This term is reserved for high throughput studies with scores." ;
rdfs:subClassOf obo:MI_2402 .
obo:MI_0201 a rdfs:Class ;
rdfs:label "demyristoylation reaction" ;
rdfs:comment "N6-myristoyl-L-lysine is cleaved and returns a K residue." ;
rdfs:subClassOf obo:MI_0212 .
obo:MI_0368 a rdfs:Class ;
rdfs:label "yellow fluorescent protein tag" ;
rdfs:comment "Yellow fluorescent protein from species such as Vibrio fischeri can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native." ;
rdfs:subClassOf obo:MI_0687 .
obo:MI_1168 a rdfs:Class ;
rdfs:label "heterotropic allostery" ;
rdfs:comment "The type of allostery that occurs when the two ligands whose binding is allosterically coupled are not chemically identical." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_1167 .
obo:MI_0549 a rdfs:Class ;
rdfs:label "alkylated cysteine" ;
rdfs:comment """Artificial residue modification enabling studies of cysteine binding status.
OBSOLETE remap to MOD:00660.""" .
obo:MI_1294 a rdfs:Class ;
rdfs:label "monophenotypic genetic suppression (partial)" ;
rdfs:comment """An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more, but not completely, \"wild type\" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a < ab < b = wt [E = a]
OR
wt = b < ab < a [E = a]
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1292 .
obo:MI_2280 a rdfs:Class ;
rdfs:label "deamidation reaction" ;
rdfs:comment "Reaction in which an amide functional group in the side chain of the amino acids asparagine or glutamine is removed or converted to another functional group. Typically, asparagine is converted to aspartic acid or isoaspartic acid and glutamine is converted to glutamic acid or pyroglutamic acid (5-oxoproline)." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_1023 a rdfs:Class ;
rdfs:label "luminogreen" ;
rdfs:comment "A nonfluorescent, biarsenical derivative of fluorescein. LumioGreen is supplied pre-complexed to EDT, is membrane-permeable, and readily enters the cell." ;
rdfs:subClassOf obo:MI_0373 .
obo:MI_0610 a rdfs:Class ;
rdfs:label "small interfering rna" ;
rdfs:comment "Ribonucleic acid used in RNAi study. These RNA have the reverse complementary sequence of a target gene's mRNA transcript and inhibit its expression." ;
rdfs:subClassOf obo:MI_0320 .
obo:MI_1254 a rdfs:Class ;
rdfs:label "atto 647" ;
rdfs:comment "Fluorescent tag - maleimide couples to thiols." ;
rdfs:subClassOf obo:MI_1092 .
obo:MI_0949 a rdfs:Class ;
rdfs:label "gdp/gtp exchange assay" ;
rdfs:comment """Experiments monitoring
interactions of GTP-GDP exchange factors with their cognate GTPases.""" ;
rdfs:subClassOf obo:MI_1036 .
obo:MI_1302 a rdfs:Class ;
rdfs:label "stable complex" ;
rdfs:comment "A stable set (2 or more) of interacting molecules which can be co-purified and have been shown to exist as a functional unit in vivo." ;
rdfs:subClassOf obo:MI_1298 .
obo:MI_0357 a rdfs:Class ;
rdfs:label "method reference" ;
rdfs:comment "Reference to a related paper which more fully describes either the experimental method or one or more of the interactors used within the experiment." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_1273 a rdfs:Class ;
rdfs:label "maximal genetic epistasis" ;
rdfs:comment """An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab = a* < b < wt
OR
wt < b < a* = ab
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1272 .
obo:MI_2416 a rdfs:Class ;
rdfs:label "ensemblbacteria" ;
rdfs:comment """Ensembl Bacteria is a browser for bacterial and archaeal genomes.
https://bacteria.ensembl.org/""" ;
rdfs:subClassOf obo:MI_1013 .
obo:MI_0011 a rdfs:Class ;
rdfs:label "beta lactamase complementation" ;
rdfs:comment "This strategy is based on a protein fragment complementation assay (PCA) of the enzyme TEM-1 beta-lactamase. The approach includes a simple colorimetric in vitro assays using the cephalosporin nitrocefin and assays in intact cells using the fluorescent substrate CCF2/AM. The combination of in vitro colorimetric and in vivo fluorescence assays of beta-lactamase in mammalian cells permits a variety of sensitive and high-throughput large-scale applications." ;
rdfs:subClassOf obo:MI_0090 .
obo:MI_0416 a rdfs:Class ;
rdfs:label "fluorescence microscopy" ;
rdfs:comment "Fluorescent microscopy uses a high intensity light to illuminate the sample. This light excites fluorescence species in the sample, which then emit light of a longer wavelength. A fluorescent microscope also produces a magnified image of the sample, but the image is based on the second light source -- the light emanating from the fluorescent species -- rather than from the light originally used to illuminate, and excite, the sample." ;
rdfs:subClassOf obo:MI_0428 .
obo:MI_0123 a rdfs:Class ;
rdfs:label "n2-acetyl-arginine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00359.""" .
obo:MI_1232 a rdfs:Class ;
rdfs:label "aggregation assay" ;
rdfs:comment "An interaction between two proteins is inferred from monitoring the effect of the presence of one of them on the aggregation state of the second." ;
rdfs:subClassOf obo:MI_0401 .
obo:MI_0930 a rdfs:Class ;
rdfs:label "epistatis" ;
rdfs:comment """An effect in which individual perturbations of two different genes result in different mutant phenotypes, and the resulting phenotype of their combination (the double mutant) is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively or quantitatively different phenotypes.""" .
obo:MI_0999 a rdfs:Class ;
rdfs:label "formylase assay" ;
rdfs:comment "Measurement of the reaction that can affect K or G residues. Reside is functionalised with a formyl group." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0263 a rdfs:Class ;
rdfs:label "suppression knockout" ;
rdfs:comment """Knocked out gene is the suppressor of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock out' MI:0788. """ .
obo:MI_2254 a rdfs:Class ;
rdfs:label "chemical activation reaction" ;
rdfs:comment "The effect of a chemical compound that results in the activation or in an increased activation of a target molecule." .
obo:MI_0539 a rdfs:Class ;
rdfs:label "gpi anchor residue" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00818.""" .
obo:MI_0898 a rdfs:Class ;
rdfs:label "putative self" ;
rdfs:comment "Molecule that is reported to self-interact but the experimental condition does not allow to resolve whether the interaction is intramolecular (true self interaction) or intermolecular (homodimer)." ;
rdfs:subClassOf obo:MI_0495 , obo:MI_0500 .
obo:MI_0528 a rdfs:Class ;
rdfs:label "omega-n-(adp-ribosyl)-arginine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00177.""" .
obo:MI_0479 a rdfs:Class ;
rdfs:label "mgd/mgi" ;
rdfs:comment """Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.
http://www.informatics.jax.org/""" ;
rdfs:subClassOf obo:MI_1094 .
obo:MI_0067 a rdfs:Class ;
rdfs:label "light scattering" ;
rdfs:comment "Dynamic and static laser light scattering probes the size, shape, and structure of biological macromolecules or of their assemblies. A beam is focused on an optically clear cylindrical cell containing the sample. Most of the light passes directly through the sample. A small portion of the light is scattered; the scattered light intensity containing information about the scattering particle is detected at an angle (typically in the range 15-180degrees) from the direction of the incident beam." ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_0257 a rdfs:Class ;
rdfs:label "antisense rna" ;
rdfs:comment "This approach is based on the observation that expression of RNA that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation." ;
rdfs:subClassOf obo:MI_0255 .
obo:MI_2293 a rdfs:Class ;
rdfs:label "5' position" ;
rdfs:comment "Term describing the upstream end of a nucleotide sequence." ;
rdfs:subClassOf obo:MI_0333 .
obo:MI_1284 a rdfs:Class ;
rdfs:label "quantitative genetic epistasis" ;
rdfs:comment """An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in any direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates quantitatively different phenotypes.""" ;
rdfs:subClassOf obo:MI_0797 .
obo:MI_0598 a rdfs:Class ;
rdfs:label "feature constraint" ;
rdfs:comment "The feature constraint free text will specificity whether a biological feature is shown to be possible (just observed) or required (experimentally demonstrated to be necessary for an interaction)." ;
rdfs:subClassOf obo:MI_0668 .
obo:MI_2441 a rdfs:Class ;
rdfs:label "lipid" ;
rdfs:comment "The term “lipid” is broadly defined as a substance of biological origin that is soluble in nonpolar solvents. Lipids include saponifiable classes such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable classes such as steroids." ;
rdfs:subClassOf obo:MI_1100 .
obo:MI_0971 a rdfs:Class ;
rdfs:label "phosphopantetheinylation" ;
rdfs:comment "The posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_1336 a rdfs:Class ;
rdfs:label "experiment database" ;
rdfs:comment "Databases that contain information used to add additional information to experiments (meta-data)." ;
rdfs:subClassOf obo:MI_0444 .
obo:MI_0246 a rdfs:Class ;
rdfs:label "cabri" ;
rdfs:comment """CABRI cell lines catalogue available at.
http://www.cabri.org/""" ;
rdfs:subClassOf obo:MI_0473 .
obo:MI_0259 a rdfs:Class ;
rdfs:label "perturbagens peptides" ;
rdfs:comment """This approach is based on the expression of peptides that bind to specific target proteins thereby interfering with their activity. In a standard approach the interfering peptide is expressed by genetic fusion to a stable protein scaffold. Interfering peptides can also be introduced into cells by fusing them to proteins or peptides (homeodomains, Tat protein.) having the property of penetrating the cell membrane. The peptide-carrier fusion protein is either synthesized chemically or produced in vivo, normally in bacteria. When the purified fusion protein is added to a cell culture, it penetrates the cell membrane thereby permitting the fused peptide to interfere with its target protein.
OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).""" .
obo:MI_1016 a rdfs:Class ;
rdfs:label "fluorescence recovery after photobleaching" ;
rdfs:comment "Slow rate of FRAP recovery when molecule is bound to another compared to inert, non-binding molecule taken as a measure of an interaction." ;
rdfs:subClassOf obo:MI_0051 .
obo:MI_0690 a rdfs:Class ;
rdfs:label "gal4 activation domain" ;
rdfs:comment "Part of the yeast transcription factor GAL4 (amino acids 766-881) specifically responsible for DNA transcription activation." ;
rdfs:subClassOf obo:MI_0689 .
obo:MI_0314 a rdfs:Class ;
rdfs:label "complex" ;
rdfs:comment "Set of interacting molecules that can be copurified. This term and its children should be use only at PARTICIPANT level." ;
rdfs:subClassOf obo:MI_0313 .
obo:MI_2389 a rdfs:Class ;
rdfs:label "mutual genetic suppression" ;
rdfs:comment "A genetic phenotype modification whereby each of two genetic perturbations suppress, or alleviate, the phenotype of the other genetic perturbation. Note that if the individual genetic perturbations have opposite phenotypes, this may be an expected result." ;
rdfs:subClassOf obo:MI_2379 .
obo:MI_1001 a rdfs:Class ;
rdfs:label "lipidase assay" ;
rdfs:comment "The covalent binding of a lipid group to a peptide chain." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_2214 a rdfs:Class ;
rdfs:label "signor" ;
rdfs:comment "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. The signaling information is mapped to the human proteome even if the experimental evidence is based on experiments on mammalian model organisms." ;
rdfs:subClassOf obo:MI_1106 .
obo:MI_2131 a rdfs:Class ;
rdfs:label "metabolite identification" ;
rdfs:comment "Identification of the breakdown products of a substance, either through chemical instability or the actions of enzymes within the body" ;
rdfs:subClassOf obo:MI_2115 .
obo:MI_0163 a rdfs:Class ;
rdfs:label "glutamic acid 5-methyl ester" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00081.""" .
obo:MI_0437 a rdfs:Class ;
rdfs:label "protein three hybrid" ;
rdfs:comment "Two hybrid assay performed with a third protein component co-transfected into a recombinant yeast strain together with a bait and a prey construct. Negative control shows that the interaction between the bait and the prey do not occur when the third protein is not co-transfected." ;
rdfs:subClassOf obo:MI_0018 , obo:MI_0588 .
obo:MI_0301 a rdfs:Class ;
rdfs:label "gene name" ;
rdfs:comment "Gene name." ;
rdfs:subClassOf obo:MI_1041 .
obo:MI_0078 a rdfs:Class ;
rdfs:label "nucleotide sequence identification" ;
rdfs:comment "Identification of a nucleotide sequence. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones." ;
rdfs:subClassOf obo:MI_0659 , obo:MI_0661 .
obo:MI_0050 a rdfs:Class ;
rdfs:label "flag tag coimmunoprecipitation" ;
rdfs:comment """The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.
OBSOLETE redundant term. Map to feature type: flag-tagged (MI:0518) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).""" .
obo:MI_0349 a rdfs:Class ;
rdfs:label "living cell" ;
rdfs:comment "Molecule is observed within in a living cell." ;
rdfs:subClassOf obo:MI_0342 .
obo:MI_0988 a rdfs:Class ;
rdfs:label "strep tag" ;
rdfs:comment "Synthetic peptide consisting of 8 amino acids Trp-Ser-His-Pro-Gln-Phe-Glu-Lys (WSHPQFEK)." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_1099 a rdfs:Class ;
rdfs:label "uniprot/trembl" ;
rdfs:comment """UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. The records in UniProtKB/TrEMBL are automatically generated and are enriched with automatic annotation and classification.
http://www.uniprot.org""" ;
rdfs:subClassOf obo:MI_0486 .
obo:MI_0963 a rdfs:Class ;
rdfs:label "interactome parallel affinity capture" ;
rdfs:comment "A specific pull down method where the protein of interest (bait) is endogenously expressed with at least two affinity tags (GFP, FLAG or others). The bait is purified in parallel using different purification protocols in contrast to tandem affinity purification (TAP) (publication currently in press)." ;
rdfs:subClassOf obo:MI_0096 .
obo:MI_0497 a rdfs:Class ;
rdfs:label "neutral component" ;
rdfs:comment "Molecule role in an experimental setting that does not have an embedded asymmetry." ;
rdfs:subClassOf obo:MI_0495 .
obo:MI_2039 a rdfs:Class ;
rdfs:label "smiles string" ;
rdfs:comment "SMILES string corresponding to drug structure" ;
rdfs:subClassOf obo:MI_1212 , obo:MI_2091 .
obo:MI_0426 a rdfs:Class ;
rdfs:label "light microscopy" ;
rdfs:comment "Light visible microscopy uses environmental light to illuminate the sample and produce a magnified image of the sample." ;
rdfs:subClassOf obo:MI_0428 .
obo:MI_0715 a rdfs:Class ;
rdfs:label "nucleic acid conjugation" ;
rdfs:comment "Bacterial conjugation is the transfer of genetic material between bacteria through cell-to-cell contact. Bacterial conjugation is often incorrectly regarded as the bacterial equivalent of sexual reproduction or mating. It is not actually sexual, as it does not involve the fusing of gametes and the creation of a zygote. It is merely the transfer of a conjugative plasmid from a donor cell to a recipient" ;
rdfs:subClassOf obo:MI_0704 .
obo:MI_1112 a rdfs:Class ;
rdfs:label "two hybrid prey pooling approach" ;
rdfs:comment "Individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners." ;
rdfs:subClassOf obo:MI_1111 .
obo:MI_1227 a rdfs:Class ;
rdfs:label "lap tag" ;
rdfs:comment "Tag encoding green fluorescent protein (GFP) , a TEV cleavage site, and a second purification tag such as S peptide or 6xHis. The tag can therefore be used for both localisation and affinity purification." ;
rdfs:subClassOf obo:MI_0677 .
obo:MI_2206 a rdfs:Class ;
rdfs:label "observed nucleic acid chemical modification" ;
rdfs:comment "Chemical modification observed on a nucleic acid molecule in the context of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition." ;
rdfs:subClassOf obo:MI_0668 .
obo:MI_1279 a rdfs:Class ;
rdfs:label "monophenotypic genetic enhancement" ;
rdfs:comment """An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation (which, on its own, has no effect on the phenotype in question) to a severity/penetrance beyond (further from wild type) that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab < a < b = wt [E = a]
OR
wt = b < a < ab [E = a]
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1271 , obo:MI_2382 .
obo:MI_2217 a rdfs:Class ;
rdfs:label "luciferase-c" ;
rdfs:comment "The c-terminus of a luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay." ;
rdfs:subClassOf obo:MI_1205 .
obo:MI_0387 a rdfs:Class ;
rdfs:label "alexa 488 label" ;
rdfs:comment "Alexa fluorescent dye analogue to Oregon Green 488 with an approximate excitation wavelength maximum of 488 nm." ;
rdfs:subClassOf obo:MI_0384 .
obo:MI_0486 a rdfs:Class ;
rdfs:label "uniprot knowledge base" ;
rdfs:comment """UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.
http://www.uniprot.org""" ;
rdfs:subClassOf obo:MI_0461 , obo:MI_0973 , obo:MI_1097 .
obo:MI_0363 a rdfs:Class ;
rdfs:label "inferred by author" ;
rdfs:comment "Evidence based on the author of a paper assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences." ;
rdfs:subClassOf obo:MI_0362 .
obo:MI_0200 a rdfs:Class ;
rdfs:label "degeranylation reaction" ;
rdfs:comment "S-geranylgeranyl-L-cysteine is cleaved and returns a C residue." ;
rdfs:subClassOf obo:MI_0212 .
obo:MI_0448 a rdfs:Class ;
rdfs:label "gene ontology" ;
rdfs:comment """The objective of Gene Ontology (GO) is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products.
http://www.ebi.ac.uk/GO""" ;
rdfs:subClassOf obo:MI_0447 , obo:MI_0461 .
obo:MI_0325 a rdfs:Class ;
rdfs:label "transfer rna" ;
rdfs:comment "The low molecular weight RNAs that specifically bind amino acids by aminoacetylation to form aminoacyl tRNA and which possess a special nucleotide triplet, the anticodon." ;
rdfs:subClassOf obo:MI_0320 .
obo:MI_2318 a rdfs:Class ;
rdfs:label "force measurement" ;
rdfs:comment "A technique that measures forces generated by interactions between molecules." ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_0960 a rdfs:Class ;
rdfs:label "mimix curation" ;
rdfs:comment "Paper has been curated to meet MIMIx specifications" ;
rdfs:subClassOf obo:MI_0955 .
obo:MI_0809 a rdfs:Class ;
rdfs:label "bimolecular fluorescence complementation" ;
rdfs:comment "The bimolecular fluorescence complementation (BiFC) is an assay for determination of protein interactions and/or their location in living cells. This approach is based on complementation between two non- fluorescent fragments of a protein fluorophore such as green fluorescent protein (GFP) or its derivatives. Interactions between proteins fused to each fragment bring the fragments together resulting in the reconstitution of a fully functional flourophore that can be identified through fluorescence spectroscopy or microscopy." ;
rdfs:subClassOf obo:MI_0051 , obo:MI_0090 .
obo:MI_1049 a rdfs:Class ;
rdfs:label "nucleicacid-protein" ;
rdfs:comment "Interaction between a nucleic acid and a corresponding protein or peptide." ;
rdfs:subClassOf obo:MI_1046 .
obo:MI_0312 a rdfs:Class ;
rdfs:label "nucleic acid transfection" ;
rdfs:comment "Introducing DNA into eukaryotic cells, such as animal cells, is called transfection. Transfection typically involves opening transient \"holes\" or gates in cells to allow the entry of extracellular molecules, typically supercoiled plasmid DNA, but also siRNA, among others. Transfection differs from transformation since the DNA is not generally incorporated into the cell's genome, it is only transiently expressed." ;
rdfs:subClassOf obo:MI_0704 .
obo:MI_0264 a rdfs:Class ;
rdfs:label "suppression partial alteration" ;
rdfs:comment """A mutation is the partial suppressor of a mutant phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock down' MI:0789. """ .
obo:MI_0792 a rdfs:Class ;
rdfs:label "antimorph" ;
rdfs:comment "The gene function has been antagonized by a mutation in another copy of the gene." ;
rdfs:subClassOf obo:MI_0787 .
obo:MI_0956 a rdfs:Class ;
rdfs:label "curation coverage" ;
rdfs:comment "Assessment to the extent of interactions captured in this paper" ;
rdfs:subClassOf obo:MI_0954 .
obo:MI_1238 a rdfs:Class ;
rdfs:label "mass spectrometry studies of subunit exchange" ;
rdfs:comment "Heavy/light isotope-labelled subunits are prepared and allowed to form their respective mature oligomeric structure. Oligomers are then mixed and subunit exchange is monitored, usually by electrospray ionisation-ion mobility spectrometry-mass spectrometry." ;
rdfs:subClassOf obo:MI_0069 .
obo:MI_0679 a rdfs:Class ;
rdfs:label "poly adenine" ;
rdfs:comment "A sequence of adenine nucleotides that is added to the 3' end of some primary transcript messenger RNA molecules in eukaryotes during post-transcriptional processing. The added tail is believed to confer stability to the molecule." ;
rdfs:subClassOf obo:MI_0320 .
obo:MI_2238 a rdfs:Class ;
rdfs:label "up-regulates quantity by expression" ;
rdfs:comment "The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B, by promoting its gene expression." ;
rdfs:subClassOf obo:MI_2237 .
obo:MI_2329 a rdfs:Class ;
rdfs:label "hydrophobic interaction chromatography" ;
rdfs:comment "Hydrophobic interaction chromatography (HIC) separates proteins according to differences in their surface hydrophobicity by utilizing a reversible interaction between these proteins and the hydrophobic surface of a HIC matrix." ;
rdfs:subClassOf obo:MI_0091 .
obo:MI_2166 a rdfs:Class ;
rdfs:label "ai" ;
rdfs:comment """The Arabidopsis Interactome network map is a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing ~6,200 highly reliable interactions between ~2,700 proteins.
http://interactome.dfci.harvard.edu/A_thaliana/index.php""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0906 a rdfs:Class ;
rdfs:label "au1 tag" ;
rdfs:comment "The protein of interest is expressed as a fusion to the peptide DTYRYI for which antibodies are commercially available." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_0468 a rdfs:Class ;
rdfs:label "hprd" ;
rdfs:comment """The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.
http://www.hprd.org/""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0010 a rdfs:Class ;
rdfs:label "beta galactosidase complementation" ;
rdfs:comment "Beta-galactosidase activity can be used to monitor the interaction of chimeric proteins. Pairs of inactive beta gal deletion mutants are capable of complementing to restore activity when fused to interacting protein partners. Critical to the success of this system is the choice of two poorly complementing mutant moieties, since strongly complementing mutants spontaneously assemble and produce functional beta-gal activity detectable in absence of any fused protein fragment." ;
rdfs:subClassOf obo:MI_0090 .
obo:MI_0156 a rdfs:Class ;
rdfs:label "n6-myristoyl-lysine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00087.""" .
obo:MI_0945 a rdfs:Class ;
rdfs:label "oxidoreductase activity electron transfer reaction" ;
rdfs:comment "An oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_1070 a rdfs:Class ;
rdfs:label "standard-based confidence" ;
rdfs:comment "Confidence scoring system based on comparison to a 'gold standard' set of known interacting molecules." ;
rdfs:subClassOf obo:MI_1064 .
obo:MI_0849 a rdfs:Class ;
rdfs:label "ncbi taxonomy" ;
rdfs:comment """The NCBI taxonomy database indexes over 55 000 organisms that are represented in the sequence databases with at least one nucleotide or protein sequence. The Taxonomy Browser can be used to view the taxonomic position or retrieve sequence and structural data for a particular organism or group of organisms. Searches of the NCBI taxonomy may be made on the basis of whole or partial organism names, and direct links to organisms commonly used in biological research are also provided. The Taxonomy Browser can also be used to display the number of nucleic acid sequences, protein sequences, and protein structures available for organisms included in the branch. From the data display for a particular organism, one can retrieve and download the sequence data for that organism, or protein 3D structure data if available.
http://www.ncbi.nlm.nih.gov/Taxonomy/""" ;
rdfs:subClassOf obo:MI_0473 .
obo:MI_0184 a rdfs:Class ;
rdfs:label "glutamyl 5-glycerylphosphorylethanolamine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00179.""" .
obo:MI_2177 a rdfs:Class ;
rdfs:label "pombase" ;
rdfs:comment """PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets.
www.pombase.org""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0360 a rdfs:Class ;
rdfs:label "secondary accession number" ;
rdfs:comment "Reference to the corresponding object in another database (like identity xref qualifier) but the identifier used in the external database is a secondary identifier or former accession number." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_0556 a rdfs:Class ;
rdfs:label "transglutamination reaction" ;
rdfs:comment "Gln-Lys cross-link catalyzed by a transglutaminase." ;
rdfs:subClassOf obo:MI_0195 .
obo:MI_1123 a rdfs:Class ;
rdfs:label "bindingdb" ;
rdfs:comment "BindingDB is a web-accessible public database of experimentally determined protein-ligand binding affinities for drug discovery. http://BindingDB.org" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0545 a rdfs:Class ;
rdfs:label "gpi-anchor amidated serine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00171.""" .
obo:MI_2109 a rdfs:Class ;
rdfs:label "solubility in dmso" ;
rdfs:comment "Solubility in DMSO" ;
rdfs:subClassOf obo:MI_2064 .
obo:MI_1038 a rdfs:Class ;
rdfs:label "silicon nanowire field-effect transistor" ;
rdfs:comment "Measures selective electrical response to molecules binding to the immobilised bait." ;
rdfs:subClassOf obo:MI_0968 .
obo:MI_0564 a rdfs:Class ;
rdfs:label "omega-n-methyl-arginine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00078.""" .
obo:MI_0274 a rdfs:Class ;
rdfs:label "synthetic growth defect" ;
rdfs:comment """Two silent mutations show growth defect when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')""" .
obo:MI_2408 a rdfs:Class ;
rdfs:label "CoVoc Coronavirus Vocabulary" ;
rdfs:comment """The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more.
https://www.ebi.ac.uk/ols/ontologies/COVOC""" ;
rdfs:subClassOf obo:MI_0473 .
obo:MI_1333 a rdfs:Class ;
rdfs:label "rogid" ;
rdfs:comment """SEGUID's are SHA-1 keys written in canonical base64 form with trailing = characters removed. ROG identifiers concatenate a SEGUID with a numerical taxonomy identifier. Therefore, the allowable characters in a SEGUID or ROG identifier are (in ascending ASCII or Unicode value):
+/0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
Lists of SEGUID or ROG identifiers were sorted in ascending ASCII-based lexicographical order.""" ;
rdfs:subClassOf obo:MI_1212 .
obo:MI_1324 a rdfs:Class ;
rdfs:label "conditioned medium" ;
rdfs:comment "Molecule present in media harvested from cultured cells." ;
rdfs:subClassOf obo:MI_0342 .
obo:MI_1307 a rdfs:Class ;
rdfs:label "defined set" ;
rdfs:comment "Two or more interactors, grouped to denote interchangeable function. Thus the addition of a single nucleotide residue during RNA transcription could be annotated with the definedSet NTP (members ATP, CTP, GTP, and UTP)." ;
rdfs:subClassOf obo:MI_1304 .
obo:MI_0741 a rdfs:Class ;
rdfs:label "peptide atlas" ;
rdfs:comment """PeptideAtlas addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms.
http://www.peptideatlas.org/""" ;
rdfs:subClassOf obo:MI_0737 .
obo:MI_1040 a rdfs:Class ;
rdfs:label "n-terminal range" ;
rdfs:comment "The N-terminal region of a sequence, exact coordinates not available." ;
rdfs:subClassOf obo:MI_0333 .
obo:MI_2003 a rdfs:Class ;
rdfs:label "commercial name" ;
rdfs:comment "Standard name of drug or any reagent as provided by its manufacturer." ;
rdfs:subClassOf obo:MI_1041 .
obo:MI_1249 a rdfs:Class ;
rdfs:label "isomerase assay" ;
rdfs:comment "Measurement of the catalysis of the structural rearrangement of isomers." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0680 a rdfs:Class ;
rdfs:label "single stranded deoxyribonucleic acid" ;
rdfs:comment "DNA that consists of only one chain of nucleotides rather than the two base pairing strands found in DNA in the double helix form." ;
rdfs:subClassOf obo:MI_0319 .
obo:MI_0336 a rdfs:Class ;
rdfs:label "greater-than" ;
rdfs:comment "Partially determined sequence position known to be in a location higher than a given position." ;
rdfs:subClassOf obo:MI_0333 .
obo:MI_2008 a rdfs:Class ;
rdfs:label "chemical formula" ;
rdfs:comment "Chemical formula describing atomic or elemental composition" ;
rdfs:subClassOf obo:MI_2086 .
obo:MI_0913 a rdfs:Class ;
rdfs:label "lc-spdp cross linker" ;
rdfs:comment """Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate, is an heterobifunctional, thiol-cleavable
and membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester
that will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond. LC-SPDP is a derivative of the classical SPDP with a longer spacer arm.""" ;
rdfs:subClassOf obo:MI_0912 .
obo:MI_2030 a rdfs:Class ;
rdfs:label "isoelectric point" ;
rdfs:comment "The isoelectric point (pI) is the pH at which a particular molecule or surface carries no net electrical charge. For an amino acid with only one amine and one carboxyl group, the pI can be calculated from the pKas of this molecule." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_1027 a rdfs:Class ;
rdfs:label "diphtamidation reaction" ;
rdfs:comment "A modification that converts an L-histidine residue to diphthamide." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0145 a rdfs:Class ;
rdfs:label "arginine amide" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00091.""" .
obo:MI_0704 a rdfs:Class ;
rdfs:label "nucleic acid delivery" ;
rdfs:comment "Method by which nucleic acids are delivered or engineered into a cell." ;
rdfs:subClassOf obo:MI_0307 .
obo:MI_0248 a rdfs:Class ;
rdfs:label "resid" ;
rdfs:comment """The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.
http://www.ebi.ac.uk/RESID/index.html""" ;
rdfs:subClassOf obo:MI_0447 .
obo:MI_1347 a rdfs:Class ;
rdfs:label "protein ontology" ;
rdfs:comment "PRO provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities, including specific modified forms, orthologous isoforms, and protein complexes." ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0083 a rdfs:Class ;
rdfs:label "peptide synthesis" ;
rdfs:comment "When one of the partners participates in the interaction with a relatively short peptide fragment, it is often convenient to precisely identify the minimal region that supports the interaction by synthesising a series of overlapping peptides and by testing them in the binding assay. Synthetic peptides that are identical with peptides synthesised in vivo are useful experimental tools for such studies. Peptides are routinely synthesised in a test tube from monomeric amino acids by condensation reactions that form peptide bonds. Peptides are constructed sequentially by coupling the C-terminus of a monomeric amino acid to the N-terminus of the growing peptide. To prevent unwanted reactions involving the amino groups and carboxyl groups of the side chains during the coupling steps, a protecting (blocking) group is attached to the side chains. Without these protecting groups, branched peptides would be generated. In the last steps of synthesis, the side chain-protecting groups are removed and the peptide is cleaved from the resin on which synthesis occurs." ;
rdfs:subClassOf obo:MI_0093 .
obo:MI_1240 a rdfs:Class ;
rdfs:label "disease causing amino-acid variant" ;
rdfs:comment "A naturally-occuring amino-acid variation to the reference sequence which results in the organism developing, or becoming susceptible to a particular disease condition." ;
rdfs:subClassOf obo:MI_1239 .
obo:MI_0710 a rdfs:Class ;
rdfs:label "nucleic acid transformation by treatment with divalent cation" ;
rdfs:comment "Stable introduction and expression of nucleic acid carried out by treatment with divalent cation." ;
rdfs:subClassOf obo:MI_0706 .
obo:MI_2380 a rdfs:Class ;
rdfs:label "genetic enhancement" ;
rdfs:comment "A genetic phenotype modification whereby one genetic perturbation enhances, or exacerbates, the phenotype of another genetic perturbation. Note that this may be an expected result." ;
rdfs:subClassOf obo:MI_2367 .
obo:MI_1321 a rdfs:Class ;
rdfs:label "ire1 reconstruction" ;
rdfs:comment "Upon interaction of N-terminal generated Ire1p-fusions, the Ire1p kinase domains oligomerize, transphosphorylate and activate their C-terminal RNAseL domains, which specifically splice the mRNA of a transcriptional activator, Hac1. The expression of the mature form of Hac1p leads to the interaction-specific expression of a reporter. Specifically designed to identify interactors of proteins found in the endoplasmic reticulum." ;
rdfs:subClassOf obo:MI_2412 .
obo:MI_0974 a rdfs:Class ;
rdfs:label "innatedb" ;
rdfs:comment "Human and mouse experimentally verified interactions and pathways involved in innate immunity." ;
rdfs:subClassOf obo:MI_0461 , obo:MI_0973 .
obo:MI_0607 a rdfs:Class ;
rdfs:label "small nuclear rna" ;
rdfs:comment "These RNA molecules are relatively short (less than 200 nucleotides each), and there are five of them (U1, U2, U4, U5, and U6) involved in the major form of pre-mRNA splicing. Known as snRNAs (small nuclear RNAs), each is complexed with at least seven protein subunits to form a snRNP (small nuclear ribonucleoprotein). These snRNPs form the core of the spliceosome." ;
rdfs:subClassOf obo:MI_0320 .
obo:MI_1187 a rdfs:Class ;
rdfs:label "damip" ;
rdfs:comment "A mutant form of DNA adenine methyltransferase (DamK9A) from E. coli is fused to the protein of interest and expressed. The fusion protein will bind to target binding sites and introduce N-6-adenine methylation in nearby sites in the genomic DNA. Methylated DNA fragments are enriched with an antibody against N-6-methyladenine and used for further analysis." ;
rdfs:subClassOf obo:MI_1184 .
obo:MI_0303 a rdfs:Class ;
rdfs:label "gene ontology synonym" ;
rdfs:comment "Synonym as used in Gene Ontology." ;
rdfs:subClassOf obo:MI_1041 .
obo:MI_0542 a rdfs:Class ;
rdfs:label "gpi-anchor amidated aspartate" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00168.""" .
obo:MI_0371 a rdfs:Class ;
rdfs:label "35s radiolabel" ;
rdfs:comment "Molecule labelled with 35 radio isotope of sulfur. Proteins are often metabolically labelled, usually be growth in 35S labelled culture medium." ;
rdfs:subClassOf obo:MI_0517 .
obo:MI_2199 a rdfs:Class ;
rdfs:label "specific site-labelling technology" ;
rdfs:comment "The interaction is detected through selective, chemical blockage of a specific site -which can be an active site- that becomes inaccessible once the participants are interacting. The interaction is detected through loss of signal of the chemical label" ;
rdfs:subClassOf obo:MI_2198 .
obo:MI_0167 a rdfs:Class ;
rdfs:label "n6,n6,n6-trimethyl-lysine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00083.""" .
obo:MI_0162 a rdfs:Class ;
rdfs:label "n5-methyl-glutamine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00080.""" .
obo:MI_0567 a rdfs:Class ;
rdfs:label "neddylation reaction" ;
rdfs:comment "Reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_1299 a rdfs:Class ;
rdfs:label "complex composition" ;
rdfs:comment "A description of the molecule types of which a macromolecular complex is composed." ;
rdfs:subClassOf obo:MI_0314 .
obo:MI_0334 a rdfs:Class ;
rdfs:label "c-terminal position" ;
rdfs:comment "Term describing the last amino acid of a peptide chain." ;
rdfs:subClassOf obo:MI_0333 .
obo:MI_2340 a rdfs:Class ;
rdfs:label "electron microscopy 3D helical reconstruction" ;
rdfs:comment "Three-dimensional (3D) reconstruction of helical objects from a collection of fiber images recorded with a transmission electron microscope." ;
rdfs:subClassOf obo:MI_0410 .
obo:MI_0726 a rdfs:Class ;
rdfs:label "reverse two hybrid" ;
rdfs:comment "Yeast strains are generated in which expression of DB-X/AD-Y or DBPX hybrid proteins is toxic under particular conditions (negative selection). Under these conditions, dissociation of an interaction should provide a selective advantage thereby facilitating detection: a few growing yeast colonies in which DB-X/AD-Y (or DBPX/binding site) fail to interact should be identified among many nongrowing colonies containing interacting DB-X/AD-Y or DBPX/binding site." ;
rdfs:subClassOf obo:MI_0003 , obo:MI_0232 .
obo:MI_1045 a rdfs:Class ;
rdfs:label "curation content" ;
rdfs:comment "Indicates source, depth and standards by which an entry has been added to a database." ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_0553 a rdfs:Class ;
rdfs:label "o4'-sulfo-tyrosine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00181.""" .
obo:MI_0400 a rdfs:Class ;
rdfs:label "affinity technology" ;
rdfs:comment "Techniques which depend upon the strength of the interaction between two entities." ;
rdfs:subClassOf obo:MI_0401 .
obo:MI_1339 a rdfs:Class ;
rdfs:label "supercharged green fluorescent protein" ;
rdfs:comment "Mutated green fluorescent protein with altered net charge and thus altered intermolecular properties, such as resistence to aggregation." ;
rdfs:subClassOf obo:MI_0367 .
obo:MI_0386 a rdfs:Class ;
rdfs:label "alexa 430 label" ;
rdfs:comment "Alexa fluorescent dye analogue to Lucifer Yellow with an approximate excitation wavelength maximum of 430 nm." ;
rdfs:subClassOf obo:MI_0384 .
obo:MI_0226 a rdfs:Class ;
rdfs:label "ion exchange chromatography" ;
rdfs:comment "Stable complexes and their component proteins can be separated on the basis of their net charge by ion-exchange chromatography. If a protein has a net positive charge at pH 7, it will usually bind to a column of beads containing carboxylate groups, and can then be eluted by increasing the concentration of sodium chloride or another salt in the eluting buffer by competition of sodium ions with positively charged groups on the protein for binding to the column. Protein that have a low density of net positive charge will tend to emerge first, followed by those having a higher charge density. Positively charged complexes or proteins (cationic proteins) can be separated on negatively charged carboxymethyl-cellulose (CM-cellulose) columns. Conversely, negatively charged complexes or proteins (anionic proteins) can be separated by chromatography on positively charged diethylaminoethyl-cellulose (DEAE-cellulose) columns." ;
rdfs:subClassOf obo:MI_0091 .
obo:MI_0107 a rdfs:Class ;
rdfs:label "surface plasmon resonance" ;
rdfs:comment "This method measures formation of complex by monitoring changes in the resonance angle of light impinging on a gold surface as a result of changes in the refractive index of the surface. A ligand of interest (small molecule, peptide, protein, sugar, lipid, nucleic acid) is immobilized on a gold surface, and the interacting partner is injected in buffer flow over it. Biomolecules that interact with the immobilized ligand are retained on the surface, and alter the resonance angle of impinging light as a result of the change in refractive index brought about by the increased biomolecule mass retained on the surface. Since all the biomolecules belonging to the same class have the same refractive index and since there is a linear correlation between resonance angle shift and biomolecule concentration near the surface, this allows one to measure changes in concentration at the surface as a consequence of interaction. Furthermore, this is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation." ;
rdfs:subClassOf obo:MI_0659 , obo:MI_0968 .
obo:MI_2084 a rdfs:Class ;
rdfs:label "organisms affected" ;
rdfs:comment "Names of organisms which are affected, positively or negatively, by the drug." ;
rdfs:subClassOf obo:MI_2089 .
obo:MI_0122 a rdfs:Class ;
rdfs:label "n-acetyl-alanine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00050.""" .
obo:MI_1216 a rdfs:Class ;
rdfs:label "cGFP" ;
rdfs:comment "c-terminal fragment of green fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC)." ;
rdfs:subClassOf obo:MI_0367 , obo:MI_1215 .
obo:MI_0935 a rdfs:Class ;
rdfs:label "converging genetic interaction" ;
rdfs:comment """An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than would be expected from the original phenotypes, in effect making the organism more \"wild type\" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
E < ab <= wt
OR
wt <= ab < E
where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0208 .
obo:MI_0924 a rdfs:Class ;
rdfs:label "camjedb" ;
rdfs:comment """Camjedb is a comprehensive database for information on the genome of Campylobacter jejuni.
http://www.sanger.ac.uk/Projects/C_jejuni/""" ;
rdfs:subClassOf obo:MI_1094 .
obo:MI_1094 a rdfs:Class ;
rdfs:label "genome databases" ;
rdfs:comment "Databases which are the responsible for the maintenance and subsequent annotation of one or more genomic sequences." ;
rdfs:subClassOf obo:MI_0683 .
obo:MI_0072 a rdfs:Class ;
rdfs:label "monoclonal antibody western blot" ;
rdfs:comment "Western blot assay carried out using monospecific antibodies produced in the supernatant of a cell line obtained by fusing a lymphocyte B to a myeloma cell line or selected by phage display technology." ;
rdfs:subClassOf obo:MI_0113 .
obo:MI_0967 a rdfs:Class ;
rdfs:label "chembl compound" ;
rdfs:comment "ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets." ;
rdfs:subClassOf obo:MI_1349 , obo:MI_2054 .
obo:MI_0795 a rdfs:Class ;
rdfs:label "asynthetic genetic interaction" ;
rdfs:comment """An effect in which individual perturbations of different genes and their combination result in the same mutant phenotype, to the same degree of severity/penetrance. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a = b = ab != wt
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0935 , obo:MI_2386 .
obo:MI_0134 a rdfs:Class ;
rdfs:label "n6-acetyl-lysine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00064.""" .
obo:MI_2391 a rdfs:Class ;
rdfs:label "transphenotypic genetic suppression (complete)" ;
rdfs:comment "A transphenotypic suppression in which the double genetic perturbation phenotype is equivalent to the wild type (or control) phenotype." ;
rdfs:subClassOf obo:MI_1281 , obo:MI_2390 .
obo:MI_1176 a rdfs:Class ;
rdfs:label "sequence based prediction of gene regulatory region binding sites" ;
rdfs:comment "Sequence analysis of the regulatory region of a gene used to predict specific elements, transcription factor binding sites (TFBS), where binding of specific transcription factors can occur." ;
rdfs:subClassOf obo:MI_0101 .
obo:MI_2249 a rdfs:Class ;
rdfs:label "post transcriptional regulation" ;
rdfs:comment "Any process that control gene expression at the RNA level, between the transcription and the translation of the gene." ;
rdfs:subClassOf obo:MI_2245 .
obo:MI_0827 a rdfs:Class ;
rdfs:label "x-ray tomography" ;
rdfs:comment "X-ray Tomography is a branch of X-ray microscopy. A series of projection images are used to calculate a three dimensional reconstruction of an object. The technique has found many applications in materials science and later in biology and biomedical research. In terms of the latter, the National Center for X-ray Tomography (NCXT) is one of the principle developers of this technology, in particular for imaging whole, hydrated cells." ;
rdfs:subClassOf obo:MI_0428 .
obo:MI_2289 a rdfs:Class ;
rdfs:label "virotrap" ;
rdfs:comment "The bait fused to a viral protein (e.g. HIV-1 GAG protein) allows the trapping of interaction partners (preys) within virus-like particles (VLPs) that bud from mammalian cells. Once the VLPs are enriched and purified, this technique allows the isolation of multimeric complexes as well as binary interactions and their subsequent identification by methods such as MS and western blots." ;
rdfs:subClassOf obo:MI_0401 .
obo:MI_0270 a rdfs:Class ;
rdfs:label "conditional synthetic lethal" ;
rdfs:comment """Two silent mutations show a conditional synthetic lethal phenotype when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)""" .
obo:MI_1268 a rdfs:Class ;
rdfs:label "nubg" ;
rdfs:comment "N-terminal ubiquitin moiety (residues 1-34) containing a Ile13Gly mutation." ;
rdfs:subClassOf obo:MI_1267 .
obo:MI_0887 a rdfs:Class ;
rdfs:label "histone acetylase assay" ;
rdfs:comment "In histone acetylation the histones are acetylated on lysine residues in the N-terminal tail as part of gene regulation. Typically, these reactions are catalyzed by enzymes with \"histone acetyltransferase\" (HAt)" ;
rdfs:subClassOf obo:MI_0889 .
obo:MI_1101 a rdfs:Class ;
rdfs:label "standard inchi key" ;
rdfs:comment "The Standard InChIKey has five distinct components, a 14-character hash of the basic (Mobile-H) InChI layer, an 8-character hash of the remaining layers (except for the /p segment, which accounts for added or removed protons: it is not hashed at all; the number of protons is encoded at the end of the standard InChIKey.) , a 1 flag character, a 1 version character and the last character is a [de]protonation indicator. The overall length of InChIKey is fixed at 27 characters, including separators (dashes)." ;
rdfs:subClassOf obo:MI_0970 .
obo:MI_2351 a rdfs:Class ;
rdfs:label "enhancer gene" ;
rdfs:comment "A gene whose genetic perturbation enhances the phenotype resulting from a different genetic perturbation." ;
rdfs:subClassOf obo:MI_0495 .
obo:MI_0517 a rdfs:Class ;
rdfs:label "radiolabel" ;
rdfs:comment "A radiolabelled molecule has radio isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule." ;
rdfs:subClassOf obo:MI_0253 .
obo:MI_0941 a rdfs:Class ;
rdfs:label "competitor" ;
rdfs:comment "Binds to an interacting molecule in competition with other interaction candidates, for example at a shared binding site." ;
rdfs:subClassOf obo:MI_0500 .
obo:MI_0952 a rdfs:Class ;
rdfs:label "imex secondary" ;
rdfs:comment "Deprecated IMEx identifiers should be exchanged in IMEx records and stored as cross reference with this qualifier." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_0235 a rdfs:Class ;
rdfs:label "14c radiolabel" ;
rdfs:comment "Molecule labelled with the radio isotope 14 of carbon atoms." ;
rdfs:subClassOf obo:MI_0517 .
obo:MI_0173 a rdfs:Class ;
rdfs:label "s-phospho-cysteine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00043.""" .
obo:MI_1120 a rdfs:Class ;
rdfs:label "cYFP" ;
rdfs:comment "c-terminal fragment of yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC)." ;
rdfs:subClassOf obo:MI_0368 , obo:MI_1215 .
obo:MI_0141 a rdfs:Class ;
rdfs:label "n-acetyl-tyrosine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00062.""" .
obo:MI_0689 a rdfs:Class ;
rdfs:label "activation domain tag" ;
rdfs:comment "Part of a transcription factor responsible for the activation of DNA transcription. Such tags are generally used in two hybrid experiments where they are fused to a prey polypeptide tested for its ability to interact with a bait fused to a DNA binding domain tag." ;
rdfs:subClassOf obo:MI_0240 .
obo:MI_2378 a rdfs:Class ;
rdfs:label "dosage growth defect (sensu BioGRID)" ;
rdfs:comment "Increased dosage of one gene causes a growth defect in (or enhances an existing growth defect of) a strain with perturbation of another gene." ;
rdfs:subClassOf obo:MI_2399 .
obo:MI_2115 a rdfs:Class ;
rdfs:label "pharmacokinetics attribute name" ;
rdfs:comment "Determination of the fate of substances administered externally to a living organism i.e. the study of what the body does to a drug." ;
rdfs:subClassOf obo:MI_2086 .
obo:MI_0411 a rdfs:Class ;
rdfs:label "enzyme linked immunosorbent assay" ;
rdfs:comment "Following non-covalent binding of a purified primary ligand to a solid phase, a blocking reagent is added to prevent any non-specific binding. A specific antigen is then allowed to bind to the primary ligand. Unbound antigen is removed by washing and a secondary antibody conjugated to an enzyme (e.g. horseradish peroxidase) is added. Following a washing step to remove unbound secondary ligand, the extent to which a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme in a given time is determined by spectrophotometry using a standard microplate absorbance reader. A similar type of approach can be utilized to detect enzymatic activities. The substrate, attached to a solid phase is incubated in the presence of the enzyme and the enzymatic modification is monitored by an antibody that is specific for the modified substrate (for instance a phosphorylated protein)." ;
rdfs:subClassOf obo:MI_0421 , obo:MI_0892 .
obo:MI_0902 a rdfs:Class ;
rdfs:label "rna cleavage" ;
rdfs:comment "Any process by which an RNA molecule is cleaved at specific sites or in a regulated manner." ;
rdfs:subClassOf obo:MI_0910 .
obo:MI_2193 a rdfs:Class ;
rdfs:label "iclip" ;
rdfs:comment """iCLIP allows for the stringent purification of UV cross-linked protein-RNA complexes, using immunoprecipitation followed by SDS-PAGE and membrane transfer. The radiolabelled protein-RNA complexes are then excised from the membrane, and treated with proteinase to release the RNA. This leaves one or two amino acids at the RNA cross-link site. The RNA is then reverse transcribed using barcoded primers. Because reverse transcription stops prematurely at the cross-link site, iCLIP allows RNA-protein interaction sites to be identified at high resolution.
https://en.wikipedia.org/wiki/ICLIP""" ;
rdfs:subClassOf obo:MI_2191 .
obo:MI_2142 a rdfs:Class ;
rdfs:label "phospholipidosis" ;
rdfs:comment "Causes excess phospholipids to accumulate within cells." ;
rdfs:subClassOf obo:MI_2135 .
obo:MI_2367 a rdfs:Class ;
rdfs:label "genetic interaction (sensu phenotype modification)" ;
rdfs:comment "A multigenic phenotype result in which the phenotype of a single genetic perturbation has been modified by the introduction of one or more additional genetic perturbations." ;
rdfs:subClassOf obo:MI_2402 .
obo:MI_0140 a rdfs:Class ;
rdfs:label "n-acetyl-tryptophan" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00785.""" .
obo:MI_0618 a rdfs:Class ;
rdfs:label "caution" ;
rdfs:comment "Warning about errors or grounds for confusion. Can be associated to an interaction, experiment, CV term or any participant." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_0665 , obo:MI_0666 , obo:MI_0667 , obo:MI_0668 , obo:MI_0669 .
obo:MI_0094 a rdfs:Class ;
rdfs:label "protein staining" ;
rdfs:comment "A wide range of dyes have been used over the years to visualise proteins in polyacrylamide gels - Coomasie Blue and silver-staining being two classical methods. Fluorescent dyes such as Nile Red and SYPRO Orange are now increasingly used due to their superior dynamic range. Use of non-denaturing gels can allow visualisation of protein protein interactions. Several dyes can be used to specifically indicate residue modification, however this methodology will give no information as the number of residues modified or their position within the protein sequence. Examples include the use of acid fuscian or the fluorescent dansyl hydrazine to show protein glycosylation." ;
rdfs:subClassOf obo:MI_0659 .
obo:MI_0737 a rdfs:Class ;
rdfs:label "peptide sequence database" ;
rdfs:comment "database storing sequences detected by peptide identification methods." ;
rdfs:subClassOf obo:MI_0683 .
obo:MI_0152 a rdfs:Class ;
rdfs:label "s-geranylgeranyl-cysteine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00113.""" .
obo:MI_2419 a rdfs:Class ;
rdfs:label "ensemblplants" ;
rdfs:comment """Ensembl Plants is a browser for plant genomes.
https://plants.ensembl.org/""" ;
rdfs:subClassOf obo:MI_1013 .
obo:MI_0112 a rdfs:Class ;
rdfs:label "ubiquitin reconstruction" ;
rdfs:comment "The split-ubiquitin system provides a method for examining the interactions of membrane proteins. In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety (\"Cub\", residues 35-76) and an N-terminal ubiquitin moiety (\"Nub\", residues 1-34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor that can be cleaved off by ubiquitin specific proteases. Upon bait-prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes." ;
rdfs:subClassOf obo:MI_2412 .
obo:MI_1344 a rdfs:Class ;
rdfs:label "erythrosin iodoacetamide label" ;
rdfs:comment "Fluoresceine-derived label." ;
rdfs:subClassOf obo:MI_0939 .
obo:MI_2148 a rdfs:Class ;
rdfs:label "investigational drug" ;
rdfs:comment "A drug currently under clinical development." ;
rdfs:subClassOf obo:MI_2040 .
obo:MI_0865 a rdfs:Class ;
rdfs:label "fluorescence acceptor donor pair" ;
rdfs:comment "Pair of fluorophores attached to the same molecule used in a fret experiment to observe the details of conformational changes." ;
rdfs:subClassOf obo:MI_2336 .
obo:MI_0133 a rdfs:Class ;
rdfs:label "n2-acetyl-lysine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00057.""" .
obo:MI_0209 a rdfs:Class ;
rdfs:label "geranylgeranylation reaction" ;
rdfs:comment "Attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).Reversible reaction that can affect C residue." ;
rdfs:subClassOf obo:MI_0211 .
obo:MI_2228 a rdfs:Class ;
rdfs:label "ceitec" ;
rdfs:comment "Interactions and complexes curated by scientists at the Central European Institute of Technology (CEITEC)." ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_2048 a rdfs:Class ;
rdfs:label "drug biotransformation" ;
rdfs:comment "The chemical conversion of drugs to other compounds in the body, excluding degradation due to any inherent chemical instability of drugs in biological media." ;
rdfs:subClassOf obo:MI_2115 .
obo:MI_1257 a rdfs:Class ;
rdfs:label "rhodamine label" ;
rdfs:comment "Rhodamines are supplements to fluoresceins, as they offer longer wavelength emission maxima and provide opportunities for multicolor labeling or staining." ;
rdfs:subClassOf obo:MI_0857 .
obo:MI_0464 a rdfs:Class ;
rdfs:label "cygd" ;
rdfs:comment """The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis.
http://mips.gsf.de/proj/yeast/CYGD.
http://mips.gsf.de/genre/proj/mpact""" ;
rdfs:subClassOf obo:MI_0489 , obo:MI_1094 , obo:MI_1106 .
obo:MI_0190 a rdfs:Class ;
rdfs:label "interaction type" ;
rdfs:comment "Connection between molecule." ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_0062 a rdfs:Class ;
rdfs:label "his tag coimmunoprecipitation" ;
rdfs:comment """The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies.
OBSOLETE redundant term. Map to feature type: his-tagged (MI:0521) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).""" .
obo:MI_1310 a rdfs:Class ;
rdfs:label "de-ADP-ribosylation reaction" ;
rdfs:comment "Measure of hydrolytic reactions that release ADP-ribose." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_1034 a rdfs:Class ;
rdfs:label "nuclease assay" ;
rdfs:comment "Measures the cleavage of phosphodiesterase bonds between the nucleotide subunits of nucleic acids." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0838 a rdfs:Class ;
rdfs:label "kelvin" ;
rdfs:comment "The kelvin (K) is the SI unit of thermodynamic temperature. It is defined by taking the fixed numerical value of the Boltzmann constant k to be 1.380649×10-23 when expressed in the unit J·K-1, which is equal to kg·m2·s-2·K-1, where the kilogram, metre and second are defined in terms of h, c and caesium frequency. It is equivalent to -273.15°C / -459.67°F." ;
rdfs:subClassOf obo:MI_0647 .
obo:MI_1171 a rdfs:Class ;
rdfs:label "composite binding site formation" ;
rdfs:comment "The preformation of a complex results in the generation of a continuous binding site that spans more than one component of this complex. The functional binding site does not exist outside the context of the preformed complex." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_1170 .
obo:MI_0101 a rdfs:Class ;
rdfs:label "sequence based prediction" ;
rdfs:comment "Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict interacting pairs." ;
rdfs:subClassOf obo:MI_0063 .
obo:MI_0629 a rdfs:Class ;
rdfs:label "complex-properties" ;
rdfs:comment "Information on the complex being annotated. Attribute generally associated to an interaction." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_0665 .
obo:MI_0251 a rdfs:Class ;
rdfs:label "gene product" ;
rdfs:comment "Reference pointing to a protein object from its genomic or nucleic acid sequence." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_2326 a rdfs:Class ;
rdfs:label "nanoluc-n" ;
rdfs:comment "The n-terminus of the nanoluc luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay." ;
rdfs:subClassOf obo:MI_2325 .
obo:MI_2366 a rdfs:Class ;
rdfs:label "multigenic phenotype result" ;
rdfs:comment "The phenotype outcome resulting from two or more genetic perturbations to an organism, individually and in combination." ;
rdfs:subClassOf obo:MI_2384 .
obo:MI_0844 a rdfs:Class ;
rdfs:label "phosphotransfer reaction" ;
rdfs:comment "Reaction where a phosphate is transferred between two proteins of a phosphorelay system." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0397 a rdfs:Class ;
rdfs:label "two hybrid array" ;
rdfs:comment "Two-hybrid screening can be done in a colony array format, in which each colony expresses a defined pair of proteins. Because the particular protein pair expressed in each colony is defined by its position in the array, positive signals identify interacting proteins without further characterization, thus obviating the need for DNA purification and sequencing. The interrogation of a two-hybrid colony array usually involves a mating strategy in which every DNA binding domain hybrid (the bait) is tested against all activation domain hybrids (the preys) in a grid pattern. Arrays usually use full-length open reading frames." ;
rdfs:subClassOf obo:MI_0018 .
obo:MI_0237 a rdfs:Class ;
rdfs:label "33p radiolabel" ;
rdfs:comment "Molecule labelled with the radio isotope 33 of phosphorus atoms." ;
rdfs:subClassOf obo:MI_0517 .
obo:MI_0089 a rdfs:Class ;
rdfs:label "protein array" ;
rdfs:comment "The protein array technology allows the screening of biochemical activities or binding abilities of hundreds or thousands of protein samples in parallel. After synthesis and purification by high-throughput methodologies, the proteins are printed onto the chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with labelled molecules to identify proteins that bind to the bait." ;
rdfs:subClassOf obo:MI_0008 .
obo:MI_0575 a rdfs:Class ;
rdfs:label "alliance for cellular signaling" ;
rdfs:comment """Alliance for Cellular Signaling (AfCS -Nature) store yeast 2-hybrid Interaction data and expression data. Information and data are freely available to all.
http://www.signaling-gateway.org""" ;
rdfs:subClassOf obo:MI_0461 , obo:MI_0489 .
obo:MI_0668 a rdfs:Class ;
rdfs:label "feature attribute name" ;
rdfs:comment "Attribute name of annotation associated to a feature element." ;
rdfs:subClassOf obo:MI_0590 .
obo:MI_2305 a rdfs:Class ;
rdfs:label "carbohydrate chemical modification increasing interaction" ;
rdfs:comment "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate." ;
rdfs:subClassOf obo:MI_2276 .
obo:MI_0268 a rdfs:Class ;
rdfs:label "suppression underexpression" ;
rdfs:comment """Underexpression is the suppressor of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'under expressed' MI:0223. """ .
obo:MI_2153 a rdfs:Class ;
rdfs:label "pdr health" ;
rdfs:comment "Hyperlink to PDRhealth entry for the given drug (if it exists)" ;
rdfs:subClassOf obo:MI_2054 .
obo:MI_0459 a rdfs:Class ;
rdfs:label "mmdb" ;
rdfs:comment """MMDB (Molecular Modeling DataBase), is a subset of three-dimensional structures obtained from the Protein Data Bank.
http://www.ncbi.nlm.nih.gov/Structure""" ;
rdfs:subClassOf obo:MI_0447 , obo:MI_0461 .
obo:MI_1090 a rdfs:Class ;
rdfs:label "bimane label" ;
rdfs:comment "Bromobimanes are low molecular weight non-fluorescent alkyl halides which react with thiol groups to produce highly fluorescent derivatives. The bimane labels, monobromobimane, dibromobimane, and monobromotrimethylammoniobimane, are derivatives of syn-9,10-dioxabimane:1,5-diazabicyclo[3.3.0]octa-3,6-diene-2,8-dione." ;
rdfs:subClassOf obo:MI_0857 .
obo:MI_2098 a rdfs:Class ;
rdfs:label "anti-bacterial" ;
rdfs:comment "Therapeutic category or general category of drug -anti-bacterial" ;
rdfs:subClassOf obo:MI_2041 .
obo:MI_0056 a rdfs:Class ;
rdfs:label "full identification by DNA sequencing" ;
rdfs:comment "Sequencing occurs during the course of the experiment. DNA sequencing is the process of determining the nucleotide order of a given DNA fragment. Thus far, most DNA sequencing has been performed using the chain termination method developed by Frederick Sanger. This technique uses sequence-specific termination of a DNA synthesis reaction using modified nucleotide substrates. However, new sequencing technologies such as Pyrosequencing are generating the majority of data." ;
rdfs:subClassOf obo:MI_0078 , obo:MI_0659 .
obo:MI_0730 a rdfs:Class ;
rdfs:label "pubchem" ;
rdfs:comment """PubChem provides information on the biological activities of small molecules.
http://pubchem.ncbi.nlm.nih.gov/""" ;
rdfs:subClassOf obo:MI_2054 .
obo:MI_1102 a rdfs:Class ;
rdfs:label "mapped-identity" ;
rdfs:comment "Sequence has been computationally remapped following removal or update of the original sequence in the underlying sequence database." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_2354 a rdfs:Class ;
rdfs:label "hypostatic gene" ;
rdfs:comment "A gene whose genetic perturbation phenotype is masked by a different genetic perturbation." ;
rdfs:subClassOf obo:MI_0495 .
obo:MI_1132 a rdfs:Class ;
rdfs:label "mutation increasing interaction strength" ;
rdfs:comment "Region of a molecule whose mutation or deletion increases significantly interaction strength." ;
rdfs:subClassOf obo:MI_0382 .
obo:MI_2381 a rdfs:Class ;
rdfs:label "aphenotypic phenotype result" ;
rdfs:comment "A phenotype result in which each of multiple perturbations results in no (or only a minimal) phenotype for the phenotype in question." ;
rdfs:subClassOf obo:MI_2384 .
obo:MI_2184 a rdfs:Class ;
rdfs:label "mtbbase" ;
rdfs:comment """Collection and Refinement of Physiological Data on Mycobacterium tuberculosis in the form of GO annitations. MTBBASE data has also been rendered as pathway information in Reactome.
http://www.ark.in-berlin.de/Site/MTBbase.html
http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_121237.1""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0643 a rdfs:Class ;
rdfs:label "ki" ;
rdfs:comment "Equilibrium constant for dissociation of an inhibitor. Unit Molar." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0578 a rdfs:Class ;
rdfs:label "maltose binding protein tag" ;
rdfs:comment "The protein is expressed and purified as a fusion to the glutathione maltose-binding protein (MBP). The MBP-fusion protein can be purified by affinity chromatography using an amylose resin." ;
rdfs:subClassOf obo:MI_0240 .
obo:MI_0323 a rdfs:Class ;
rdfs:label "heterogeneous nuclear rna" ;
rdfs:comment "A heterogeneous mixture of RNA molecules with a rapid turnover rate that occurs in cell nuclei during protein synthesis; it is the form of RNA synthesized in eukaryotes by RNA polymerase II, which is translated into protein." ;
rdfs:subClassOf obo:MI_0320 .
obo:MI_1211 a rdfs:Class ;
rdfs:label "liposome binding assay" ;
rdfs:comment "Lipid binding proteins incubated with liposomes of known lipid content. Mixture is then centrifuged and proteins bound to liposomes separated out." ;
rdfs:subClassOf obo:MI_0027 .
obo:MI_2204 a rdfs:Class ;
rdfs:label "micro rna" ;
rdfs:comment "A micro RNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals, and some viruses, which functions in RNA silencing and post-transcriptional regulation of gene expression." ;
rdfs:subClassOf obo:MI_0320 .
obo:MI_0342 a rdfs:Class ;
rdfs:label "sample process" ;
rdfs:comment "Indicates the sample context in which each interacting molecule is presented to its partner." ;
rdfs:subClassOf obo:MI_0346 .
obo:MI_2321 a rdfs:Class ;
rdfs:label "high-throughput sequencing" ;
rdfs:comment "High-throughput (a.k.a. \"next-generation\") sequencing applies to methods that allow for sequencing of genome-scale number of bases." ;
rdfs:subClassOf obo:MI_0078 .
obo:MI_0536 a rdfs:Class ;
rdfs:label "glycosyl-threonine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00164.""" .
obo:MI_0461 a rdfs:Class ;
rdfs:label "interaction database" ;
rdfs:comment "Databases that contain experimental or predictive molecular interaction data." ;
rdfs:subClassOf obo:MI_0444 .
obo:MI_1165 a rdfs:Class ;
rdfs:label "allosteric change in structure" ;
rdfs:comment "The allosteric mechanism where changes in the local structure of an allosteric molecule result in altered binding or catalytic properties." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_1164 .
obo:MI_0096 a rdfs:Class ;
rdfs:label "pull down" ;
rdfs:comment "A specific affinity chromatography method where a molecule of interest (bait) is bound to a column, often via an affinity tag expressed as a protein fusion (GST, HIS tag and others) or chemically linked to the bait molecule . The molecule may be expressed or synthesised and purified first, often in an heterologous system, bound to the matrix at high concentration and then challenged with a solution or cellular extract containing the candidate partner molecules. Alternatively, a multi-molecular complex may be adsorbed to the resin and the retained binding molecules subsequently identified." ;
rdfs:subClassOf obo:MI_0004 .
obo:MI_0353 a rdfs:Class ;
rdfs:label "cross-reference type" ;
rdfs:comment "Qualifier to describe the type of information a cross-reference is pointing to." ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_0817 a rdfs:Class ;
rdfs:label "molecular weight estimation by silver staining" ;
rdfs:comment "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with silver." ;
rdfs:subClassOf obo:MI_0816 .
obo:MI_0477 a rdfs:Class ;
rdfs:label "entrez gene/locuslink" ;
rdfs:comment """LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci.
http://www.ncbi.nlm.nih.gov/LocusLink/""" ;
rdfs:subClassOf obo:MI_1109 .
obo:MI_0687 a rdfs:Class ;
rdfs:label "fluorescent protein tag" ;
rdfs:comment "Protein having well characterized fluorescence excitation and emission spectra used as fusion with a protein under study to facilitate its localisation or identification." ;
rdfs:subClassOf obo:MI_0240 .
obo:MI_0590 a rdfs:Class ;
rdfs:label "attribute name" ;
rdfs:comment "Collection of topics describing the free text stored as an attribute value." ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_2400 a rdfs:Class ;
rdfs:label "monophenotypic neutral multigenic phenotype result" ;
rdfs:comment """A phenotype result in which only one of two perturbations results in the phenotype in question and the phenotype of the combined perturbations a and b result in the expected phenotype, namely the same phenotype as the single perturbation that exhibits that phenotype. The interpretation is that no interaction was observed between the two genes, for the indicated phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab = a ≠ wt = b [E = a]
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0932 , obo:MI_2382 .
obo:MI_0217 a rdfs:Class ;
rdfs:label "phosphorylation reaction" ;
rdfs:comment "Reversible reaction that can affect D,C,H,S,T,Y,R residues." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0466 a rdfs:Class ;
rdfs:label "ecocyc" ;
rdfs:comment """EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli K12 MG1655.
http://ecocyc.org/""" ;
rdfs:subClassOf obo:MI_1106 .
obo:MI_1160 a rdfs:Class ;
rdfs:label "allosteric effector" ;
rdfs:comment "A ligand that elicits an allosteric response upon binding to a target molecule." ;
rdfs:subClassOf obo:MI_0500 , obo:MI_0664 , obo:MI_1149 .
obo:MI_0354 a rdfs:Class ;
rdfs:label "cellular component" ;
rdfs:comment "Cross reference pointing to a Gene Ontology -'cellular component' term." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_0832 a rdfs:Class ;
rdfs:label "half cystine" ;
rdfs:comment "A protein modification that is effectively either one half of a cystine cross-link, or a cysteine residue with one hydrogen atom or proton removed" .
obo:MI_0791 a rdfs:Class ;
rdfs:label "hypomorph" ;
rdfs:comment "The gene function has been partially reduced compared to wild-type by altering its sequence e.g. a temperature sensitive mutant." ;
rdfs:subClassOf obo:MI_0787 .
obo:MI_0051 a rdfs:Class ;
rdfs:label "fluorescence technology" ;
rdfs:comment "Techniques based upon the measurement of the emission of one or more photons by a molecule activated by the absorption of a quantum of electro-magnetic radiation. Typically the emission, which is characterised by a wavelength that is longer than the one of excitatory radiation, occurs within 10-8 seconds." ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_0476 a rdfs:Class ;
rdfs:label "ensembl" ;
rdfs:comment """Ensembl is a joint project between the EMBL-EBI and the Wellcome Trust Sanger Institute that aims at developing a system that maintains automatic annotation of large eukaryotic genomes.
http://www.ensembl.org""" ;
rdfs:subClassOf obo:MI_1094 .
obo:MI_0595 a rdfs:Class ;
rdfs:label "translocation end" ;
rdfs:comment "Xref pointing to a GO compartment term describing the end location of a migrating molecule." ;
rdfs:subClassOf obo:MI_0593 .
obo:MI_0531 a rdfs:Class ;
rdfs:label "o-(adp-ribosyl)-serine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00242.""" .
obo:MI_2101 a rdfs:Class ;
rdfs:label "biotech drug" ;
rdfs:comment "A natural product, such as a protein or peptide, which is produced used biotechnology as a drug." ;
rdfs:subClassOf obo:MI_2040 .
obo:MI_0503 a rdfs:Class ;
rdfs:label "self" ;
rdfs:comment "Molecule that makes intramolecular interactions." ;
rdfs:subClassOf obo:MI_0495 , obo:MI_0500 .
obo:MI_2024 a rdfs:Class ;
rdfs:label "patent number" ;
rdfs:comment "number of the patent describing a drug's synthesis or use." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_1091 a rdfs:Class ;
rdfs:label "publication title" ;
rdfs:comment "Title of the publication." ;
rdfs:subClassOf obo:MI_1093 .
obo:MI_2164 a rdfs:Class ;
rdfs:label "mind" ;
rdfs:comment "The Membrane-based Interactome Network Database (MIND) holds a network of over 25,000 putative PPI (PPPI) obtained by screening of over 3,000 unique Arabidopsis ORFs for pair-wise interactions using the yeast mating-based split-ubiquitin system (mbSUS). http://cas-biodb.cas.unt.edu/project/mind/index.php" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0085 a rdfs:Class ;
rdfs:label "phylogenetic profile" ;
rdfs:comment "The phylogenetic profile of a protein stores information about the presence and the absence of that protein in a set of genomes. By clustering identical or similar profiles, proteins with similar functions and potentially interacting are identified." ;
rdfs:subClassOf obo:MI_0058 .
obo:MI_0196 a rdfs:Class ;
rdfs:label "covalent interaction" ;
rdfs:comment """Physical interaction mediated by covalent bond rearrangement.
OBSOLETE use covalent binding (MI:0195) instead.""" .
obo:MI_1352 a rdfs:Class ;
rdfs:label "uracil interference assay" ;
rdfs:comment "In uracil interference assays, the DNA will be amplified by PCR in the presence of a mixture of TTP and dUTP to randomly replace thymine by deoxyuracil residues before the binding assay. If T nucleotides involved in protein-DNA interactions are replaced by deoxyuracil, protein binding is prevented. After isolating the protein-DNA complex, DNA is cleaved with uracil-N-glycosylase, which specifically targets uracil bases, and the products are electrophoresed on a denaturing polyacrylamide gel. As a result, DNA in which a thymine involved in binding is replaced by uracil will be depleted. Hence, although the pattern looks like a footprint, the blank region means \"contact points\"." ;
rdfs:subClassOf obo:MI_0605 .
obo:MI_1207 a rdfs:Class ;
rdfs:label "renilla-c" ;
rdfs:comment "The c-terminus of the renilla luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay." ;
rdfs:subClassOf obo:MI_0896 , obo:MI_1215 .
obo:MI_0206 a rdfs:Class ;
rdfs:label "farnesylation reaction" ;
rdfs:comment "Reversible reaction that can affect C residue." ;
rdfs:subClassOf obo:MI_0211 .
obo:MI_0520 a rdfs:Class ;
rdfs:label "ha tag" ;
rdfs:comment "The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemagglutinin protein) for which antibodies are commercially available." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_2195 a rdfs:Class ;
rdfs:label "clash" ;
rdfs:comment "This method is a variation of CRAC where after combined cross-linking and affinity purification of protein-RNA complexes, RNA-RNA interactions are specifically detected. Base-paired RNA molecules can be linked together while tagging RNA with oligonucleotides, generating chimeric RNAs that allow identification of RNA-RNA pairs." ;
rdfs:subClassOf obo:MI_2194 .
obo:MI_1341 a rdfs:Class ;
rdfs:label "set member" ;
rdfs:comment "Indicates that this protein is a member of a set of proteins with similar sequence and/or function." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_1247 a rdfs:Class ;
rdfs:label "microscale thermophoresis" ;
rdfs:comment "Measurement of the directed movement of particles in a microscopic temperature gradient. Any change of the hydration shell of biomolecules due to changes in their structure/conformation results in a relative change of movement along the temperature gradient and is used to determine binding affinities, binding kinetics and activity kinetics. Events such as the phosphorylation of a protein or the binding of small molecules to a target can be monitored." ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_1084 a rdfs:Class ;
rdfs:label "photon donor" ;
rdfs:comment "Any molecule that is able to transfer a photon to another chemical species." ;
rdfs:subClassOf obo:MI_0918 .
obo:MI_2013 a rdfs:Class ;
rdfs:label "pubchem" ;
rdfs:comment """NCBI's PubChem database identification number (if molecule is in PubChem).
OBSOLETE as redudant with MI:0730""" .
obo:MI_2302 a rdfs:Class ;
rdfs:label "carbohydrate chemical modification disrupting interaction" ;
rdfs:comment "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate." ;
rdfs:subClassOf obo:MI_2299 .
obo:MI_2225 a rdfs:Class ;
rdfs:label "zinc" ;
rdfs:comment """ZINC is a database of commercially available compounds for virtual screening. It uses publicly available bioactivity data to allow investigators to access chemical tools for biology.
http://zinc15.docking.org/""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_2377 a rdfs:Class ;
rdfs:label "dosage lethality (sensu BioGRID)" ;
rdfs:comment "Increased dosage of one gene causes lethality in combination with another viable genetic perturbation." ;
rdfs:subClassOf obo:MI_0794 , obo:MI_2394 .
obo:MI_1064 a rdfs:Class ;
rdfs:label "interaction confidence" ;
rdfs:comment "A method used to derive a numerical or empirical measure of confidence in a particular interaction, or in the identification of the participants in an interaction." ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_0195 a rdfs:Class ;
rdfs:label "covalent binding" ;
rdfs:comment "Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners." ;
rdfs:subClassOf obo:MI_0407 .
obo:MI_0139 a rdfs:Class ;
rdfs:label "n-acetyl-threonine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00061.""" .
obo:MI_0698 a rdfs:Class ;
rdfs:label "dna directed rna polymerase assay" ;
rdfs:comment "Measures the catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." ;
rdfs:subClassOf obo:MI_0696 .
obo:MI_0806 a rdfs:Class ;
rdfs:label "pdbj" ;
rdfs:comment """PDBj(Protein Data Bank Japan) maintains the database for the protein structures with financial assistance from the Institute for Bioinformatics Research and Development of Japan Science and Technology Corporation(BIRD-JST), collaborating with the Research Collaboration for Structural Bioinformatics(RCSB) and the MSD in the European Bioinformatics Institute(MSD-EBI) in EU. All three organizations serve as deposition, data processing and distribution sites.
http://www.pdbj.org/""" ;
rdfs:subClassOf obo:MI_0805 .
obo:MI_0365 a rdfs:Class ;
rdfs:label "enzyme tag" ;
rdfs:comment "Molecule under study is fused to an enzyme, for example alkaline phosphatase, and measure of enzyme activity can be taken as indicative of presence of protein." ;
rdfs:subClassOf obo:MI_0240 .
obo:MI_2136 a rdfs:Class ;
rdfs:label "herg binding" ;
rdfs:comment "Binds to the hERG (human Ether-a-go-go Related Gene) (Q12809) which encodes the Kv11.1 potassium ion channel responsible for the repolarizing IKr current in the cardiac action potential." ;
rdfs:subClassOf obo:MI_2135 .
obo:MI_0671 a rdfs:Class ;
rdfs:label "antibodies" ;
rdfs:comment "This annotation topic should contain information about antibodies when specific antibodies (monoclonal or polyclonal raised against specific regions of the proteins or purified in a specific manner) have been used." ;
rdfs:subClassOf obo:MI_0665 .
obo:MI_1172 a rdfs:Class ;
rdfs:label "altered physicochemical compatibility" ;
rdfs:comment "The addition of a PTM to an interaction interface affects the physicochemical compatibility of the binding site with its binding partner. This can either induce or enhance an interaction, or result in inhibition or even abrogation of an interaction. Multisite modification can mediate rheostatic regulation of the interaction." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_1170 .
obo:MI_1261 a rdfs:Class ;
rdfs:label "oregon green label" ;
rdfs:comment "Oregon Green 488 and Oregon Green 514 dyes are fluorinated analogs of fluoresceins" ;
rdfs:subClassOf obo:MI_0939 .
obo:MI_0440 a rdfs:Class ;
rdfs:label "saturation binding" ;
rdfs:comment "Saturation binding experiments measure specific ligand binding at equilibrium at various concentrations of the ligand. Analysis of these data can determine receptor number and affinity." ;
rdfs:subClassOf obo:MI_0400 .
obo:MI_1053 a rdfs:Class ;
rdfs:label "data source" ;
rdfs:comment "The source of the data entered into the database." ;
rdfs:subClassOf obo:MI_1045 .
obo:MI_2265 a rdfs:Class ;
rdfs:label "de-acetylated residue" ;
rdfs:comment "A protein modification that effectively remove an acyl group from a protein." ;
rdfs:subClassOf obo:MI_2262 .
obo:MI_1330 a rdfs:Class ;
rdfs:label "dnp" ;
rdfs:comment "Fluorescent dye. Also acts as an uncoupler of oxidative phosphorylation in the mitochondria." ;
rdfs:subClassOf obo:MI_0857 .
obo:MI_2392 a rdfs:Class ;
rdfs:label "mutual genetic enhancement (expected)" ;
rdfs:comment "A genetic enhancement in which the double genetic perturbation phenotype is equivalent to the expected phenotype, according to some chosen neutrality function." ;
rdfs:subClassOf obo:MI_0932 , obo:MI_2401 .
obo:MI_2112 a rdfs:Class ;
rdfs:label "chemical stability at pH 2" ;
rdfs:comment "Chemical stability at pH 2" ;
rdfs:subClassOf obo:MI_2055 .
obo:MI_0525 a rdfs:Class ;
rdfs:label "v5 tag" ;
rdfs:comment "The protein of interest is expressed as a fusion to the peptide GKPIPNPLLGLDST for which antibodies are commercially available." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_2012 a rdfs:Class ;
rdfs:label "kegg compound" ;
rdfs:comment "Kyoto Encyclopedia of Genes and Genomes compound identification number (if molecule is in KEGG)" ;
rdfs:subClassOf obo:MI_0470 .
obo:MI_2337 a rdfs:Class ;
rdfs:label "chemiluminiscence donor" ;
rdfs:comment "Luminiscence source which emits electromagnetic radiation of given wavelength through a chemical process." ;
rdfs:subClassOf obo:MI_2334 .
obo:MI_1183 a rdfs:Class ;
rdfs:label "nuclease footprinting" ;
rdfs:comment "Binding of a molecule to a strand of nucleic acid protects that region of nucleic acid from the action of a nuclease. The protected region can subsequently be sequenced and the binding site identified." ;
rdfs:subClassOf obo:MI_0605 .
obo:MI_2296 a rdfs:Class ;
rdfs:label "3' range" ;
rdfs:comment "Term describing the downstream region of a nucleotide sequence, exact coordinates not available." ;
rdfs:subClassOf obo:MI_0333 .
obo:MI_0514 a rdfs:Class ;
rdfs:label "in gel phosphatase assay" ;
rdfs:comment "Substrate pre-radiolabelled either synthetically or through the action of a kinase transferring an isotope of phosphate from a nucleotide. Substrate then exposed to phosphate under assay conditions. Substrate isolated by gel electrophoresis and loss of radiolabelling confirmed by autoradiography." ;
rdfs:subClassOf obo:MI_0434 .
obo:MI_1124 a rdfs:Class ;
rdfs:label "pathwaycommons" ;
rdfs:comment """Allows the user to browse and search pathways across multiple public pathway databases.
http://www.pathwaycommons.org""" ;
rdfs:subClassOf obo:MI_1106 .
obo:MI_0045 a rdfs:Class ;
rdfs:label "experimental interaction detection" ;
rdfs:comment "Methods based on laboratory experiments to determine an interaction." ;
rdfs:subClassOf obo:MI_0001 .
obo:MI_2343 a rdfs:Class ;
rdfs:label "genomic coordinates" ;
rdfs:comment "Coordinates of a reference DNA sequence in the genome, providing information about the chromosome name, start and end of the sequence, optionally including the strand as well if it applies." ;
rdfs:subClassOf obo:MI_0666 , obo:MI_0668 .
obo:MI_2411 a rdfs:Class ;
rdfs:label "mac tag" ;
rdfs:comment "The protein of interest is expressed as a fusion to a MAC-tag, which contains a twin-strep affinity tag and BirA* in one construct, requires generation of only one isogenic cell line and allows one-step protein purification by Strep-Tactin matrix for both AP–MS and BioID pipelines." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_1143 a rdfs:Class ;
rdfs:label "aminoacylation reaction" ;
rdfs:comment "Aminoacylation is the process of adding an aminoacyl group to a compound." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_2332 a rdfs:Class ;
rdfs:label "g1 spin label" ;
rdfs:comment "Paramagnetic molecule formed by a gadolinium complex based on 4-mercaptomethyl-dipicolinic acid (4MMDPA) attached to a cysteine side chain." ;
rdfs:subClassOf obo:MI_0845 .
obo:MI_0376 a rdfs:Class ;
rdfs:label "cy5 label" ;
rdfs:comment "The organic cyanine Cy5 emits maximally at 670 nm." ;
rdfs:subClassOf obo:MI_0374 .
obo:MI_1222 a rdfs:Class ;
rdfs:label "mbinfo" ;
rdfs:comment "MBInfo is a wiki based, multimedia, educational resource providing up to date reviews on topics relating to mechanobiology (http://www.mechanobio.info/)." ;
rdfs:subClassOf obo:MI_0461 , obo:MI_0973 .
obo:MI_1154 a rdfs:Class ;
rdfs:label "positive cooperative effect" ;
rdfs:comment "This term specifies that an interaction augments a subsequent interaction." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_1153 .
obo:MI_0800 a rdfs:Class ;
rdfs:label "single nonmonotonic genetic interaction defined by inequality" ;
rdfs:comment "The phenotype resulting from genetic perturbation of B shows opposing effects in the WT and a backgrounds (for example, b > WT and ab < a); or, a shows opposing effects in the WT and b backgrounds, but not both. E.g., WT > a > ab > b." .
obo:MI_1048 a rdfs:Class ;
rdfs:label "smallmolecule-protein" ;
rdfs:comment "Interaction between a small molecule and a corresponding protein or peptide." ;
rdfs:subClassOf obo:MI_1046 .
obo:MI_2433 a rdfs:Class ;
rdfs:label "turbo id tag" ;
rdfs:comment "An engineered biotin ligase that uses ATP to convert biotin into biotin–AMP, a reactive intermediate that covalently labels proximal proteins. TurboID has faster labeling kinetics than \\bir\\a and will operate at lower temperatures." ;
rdfs:subClassOf obo:MI_2431 .
obo:MI_0409 a rdfs:Class ;
rdfs:label "dna footprinting" ;
rdfs:comment """Experimental method used to identify the region of a nucleic acid involved in an interaction with a protein. One sample of a radiolabeled nucleic acid of known sequence is submitted to partial digestion. A second sample is incubated with its interacting partner and then is submitted to the same partial digestion. The two samples are then analyzed in parallel by electrophoresis on a denaturing acrylamide gel. After autoradiography the identification of the bands that correspond to fragments missing from the lane loaded with the second sample reveals the region of the nucleic acid that is protected from nuclease digestion upon binding.
OBSOLETE because redundant with MI:0417 'footprinting' combined with interactor type MI:0319 'DNA'
replace by:MI:0417""" .
obo:MI_0584 a rdfs:Class ;
rdfs:label "fluorescence acceptor" ;
rdfs:comment "Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific donor fluorophore, then re-emiting its own characteristic fluorescence." ;
rdfs:subClassOf obo:MI_2335 .
obo:MI_2276 a rdfs:Class ;
rdfs:label "carbohydrate chemical modification" ;
rdfs:comment "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction. The process can involve covalent modifications (i.e. sulfations) or other forms of chemical modification." ;
rdfs:subClassOf obo:MI_0252 .
obo:MI_1000 a rdfs:Class ;
rdfs:label "hydroxylase assay" ;
rdfs:comment "Measurement of the irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_2157 a rdfs:Class ;
rdfs:label "experimental water solubility" ;
rdfs:comment "Water solubility in mg/mL or g/L." ;
rdfs:subClassOf obo:MI_2027 , obo:MI_2161 .
obo:MI_0821 a rdfs:Class ;
rdfs:label "molecular weight estimation by autoradiography" ;
rdfs:comment "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining by autoradiography." ;
rdfs:subClassOf obo:MI_0815 .
obo:MI_0488 a rdfs:Class ;
rdfs:label "psi-mi" ;
rdfs:comment "PSI-MI." ;
rdfs:subClassOf obo:MI_0444 .
obo:MI_2236 a rdfs:Class ;
rdfs:label "up-regulates activity" ;
rdfs:comment "The effect of a modulator entity A on a modulated entity B that increases the frequency, rate or extent of the molecular function of B, an elemental biological activity occurring at the molecular level, such as catalysis or binding (GO:0044093)." ;
rdfs:subClassOf obo:MI_2235 .
obo:MI_0465 a rdfs:Class ;
rdfs:label "dip" ;
rdfs:comment """The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions.
http://dip.doe-mbi.ucla.edu/""" ;
rdfs:subClassOf obo:MI_0461 , obo:MI_0973 .
obo:MI_1290 a rdfs:Class ;
rdfs:label "genetic suppression (complete)" ;
rdfs:comment """An effect in which the perturbation of one gene results in complete suppression (to wild type) of the mutant phenotype caused by perturbation of another gene. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
wt = ab != a = E
where 'a' is the observed phenotype values of an individual perturbation, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_2379 .
obo:MI_2399 a rdfs:Class ;
rdfs:label "deleterious multigenic phenotype result" ;
rdfs:comment "A phenotype modification whereby introduction of a genetic perturbation in an organism with another genetic perturbation results in, or enhances, a phenotype in that organism." ;
rdfs:subClassOf obo:MI_2366 .
obo:MI_1236 a rdfs:Class ;
rdfs:label "proline isomerase assay" ;
rdfs:comment "Measurment of the conversion between cis- and trans- peptide bonds formed by the amine group of a proline. Peptide bonds to proline, and to other N-substituted amino acids (such as sarcosine), are able to populate both the cis and trans isomers the cis and trans isomers of the X-Pro peptide bond (where X represents any amino acid) both experience steric clashes with the neighboring substitution and are nearly equal energetically. Hence, the fraction of X-Pro peptide bonds in the cis isomer under unstrained conditions ranges from 10-40%; the fraction depends slightly on the preceding amino acid, with aromatic residues favoring the cis isomer slightly." ;
rdfs:subClassOf obo:MI_1249 .
obo:MI_0080 a rdfs:Class ;
rdfs:label "partial DNA sequence identification by hybridization" ;
rdfs:comment "Genes are recognised by hybridization of a probe with a fragment of the gene sequence." ;
rdfs:subClassOf obo:MI_1180 .
obo:MI_0507 a rdfs:Class ;
rdfs:label "tag" ;
rdfs:comment "Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule." ;
rdfs:subClassOf obo:MI_0505 .
obo:MI_1255 a rdfs:Class ;
rdfs:label "stilbene label" ;
rdfs:comment "1,2-Diphenylethene" ;
rdfs:subClassOf obo:MI_0857 .
obo:MI_1326 a rdfs:Class ;
rdfs:label "CLONE OF phosphotransfer reaction" ;
rdfs:comment "Reaction where a phosphate is transferred between two proteins of a phosphorelay system. " .
obo:MI_1350 a rdfs:Class ;
rdfs:label "orphanet" ;
rdfs:comment "Orphanet is a reference portal for information on rare diseases and orphan drugs. Its aim is to help improve the diagnosis, care and treatment of patients with rare diseases." ;
rdfs:subClassOf obo:MI_1336 .
obo:MI_0667 a rdfs:Class ;
rdfs:label "controlled vocabulary attribute name" ;
rdfs:comment "Attribute name of annotation associated to a CV term." ;
rdfs:subClassOf obo:MI_0590 .
obo:MI_2055 a rdfs:Class ;
rdfs:label "chemical stability" ;
rdfs:comment "chemical stability occurs when a substance is in a (dynamic) chemical equilibrium with its environment. In this well-defined state, the substance is expected to persist indefinitely (assuming that the environment does not change). A substance which is not chemically stable (yet exists) is metastable or kinetically persistent." ;
rdfs:subClassOf obo:MI_2086 .
obo:MI_1169 a rdfs:Class ;
rdfs:label "homotropic allostery" ;
rdfs:comment "The type of allostery that occurs when the two ligands whose binding is allosterically coupled are chemically identical." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_1167 .
obo:MI_1008 a rdfs:Class ;
rdfs:label "sumoylase assay" ;
rdfs:comment "Measurement of the reversible reaction that creates a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0413 a rdfs:Class ;
rdfs:label "electrophoretic mobility shift assay" ;
rdfs:comment "This method proves the interaction between a nucleic acid and a protein partner. On the same electrophoresis gel 1 lane is loaded with a nucleic acid of known sequence, a second lane is loaded with the same nucleic acid together with a purified protein (or a protein mixture). The nucleic acid is often radio-labelled to enable visualisation by autoradiography. Comparison of the nucleic acid migration in the two lanes enables the retardation of the nucleic acid due to its interaction with a protein to be observed." ;
rdfs:subClassOf obo:MI_0807 .
obo:MI_2017 a rdfs:Class ;
rdfs:label "heterogen" ;
rdfs:comment """The HET records are used to describe non-standard residues, such as prosthetic groups, inhibitors, solvent molecules, and ions for
which coordinates are supplied. Groups are considered HET if they are:
- not one of the standard amino acids, and
- not one of the nucleic acids (C, G, A, T, U, and I), and
- not one of the modified versions of nucleic acids (+C, +G, +A,
+T, +U, and +I), and
- not an unknown amino acid or nucleic acid where UNK is used to
indicate the unknown residue name.
Het records also describe heterogens for which the chemical identity is unknown, in which case the group is assigned the hetID UNK.""" ;
rdfs:subClassOf obo:MI_0460 , obo:MI_0472 , obo:MI_0806 .
obo:MI_2388 a rdfs:Class ;
rdfs:label "genetic over-suppression" ;
rdfs:comment "A genetic phenotype modification whereby introduction of one genetic perturbation to another genetic perturbation results in the opposite phenotype compared to the phenotype of the starting individual genetic perturbation. For example, one perturbation results in an increased quality phenotype and introduction of the second perturbation results in a decreased quality phenotype. Note that if the individual genetic perturbations have opposite phenotypes, this may be an expected result." ;
rdfs:subClassOf obo:MI_2379 .
obo:MI_0061 a rdfs:Class ;
rdfs:label "his pull down" ;
rdfs:comment """The bait protein is expressed and purified fused to an amino or carboxyterminal tail containing a variable number of histidines. The bait protein is normally attached to a metal (usually nickel) resin.
OBSOLETE redundant term. Map to feature type : his-tagged (MI:0521) and Interaction detection method: pull down (MI:0096).""" .
obo:MI_1288 a rdfs:Class ;
rdfs:label "transphenotypic enhancing genetic interaction" ;
rdfs:comment """An effect in which two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is more severe than the phenotype observed with the same directionality. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a < wt < b < ab
OR
ab < a < wt < b
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0208 , obo:MI_2387 .
obo:MI_2023 a rdfs:Class ;
rdfs:label "material safety data sheet" ;
rdfs:comment "Material Safety Data Sheet (if it exists). A Material Safety Data Sheet (MSDS) is designed to provide both workers and emergency personnel with the proper procedures for handling or working with a particular substance. MSDS's include information such as physical data (melting point, boiling point, flash point etc.), toxicity, health effects, first aid, reactivity, storage, disposal, protective equipment, andspill/leak procedures. These are of particular use if a spill or other accident occurs." ;
rdfs:subClassOf obo:MI_2086 .
obo:MI_2348 a rdfs:Class ;
rdfs:label "sequential bret-fret" ;
rdfs:comment "In sequential BRET-FRET (BRET combined with FRET) bioluminiscence generated by a luciferase triggers acceptor excitation by BRET and subsequent energy transfer to a FRET acceptor. This technique can identify multimolecular complexes through detection of the resulting fluoresecence." ;
rdfs:subClassOf obo:MI_0051 .
obo:MI_1295 a rdfs:Class ;
rdfs:label "monophenotypic genetic over-suppression" ;
rdfs:comment """An effect in which the perturbation of one gene (which has no individual effect on the phenotype in question), when combined with a perturbation of another gene (which causes the phenotype in question), results in a mutant phenotype opposite (relative to wild type) to that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
E = a < b = wt < ab
OR
ab < wt = b < a = E
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1286 , obo:MI_2382 , obo:MI_2388 .
obo:MI_2191 a rdfs:Class ;
rdfs:label "clip" ;
rdfs:comment """Combination of cross-linking and co-immunoprecipitation aimed to find protein-RNA interactions. The canonical method uses first a cross-linking procedure over a tissue sample or lysate, and the immunoprecipitated with specific antibodies for the protein of interest. Unspecific proteins are digested via proteinase K treatment. RNA can be then identified via Northern blotting or using RT-PCR and then sequencing of the generated cDNA.
https://en.wikipedia.org/wiki/CLIP""" ;
rdfs:subClassOf obo:MI_0430 .
obo:MI_0131 a rdfs:Class ;
rdfs:label "n-acetyl-isoleucine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00056.""" .
obo:MI_0318 a rdfs:Class ;
rdfs:label "nucleic acid" ;
rdfs:comment "Linear polymers of nucleotides, linked by 3',5' phosphodiester linkages." ;
rdfs:subClassOf obo:MI_0383 .
obo:MI_2135 a rdfs:Class ;
rdfs:label "toxicity attribute name" ;
rdfs:comment "The mechanism by which a substance can harm humans or animals." ;
rdfs:subClassOf obo:MI_2089 .
obo:MI_0023 a rdfs:Class ;
rdfs:label "colocalization/visualisation technologies" ;
rdfs:comment """Techniques enabling the identification of the subcellular localisation of a protein or complex. Two different proteins show a similar distribution in the cell are said to co-localise. Obsolete since combination of Interaction Detection Method and Interaction Type.
OBSOLETE. Consider using imaging techniques (MI:0428) as interaction detection method coupled with colocalisation (MI:0401) as interaction type and predetermined (MI:0396) as participant detection.""" .
obo:MI_2054 a rdfs:Class ;
rdfs:label "bioactive entity reference" ;
rdfs:comment "General on-line reference to other details about a drug or other bioactive entity." ;
rdfs:subClassOf obo:MI_0473 .
obo:MI_0040 a rdfs:Class ;
rdfs:label "electron microscopy" ;
rdfs:comment "Electron microscopy methods provide insights into the structure of biological macromolecules and their supramolecular assemblies. Resolution is on average around 10 Angstroms but can reach the atomic level when the samples analysed are 2D crystals. Different types of samples can be analysed by electron microscopy: crystals, single particles like viruses, macromolecular complexes or entire cells and tissue sections. Samples can be chemically fixed or vitrified by rapid freezing in liquid ethane, and then transferred into the electron microscope. Data collection consists of the recording of electron diffraction data (2D crystals) and images. Depending on the type of sample, different approaches are used to analyse and merge images and electron diffraction data." ;
rdfs:subClassOf obo:MI_0428 .
obo:MI_0012 a rdfs:Class ;
rdfs:label "bioluminescence resonance energy transfer" ;
rdfs:comment "In this variation of the FRET assay the donor fluorophore is replaced by a luciferase (typically Renilla luciferase). In the presence of its substrate, the luciferase catalyses a bioluminescent reaction that excites the acceptor fluorophore through a resonance energy transfer mechanism. As with FRET the energy transfer occurs only if the protein fused to the luciferase and the one fused to the acceptor fluorophore are in close proximity (10-100 Angstrom)." ;
rdfs:subClassOf obo:MI_0051 .
obo:MI_0708 a rdfs:Class ;
rdfs:label "monoclonal antibody immunostaining" ;
rdfs:comment "A monospecific antibody for the protein of interest is available, this is used to detect a specific protein within a cell or tissue sample." ;
rdfs:subClassOf obo:MI_0422 .
obo:MI_1272 a rdfs:Class ;
rdfs:label "converging genetic epistasis" ;
rdfs:comment """An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in the same direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
((a* < b < wt) OR (wt < b < a*)) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0935 , obo:MI_1284 , obo:MI_2385 .
obo:MI_2231 a rdfs:Class ;
rdfs:label "coexpression" ;
rdfs:comment "This approach infers interacting pairs of proteins looking at expression data coming from transcript expression datasets. Co-expressed pairs of genes are ranked and predicted to be interacting proteins as well." ;
rdfs:subClassOf obo:MI_0046 .
obo:MI_0654 a rdfs:Class ;
rdfs:label "fentomolar" ;
rdfs:comment """10E-15 moles per liter of solution.
OBSOLETE: term redundant with the schema exponent attribute of the parameter.""" .
obo:MI_0343 a rdfs:Class ;
rdfs:label "cdna library" ;
rdfs:comment "Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process." ;
rdfs:subClassOf obo:MI_0342 .
obo:MI_0276 a rdfs:Class ;
rdfs:label "blue native page" ;
rdfs:comment "Blue native PAGE (BN-PAGE) permits a high-resolution separation of multi-protein complexes under native conditions. Blue native (BN)-PAGE is a charge shift method, in which the electrophoretic mobility of a complex is determined by the negative charge of the bound Coomassie dye and the size and shape of the complex. Coomassie does not act as a detergent and preserves the structure of complexes. Importantly, the resolution of BN-PAGE is much higher than that of other methods such as gel filtration or sucrose-gradient ultracentrifugation. Combined with other pre-purifications or dialysis steps this method permits the analysis of multi-protein complexes of whole cellular lysates by BN-PAGE." ;
rdfs:subClassOf obo:MI_0404 .
obo:MI_0613 a rdfs:Class ;
rdfs:label "function" ;
rdfs:comment "Biological function of a participant or of an interaction." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_0666 .
obo:MI_1283 a rdfs:Class ;
rdfs:label "cisphenotypic inter-suppressing genetic interaction" ;
rdfs:comment """An effect in which individual perturbations of different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination has a phenotype more severe/penetrant than the least severe/penetrant and less severe/penetrant than the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* < ab < b < wt [E = a*]
OR
wt < b < ab < a* [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1282 .
obo:MI_0955 a rdfs:Class ;
rdfs:label "curation depth" ;
rdfs:comment "Assessment of the depth to which a paper has been curated" ;
rdfs:subClassOf obo:MI_0954 .
obo:MI_0599 a rdfs:Class ;
rdfs:label "figure legend" ;
rdfs:comment "Text pointing to a specific paper figure legend where the experimental evidences for an interaction are to be found." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_0665 .
obo:MI_2124 a rdfs:Class ;
rdfs:label "total clearance" ;
rdfs:comment "The clearance of a drug is the volume of plasma from which the drug is completely removed per unit time. The amount eliminated is proportional to the concentration of the drug in the blood." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0151 a rdfs:Class ;
rdfs:label "s-farnesyl-cysteine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00111.""" .
obo:MI_0693 a rdfs:Class ;
rdfs:label "gal4 dna binding domain" ;
rdfs:comment """Part of the yeast transcription factor GAL4 (amino acids 11-38) specifically responsible for DNA binding of a 17 base-pair long sequence in the upstream activating sequence of galactose-induced genes.
""" ;
rdfs:subClassOf obo:MI_0688 .
obo:MI_0472 a rdfs:Class ;
rdfs:label "pdbe" ;
rdfs:comment """The Protein Data Bank in Europe - the European project for the collection, management and distribution of data about macromolecular structures, derived in part from the Protein Data Bank (PDB).
http://www.ebi.ac.uk/pdbe/""" ;
rdfs:subClassOf obo:MI_0805 .
obo:MI_0676 a rdfs:Class ;
rdfs:label "tandem affinity purification" ;
rdfs:comment "Tandem affinity purification allows rapid purification under native conditions of complexes, even when expressed at their natural level. Prior knowledge of complex composition or function is not required. The TAP method requires fusion of the a multiple tag, either N- or C-terminally, to the target (or bait) protein of interest. The multiple tag allows two steps purification steps ensuring a highly selective complex purification." ;
rdfs:subClassOf obo:MI_0004 .
obo:MI_2006 a rdfs:Class ;
rdfs:label "biotech product preparation" ;
rdfs:comment "Description of the drug (for biotech drugs) describing its composition and/or preparation." ;
rdfs:subClassOf obo:MI_2089 .
obo:MI_2203 a rdfs:Class ;
rdfs:label "primer extension assay" ;
rdfs:comment "Primer extension can be used to determine the 3' end of a given sequence of RNA. This technique requires a radiolabelled primer which is complementary to a region near the 3' end of the RNA. The primer is allowed to anneal to the RNA and reverse transcriptase is used to synthesize a strand of DNA from the RNA until it reaches the 5' end of the RNA. By denaturing the hybrid and using the extended primer DNA strand as a marker on an electrophoretic gel, it is possible to determine the transcriptional start site." ;
rdfs:subClassOf obo:MI_1193 .
obo:MI_1075 a rdfs:Class ;
rdfs:label "beilstein" ;
rdfs:comment "The Beilstein database is in the field of organic chemistry, in which compounds are uniquely identified by their Beilstein Registry Number." ;
rdfs:subClassOf obo:MI_2054 .
obo:MI_1308 a rdfs:Class ;
rdfs:label "resulting sequence" ;
rdfs:comment """Used to specify the identity of the residue (or residues) introduced by mutation or variant (of child terms). The attribute would be used concurrently with the description
provided in the feature name.""" ;
rdfs:subClassOf obo:MI_0668 .
obo:MI_2243 a rdfs:Class ;
rdfs:label "down-regulates quantity by repression" ;
rdfs:comment "The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B, by preventing its gene expression." ;
rdfs:subClassOf obo:MI_2242 .
obo:MI_0229 a rdfs:Class .
obo:MI_1315 a rdfs:Class ;
rdfs:label "complex recommended name" ;
rdfs:comment "The most accepted name in the literature for this complex." ;
rdfs:subClassOf obo:MI_1041 .
obo:MI_2370 a rdfs:Class ;
rdfs:label "synthetic lethality (sensu BioGRID)" ;
rdfs:comment "Mutation of multiple genes in combination that results in lethality when individual single mutations are viable." ;
rdfs:subClassOf obo:MI_0794 , obo:MI_2394 .
obo:MI_2180 a rdfs:Class ;
rdfs:label "agbase" ;
rdfs:comment """AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products. Their long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. They use the Gene Ontology for functional annotation.
http://www.agbase.msstate.edu/""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_2041 a rdfs:Class ;
rdfs:label "drug category" ;
rdfs:comment "Therapeutic category or general category of drug (anti-convulsant, antibacterial, etc.)." ;
rdfs:subClassOf obo:MI_2089 .
obo:MI_0719 a rdfs:Class ;
rdfs:label "calcium phosphate nucleic acid transfection" ;
rdfs:comment "Transient introduction and expression of nucleic acid carried out by treatment with calcium phosphate." ;
rdfs:subClassOf obo:MI_0718 .
obo:MI_0602 a rdfs:Class ;
rdfs:label "chemical footprinting" ;
rdfs:comment "Binding sites are identified by altered reactivity of a complex to a chemical treatment compared to the unbound molecules. Residues in close contact with the binding partner are protected from chemical modification. When these chemicals are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein or protein-protein interactions in vivo." ;
rdfs:subClassOf obo:MI_0417 .
obo:MI_1194 a rdfs:Class ;
rdfs:label "reverse transcription pcr" ;
rdfs:comment "Reverse Transcription PCR (RT-PCR) is used for amplifying DNA from RNA. Reverse transcriptase reverse transcribes RNA into cDNA, which is then amplified by PCR." ;
rdfs:subClassOf obo:MI_0088 .
obo:MI_2359 a rdfs:Class ;
rdfs:label "ds rna" ;
rdfs:comment "RNA that consists of two base pairing strands. The 2 nucleotide chains are held together by hydrogen bonds between base pairs of nucleotides." ;
rdfs:subClassOf obo:MI_0320 .
obo:MI_1056 a rdfs:Class ;
rdfs:label "text-mining" ;
rdfs:comment "The data has been entered into the database following extraction from the literature by a computational process." ;
rdfs:subClassOf obo:MI_1053 .
obo:MI_1356 a rdfs:Class ;
rdfs:label "validated two hybrid" ;
rdfs:comment "The protein pairs, often initially identified by a separate 2-hybrid screening methodology, are subjected to a rigorous re-analysis which may include independent re-screening of the entire search space, retesting the assay in different strain backgrounds, and multiple retesting of identified protein pairs reversing bait-prey orientations. Orthogonal data from other experimental and bioinformatic approaches may also be used to support the identification of the final high-confidence protein pairs but the primary means of selection must be experimentally based. This method would be expected to identify protein pairs with a higher degree of confidence than any single protein complementation technique." ;
rdfs:subClassOf obo:MI_0018 .
obo:MI_2120 a rdfs:Class ;
rdfs:label "tissue distribution" ;
rdfs:comment "Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0682 a rdfs:Class ;
rdfs:label "cofactor" ;
rdfs:comment "A cofactor is a small molecule required for the catalysis of an enzyme." ;
rdfs:subClassOf obo:MI_0500 .
obo:MI_1067 a rdfs:Class ;
rdfs:label "function-based confidence" ;
rdfs:comment "Confidence in an interaction is based on shared functionality of interacting molecules e.g. co-occurrence of GO function terms." ;
rdfs:subClassOf obo:MI_1064 , obo:MI_1221 .
obo:MI_1338 a rdfs:Class ;
rdfs:label "eef tag" ;
rdfs:comment "Glu-Glu-Phe epitope tag, allowing its detection with rat monoclonal antibody YL1/2" ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_2422 a rdfs:Class ;
rdfs:label "mass photometry" ;
rdfs:comment "Mass photometry measures mass at the single molecule level in solution and enables the quantification of protein–protein interactions in solution with sufficient sensitivity to accurately determine stoichiometry and rate of reactions." ;
rdfs:subClassOf obo:MI_0067 .
obo:MI_0632 a rdfs:Class ;
rdfs:label "3d-resolution" ;
rdfs:comment "Resolution of the 3D structure. This attribute is generally associated to an interaction." ;
rdfs:subClassOf obo:MI_0664 .
obo:MI_2146 a rdfs:Class ;
rdfs:label "solubility ph 2.0" ;
rdfs:comment "Solubility pH 2.0" ;
rdfs:subClassOf obo:MI_2064 .
obo:MI_2002 a rdfs:Class ;
rdfs:label "drugbank" ;
rdfs:comment "DrugBank Accession number consisting of the 4 letter prefix and a 5 number suffix. Each Accession number is unique to the drug's generic name. The 4 letter suffix (APRD, EXPT, BIOD, NUTR) indicates the type of drug (APRD=approved small molecule drug, EXPT=experimental drug, BIOD=biotech drug, NUTR=nutraceutical or natural product). Biotech drugs consist of FDA approved peptide, protein or nucleic acid drugs, approved small molecule drugs are FDA approved non-biotech drugs, nutraceuticals are natural products (amino acids, vitamins, other metabolites) and experimental drugs include drugs under trial, pre-clinical drugs, unapproved drugs, well known inhibitors and possible toxins." ;
rdfs:subClassOf obo:MI_2054 .
obo:MI_2189 a rdfs:Class ;
rdfs:label "avexis" ;
rdfs:comment "Low-affinity interaction detection method designed specifically to detect interactions between extracellular proteins. Recombinant soluble fragments of these proteins are produced in a (generally) mammalian expression cell line and secreted into the medium and produced in two forms: a biotinylated bait which can be captured on a streptavidin-coated solid phase suitable for screening, and a pentamerised enzyme-tagged (beta-lactamase) prey. The bait and prey proteins are presented to each other in a binary fashion to detect direct interactions between them, similar to a conventional ELISA. The pentamerisation of the proteins in the prey is achieved through a peptide sequence from the cartilage oligomeric matrix protein (COMP) and increases the local concentration of the ectodomains thereby providing significant avidity gains to enable even very transient interactions to be detected. By normalising the activities of both the bait and prey to predetermined levels prior to screening, interactions having monomeric half-lives of 0.1 sec can be detected with low false positive rates." ;
rdfs:subClassOf obo:MI_0892 .
obo:MI_2220 a rdfs:Class ;
rdfs:label "gaussia-c" ;
rdfs:comment "The c-terminus of the gaussia luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay." ;
rdfs:subClassOf obo:MI_2219 .
obo:MI_0483 a rdfs:Class ;
rdfs:label "rgd" ;
rdfs:comment """The Rat Genome Database (RGD) curates and integrates rat genetic and genomic data.
http://rgd.mcw.edu/""" ;
rdfs:subClassOf obo:MI_1094 .
obo:MI_1214 a rdfs:Class ;
rdfs:label "c-venus" ;
rdfs:comment "C-terminal region of the Venus fusion protein, created by the introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L). This tag is used for split flurescence complementation assays." ;
rdfs:subClassOf obo:MI_1135 , obo:MI_1215 .
obo:MI_0588 a rdfs:Class ;
rdfs:label "three hybrid" ;
rdfs:comment "Group of methods based on complementation assay where a third participant is shown to be necessary for the binding of a given bait prey pair. The molecule fused to the DNA binding domain is the bait, that fused to the transcriptional activator is the prey." ;
rdfs:subClassOf obo:MI_0232 .
obo:MI_0811 a rdfs:Class ;
rdfs:label "insertion analysis" ;
rdfs:comment "In this approach, once a molecule is demonstrated to participate in an interaction, several insertion derivatives are produced and tested in the binding assay to detect the regions that are important for the interaction." ;
rdfs:subClassOf obo:MI_0074 .
obo:MI_0929 a rdfs:Class ;
rdfs:label "northern blot" ;
rdfs:comment """A standard procedure to identify RNA fragments containing specific
sequences. In this procedure RNA fragments are separated by
electrophoresis, the fragments are transferred to a membrane and the
membrane is incubated with a radio labelled probe that hybridises any
complementary subsequence.""" ;
rdfs:subClassOf obo:MI_0078 .
obo:MI_1113 a rdfs:Class ;
rdfs:label "two hybrid bait and prey pooling approach" ;
rdfs:comment "def" ;
rdfs:subClassOf obo:MI_0398 .
obo:MI_0402 a rdfs:Class ;
rdfs:label "chromatin immunoprecipitation assay" ;
rdfs:comment "Chromatin immunoprecipitation (ChIP) is a powerful approach that allows one to define the interaction of factors with specific chromosomal sites in living cells. An antibody against a protein suspected of binding a given cis-element is used to immunoprecipitate fragmented chromatin fragments. Cells or tissue may first be briefly treated with an agent such formaldehyde to crosslink proteins to DNA. Nucleic acids are then identified by sequencing, for example polymerase chain reaction analysis of the immunoprecipitate with primers flanking the cis-element or next-generation sequencing techniques" ;
rdfs:subClassOf obo:MI_0019 .
obo:MI_0230 a rdfs:Class ;
rdfs:label "membrane bound complementation assay" ;
rdfs:comment "OBSOLETE remap to MI:0090 protein complementation assay." .
obo:MI_0621 a rdfs:Class ;
rdfs:label "author-confidence" ;
rdfs:comment "Confidence classification assigned by the author of the publication to a specific interaction." ;
rdfs:subClassOf obo:MI_0664 .
obo:MI_0265 a rdfs:Class ;
rdfs:label "suppression expression alteration" ;
rdfs:comment """An altered expression is the suppressor of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803. """ .
obo:MI_2160 a rdfs:Class ;
rdfs:label "logs" ;
rdfs:comment "Solubility of a molecule in a given solvant." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_2173 a rdfs:Class ;
rdfs:label "cgd" ;
rdfs:comment """Candida Genome Database is a resource for genomic sequence data and gene and protein information for Candida albicans and related species. CGD is based on the Saccharomyces Genome Database and is funded by the National Institute of Dental & Craniofacial Research at the US National Institutes of Health.
www.candidagenome.org/""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_1225 a rdfs:Class ;
rdfs:label "ptm disrupting an interaction" ;
rdfs:comment "Post translational modification on a protein observed to disrupt the strength or rate of an interaction." ;
rdfs:subClassOf obo:MI_0925 .
obo:MI_0381 a rdfs:Class ;
rdfs:label "2h label" ;
rdfs:comment "Molecules labelled with isotope 2 of hydrogen atoms." ;
rdfs:subClassOf obo:MI_0378 .
obo:MI_0660 a rdfs:Class ;
rdfs:label "feature prediction" ;
rdfs:comment "Feature detection based on computational analysis." ;
rdfs:subClassOf obo:MI_0003 .
obo:MI_0074 a rdfs:Class ;
rdfs:label "mutation analysis" ;
rdfs:comment "Mutant molecules are produced by random or directed techniques and assayed for their ability to support binding." ;
rdfs:subClassOf obo:MI_0659 .
obo:MI_0120 a rdfs:Class ;
rdfs:label "post translation modification" ;
rdfs:comment """Residue covalent modifications occurring in the specific protein form involved in an interaction.
OBSOLETE remap to MOD:00000.""" .
obo:MI_0091 a rdfs:Class ;
rdfs:label "chromatography technology" ;
rdfs:comment "Used to separate and/or analyse complex mixtures. The components to be separated are distributed between two phases: a stationary phase (bed) and a mobile phase which percolates through the stationary bed. The nature of the two phases determines the separation criteria exploited by the column such as affinity, ionic charges, size or hydrophobicity of the molecules under analysis. Each type of column can be implemented with the mobile phase under atmospheric or high pressure condition. In this later case columns are designated as High Pressure Liquid Chromatography (HPLC)." ;
rdfs:subClassOf obo:MI_0401 .
obo:MI_0518 a rdfs:Class ;
rdfs:label "flag tag" ;
rdfs:comment "The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_2292 a rdfs:Class ;
rdfs:label "magnetic tweezers" ;
rdfs:comment "Magnetic tweezers are instruments that use a set of magnets to apply forces to physically hold and move individual molecules attached to ferromagnetic beads. Such instruments allow to measure the forces generated between interacting molecules - either at the level of just single interacting pair of molecules or at the level of larger molecular assemblies." ;
rdfs:subClassOf obo:MI_0859 .
obo:MI_0451 a rdfs:Class ;
rdfs:label "pfam" ;
rdfs:comment """Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.
http://www.sanger.ac.uk/Software/Pfam""" ;
rdfs:subClassOf obo:MI_0449 .
obo:MI_0990 a rdfs:Class ;
rdfs:label "cleavage assay" ;
rdfs:comment "The cleavage of a biomolecule either into its component parts or sub-parts." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0034 a rdfs:Class ;
rdfs:label "display technology" ;
rdfs:comment "All the methods that permit the physical linking of a protein/peptide to its coding sequence. As a consequence affinity purification of the displayed peptide results in the genetic enrichment of its coding sequence. By these technologies genes encoding a peptide with desired binding properties can be selected over an excess of up to 1012 unrelated molecules." ;
rdfs:subClassOf obo:MI_0400 .
obo:MI_2044 a rdfs:Class ;
rdfs:label "mechanism of action" ;
rdfs:comment "Description of how the drug works or what it binds to at a molecular level." ;
rdfs:subClassOf obo:MI_2089 .
obo:MI_2226 a rdfs:Class ;
rdfs:label "mutation with no effect" ;
rdfs:comment "A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that does not have any effect over an interaction when compared with the wild-type." ;
rdfs:subClassOf obo:MI_0118 .
obo:MI_0001 a rdfs:Class ;
rdfs:label "interaction detection method" ;
rdfs:comment "Method to determine the interaction." ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_1266 a rdfs:Class ;
rdfs:label "cub" ;
rdfs:comment "A C-terminal ubiquitin moiety (cub, residues 35-76) plus a transcription factor that can be cleaved off by ubiquitin specific proteases. Regarded as attached to the bait molecules in ubiquitin reconstruction assays." ;
rdfs:subClassOf obo:MI_1265 .
obo:MI_0211 a rdfs:Class ;
rdfs:label "lipid addition" ;
rdfs:comment "Covalent or non covalent binding of lipid group on a protein residue." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_2091 a rdfs:Class ;
rdfs:label "structure representation attribute name" ;
rdfs:comment "Human artefact to describe and report the structure of a molecule." ;
rdfs:subClassOf obo:MI_0590 .
obo:MI_1019 a rdfs:Class ;
rdfs:label "protein phosphatase assay" ;
rdfs:comment "Measures the catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate." ;
rdfs:subClassOf obo:MI_0434 .
obo:MI_1158 a rdfs:Class ;
rdfs:label "pre-assembly" ;
rdfs:comment "A non-allosteric mechanism where the strength of an interaction depends on whether or not a particular molecular complex already exists." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_1156 .
obo:MI_0375 a rdfs:Class ;
rdfs:label "cy3 label" ;
rdfs:comment "The organic cyanine Cy3 emits maximally at 570 nm." ;
rdfs:subClassOf obo:MI_0374 .
obo:MI_1277 a rdfs:Class ;
rdfs:label "qualitative genetic epistasis" ;
rdfs:comment """An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits that cannot be measured on the same scale and, hence, qualitatively different), and the resulting phenotype of their combination is equal to that of only one of the perturbations. This may be expressed as an inequality as:
(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotypes of the individual perturbations, 'ab' is the observed phenotype of the double perturbation, 'wt' is the wild type phenotype and 'a != b' indicates qualitatively different phenotypes.""" ;
rdfs:subClassOf obo:MI_0797 .
obo:MI_1204 a rdfs:Class ;
rdfs:label "split firefly luciferase complementation" ;
rdfs:comment "Two proteins of interest, a bait and prey, which are genetically fused to amino- and carboxy-terminal fragments of firefly (Photinus pyralis) luciferase, are transiently expressed. Physical interactions of these bait and prey proteins reconstitute some of the luciferase activity and result in light emission in the presence of the luciferase substrate." ;
rdfs:subClassOf obo:MI_1203 .
obo:MI_2215 a rdfs:Class ;
rdfs:label "barcode fusion genetics two hybrid" ;
rdfs:comment "This method allows screening of a full matrix of protein pairs in a single multiplexed strain pool. A doubly engineered clone pool is prepared so that each clone bears two distinct DNA barcodes flanked by site specific recombination sequences. Positive bait-prey combinations allow activation of reporter genes and their respective barcodes undergo recombination, creating unique barcode combinations. Recombined barcode tags are then fused, extracted and sequenced for identification of interacting pairs." ;
rdfs:subClassOf obo:MI_1113 .
obo:MI_0499 a rdfs:Class ;
rdfs:label "unspecified role" ;
rdfs:comment "Role not specified or not applicable to the data." ;
rdfs:subClassOf obo:MI_0495 , obo:MI_0500 .
obo:MI_2313 a rdfs:Class ;
rdfs:label "attached carbohydrate increasing interaction strength" ;
rdfs:comment "Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction strength when compared with the non-glycosylated molecule." ;
rdfs:subClassOf obo:MI_2312 .
obo:MI_0494 a rdfs:Class ;
rdfs:label "in situ" ;
rdfs:comment """Literally, in place i.e. the protein is in its natural environment during the experiment.
OBSOLETE as a full host organisms is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.""" .
obo:MI_0678 a rdfs:Class ;
rdfs:label "antibody array" ;
rdfs:comment "A microarray consisting of antibodies spotted on a solid support in appropriate orientation is incubated with a biological sample (or antigen). Some proteins are captured by the antibodies in the array. Protein of forming complexes on the array are identified according to their prior labelling (tag, ELISA, biotin and others)." ;
rdfs:subClassOf obo:MI_0089 .
obo:MI_0989 a rdfs:Class ;
rdfs:label "amidase assay" ;
rdfs:comment "The measurement of the addition of an amine group to a molecule." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_1250 a rdfs:Class ;
rdfs:label "isomerase reaction" ;
rdfs:comment "The catalysis of the structural rearrangement of isomers." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_1004 a rdfs:Class ;
rdfs:label "palmitoylase assay" ;
rdfs:comment "Measurement of the covalent attachment of palmitic acid to a protein." ;
rdfs:subClassOf obo:MI_1001 .
obo:MI_0665 a rdfs:Class ;
rdfs:label "experiment attribute name" ;
rdfs:comment "Attribute name of annotation associated to an experiment element." ;
rdfs:subClassOf obo:MI_0590 .
obo:MI_0944 a rdfs:Class ;
rdfs:label "mass spectrometry study of hydrogen/deuterium exchange" ;
rdfs:comment "Mass spectroscopy based measurement of the rate and/or extent of the hydrogen/deuterium exchange." ;
rdfs:subClassOf obo:MI_0943 .
obo:MI_0417 a rdfs:Class ;
rdfs:label "footprinting" ;
rdfs:comment "Footprinting analysis is used to identify regions of molecules involved in binding other macromolecules and therefore protected from the effects of degradative enzymes, chemical treatment or other deleterious treatments." ;
rdfs:subClassOf obo:MI_0401 .
obo:MI_0135 a rdfs:Class ;
rdfs:label "n-acetyl-methionine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00058.""" .
obo:MI_0863 a rdfs:Class ;
rdfs:label "thiol reactive lanthanide label" ;
rdfs:comment "Thiol-reactive lanthanide complexes have been synthesized that are luminescent when bound to terbium and/or europium. The Tb3+-DTPA-cs124-EMCH complexes consist of a diethylenetriaminepentaacetate (DTPA) chelate covalently joined through one amide bond to a chromophore, carbostyril 124, and via a second amide bond to a maleimide, bromoacetamide, or pyridyldithio moiety. This label can be Site-specific attached to both proteins and DNA." ;
rdfs:subClassOf obo:MI_1256 .
obo:MI_2009 a rdfs:Class ;
rdfs:label "chemical structure" ;
rdfs:comment "Image of the drug structure (if small molecule) or its sequence (if biotech drug)" ;
rdfs:subClassOf obo:MI_2086 .
obo:MI_0511 a rdfs:Class ;
rdfs:label "protease homogeneous time resolved fluorescence" ;
rdfs:comment "Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Fluorescence donor and acceptor are on the same peptide molecule and separated by the action of the protease." ;
rdfs:subClassOf obo:MI_0435 , obo:MI_0510 .
obo:MI_0996 a rdfs:Class ;
rdfs:label "deformylase assay" ;
rdfs:comment "Measures the removal of N6-formyl-L-lysine, which is cleaved and returns a K residue." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_1015 a rdfs:Class ;
rdfs:label "dictybase" ;
rdfs:comment "dictyBase (http://dictybase.org) is the model organism database for Dictyostelium discoideum. It houses the complete genome sequence, ESTs and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome." ;
rdfs:subClassOf obo:MI_1094 .
obo:MI_2403 a rdfs:Class ;
rdfs:label "bira tag" ;
rdfs:comment "E. coli BirA* biotin ligase tag used in BioID experiments. This generally refers to a promiscuous mutant version of the biotin ligase with an R118H mutation." ;
rdfs:subClassOf obo:MI_2431 .
obo:MI_0983 a rdfs:Class ;
rdfs:label "gemma" ;
rdfs:comment """GEMMA is a method to study protein complexes in solution: a diluted protein sample is transmitted
into the gas phase by a charged reduced electrospray process. The generated particles, each
containing one protein molecule with a +1 charge, are separated according to size in a differential
mobility analyzer and subsequently quantified by a particle counter. In contrast to mass spectrometry,
this method is run at atmospheric pressure and measures the diameter of the particle rather than the mass.""" ;
rdfs:subClassOf obo:MI_0982 .
obo:MI_1219 a rdfs:Class ;
rdfs:label "enzyme-mediated activation of radical sources" ;
rdfs:comment "Enzyme-mediated activation of radical sources is used to identify partners of a given molecule on the cell surface in living cells Activation of the cross-linking reagent arylazide-biotin tag is accomplished by an enzyme, horseradish peroxidase is featured by radical formation of the labelling reagent by horseradish peroxidase (HRP)." ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_0106 a rdfs:Class ;
rdfs:label "surface patches" ;
rdfs:comment "Surface patches are built using 6 criteria: solvation potential, residue interface propensity, hydrophobicity, planarity, protrusion and accessible surface area. Protein structures having similar patches are likely to have the same interactions." ;
rdfs:subClassOf obo:MI_0577 .
obo:MI_0843 a rdfs:Class ;
rdfs:label "phosphate acceptor" ;
rdfs:comment "Molecule to which a phosphate group may be transferred from a phosphate donor." ;
rdfs:subClassOf obo:MI_0919 .
obo:MI_0837 a rdfs:Class ;
rdfs:label "pH of interaction" ;
rdfs:comment "pH at which interaction was determined." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0546 a rdfs:Class ;
rdfs:label "gpi-anchor amidated threonine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00173.""" .
obo:MI_0787 a rdfs:Class ;
rdfs:label "genetic experimental form" ;
rdfs:comment "Descriptor of an experimental form involved in a genetic interaction" ;
rdfs:subClassOf obo:MI_0346 .
obo:MI_1349 a rdfs:Class ;
rdfs:label "chembl" ;
rdfs:comment "ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets." ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0427 a rdfs:Class ;
rdfs:label "Identification by mass spectrometry" ;
rdfs:comment "identification by mass spectrometry." ;
rdfs:subClassOf obo:MI_0661 .
obo:MI_0037 a rdfs:Class ;
rdfs:label "domain profile pairs" ;
rdfs:comment "This approach uses a protein interaction network of a given organism to infer interaction in another organism using information about the interacting region. The regions or domains involved in interactions are clustered if they share sequence similarity and have common interacting partners. The resulting domain profiles are then used to screen the proteome of another organism and domain-domain interactions are inferred. Ultimately, an inferred protein interaction map is built in this second organism." ;
rdfs:subClassOf obo:MI_0046 , obo:MI_0101 , obo:MI_0660 .
obo:MI_0117 a rdfs:Class ;
rdfs:label "binding-associated region" ;
rdfs:comment "A region of a molecule or a component of a complex identified as being involved in an interaction. This may or may not be a region of the molecule in direct contact with the interacting partner." ;
rdfs:subClassOf obo:MI_0252 .
obo:MI_0150 a rdfs:Class ;
rdfs:label "lipid modification" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:01155.""" .
obo:MI_0794 a rdfs:Class ;
rdfs:label "synthetic genetic interaction" ;
rdfs:comment """An effect in which two genetic perturbations, when combined, result in a mutant phenotype that is not observed (or minimally observed) as a result of any of the individual perturbations.
wt = a = b = E (not=) ab""" ;
rdfs:subClassOf obo:MI_0933 , obo:MI_2381 .
obo:MI_0923 a rdfs:Class ;
rdfs:label "irefindex" ;
rdfs:comment """iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein. iRefIndex uses the Sequence Global Unique Identifier (SEGUID) to group proteins and interactions into redundant groups. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once.
http://irefindex.uio.no/""" ;
rdfs:subClassOf obo:MI_0461 , obo:MI_0489 .
obo:MI_2202 a rdfs:Class ;
rdfs:label "RNA chemical modification" ;
rdfs:comment "Chemical alterations occurring at the nucleotide level in the specific RNA molecule involved in an interaction. The process can involve covalent modifications (i.e. 2'-O-methylation) or other forms of chemical modification, such as isomerizations (i.e. pseudouridylation)." ;
rdfs:subClassOf obo:MI_0252 .
obo:MI_2242 a rdfs:Class ;
rdfs:label "down-regulates quantity" ;
rdfs:comment "The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B." ;
rdfs:subClassOf obo:MI_2240 .
obo:MI_0714 a rdfs:Class ;
rdfs:label "nucleic acid transduction" ;
rdfs:comment "Transduction is the process by which bacterial DNA is moved from one bacterium to another by a virus." ;
rdfs:subClassOf obo:MI_0704 .
obo:MI_2040 a rdfs:Class ;
rdfs:label "drug type" ;
rdfs:comment "Type of drug (approved, experimental, biotech, nutraceutical)" ;
rdfs:subClassOf obo:MI_2089 .
obo:MI_1244 a rdfs:Class ;
rdfs:label "mkate2" ;
rdfs:comment "Monomeric far-red fluorescent protein generated from the wild-type RFP from sea anemone Entacmaea quadricolor. It possesses bright fluorescence with excitation/emission maxima at 588 and 635 nm, respectively." ;
rdfs:subClassOf obo:MI_0732 .
obo:MI_2050 a rdfs:Class ;
rdfs:label "dosage form" ;
rdfs:comment "How the drug is dispensed (tablets, capsules, solutions), packing material." ;
rdfs:subClassOf obo:MI_2089 .
obo:MI_2247 a rdfs:Class ;
rdfs:label "transcriptional regulation" ;
rdfs:comment "Any process that modulates the frequency, rate or extent of the chemical reactions resulting in the transcription of DNA to RNA and gene activity regulation." ;
rdfs:subClassOf obo:MI_2245 .
obo:MI_0950 a rdfs:Class ;
rdfs:label "trapping mutant" ;
rdfs:comment "Permits the identification of substrates of enzymes by mutating residues, usually in the active site such that the enzyme will bind but not act on its substrate." ;
rdfs:subClassOf obo:MI_0505 .
obo:MI_0307 a rdfs:Class ;
rdfs:label "delivery method" ;
rdfs:comment "Method by which molecule is delivered or engineered into a cell." ;
rdfs:subClassOf obo:MI_0346 .
obo:MI_0826 a rdfs:Class ;
rdfs:label "x ray scattering" ;
rdfs:comment "Method where the internal structure of a sample is derived from the intensity distribution of the scattered monochromatic X-ray beam at very low scattering angles." ;
rdfs:subClassOf obo:MI_0067 .
obo:MI_0487 a rdfs:Class ;
rdfs:label "wormbase" ;
rdfs:comment """WormBase is the central worm database that houses the gene reports, locus reports, translation reports, expression pattern data and genome browser.
http://www.wormbase.org/""" ;
rdfs:subClassOf obo:MI_1094 .
obo:MI_1026 a rdfs:Class ;
rdfs:label "diphtamidase assay" ;
rdfs:comment "Measurement of a modification that converts an L-histidine residue to diphthamide." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0099 a rdfs:Class ;
rdfs:label "scintillation proximity assay" ;
rdfs:comment "SPA relies upon the fact that a beta particle emitted from a radioisotope decay can excite a fluorophore only when it is at a very short distance in water solution (few micrometers). The ligand is labelled with a radioactive atom and its potential partner is fixed to fluorophore containing beads, the emitted fluorescence proving their interaction can be measured in a scintillation counter. The scintillator measures only the amount of bound radiolabelled ligand. Competition experiment with cold competitor can be done to estimate the binding affinities (50% inhibitory concentration [IC50], cold ligand versus labelled ligand). Loss of signal can also be used to measure substrate cleavage by an enzyme, and labelled antibodies used to titrate the degree of modified residue present." ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_0146 a rdfs:Class ;
rdfs:label "formylated residue" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00493.""" .
obo:MI_0009 a rdfs:Class ;
rdfs:label "bacterial display" ;
rdfs:comment "The protein of interest is presented on the outer membrane of Gram negative bacteria by expressing it as a fusion partner to peptide signals that direct heterologous proteins to the cell surface. For instance, a single chain Fv (scFv) antibody fragment, consisting of the variable heavy and variable light domains from two separate anti-digoxin monoclonal antibodies, was displayed on the outer membrane of Escherichia coli by fusing it to an Lpp-OmpA. Similar systems have also been developed for gram positive bacteria. Fluorescence-activated cell sorting (FACS), is used to specifically select clones displaying a protein binding to scFv-producing cells." ;
rdfs:subClassOf obo:MI_0034 , obo:MI_0054 .
obo:MI_0650 a rdfs:Class ;
rdfs:label "millimolar" ;
rdfs:comment """10E-3 moles per liter of solution.
OBSOLETE: term redundant with the schema exponent attribute of the parameter.""" .
obo:MI_1007 a rdfs:Class ;
rdfs:label "glycosylase assay" ;
rdfs:comment "Measurement of the covalently attachment of glycosyl residues to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0370 a rdfs:Class ;
rdfs:label "tox-r dimerization assay" ;
rdfs:comment "This assay allow identification of interactions in the inner membrane of E. coli. by using a chimeric construct ToxR-TM-MBP composed of the N-terminal DNA binding/transcriptional activation domain of ToxR (a dimerization dependant transcription factor) fused to a transmembrane domain of interest (TM) and a monomeric periplasmic anchor (the maltose binding protein). Association of the two TM results in the ToxR-mediated activation of a reporter gene such as CAT (chloroamphenicol acetyltransferase activity). The level of CAT expression indicates the strength of TM association. CAT expression can then be tested and quantify by measuring CAM resistance with disk diffusion assay or CAT activity assays on cell-free extracts." ;
rdfs:subClassOf obo:MI_0090 .
obo:MI_0410 a rdfs:Class ;
rdfs:label "3D electron microscopy" ;
rdfs:comment "Three-dimensional (3D) reconstruction of single, transparent objects from a collection of projection images recorded with a transmission electron microscope. It offers the opportunity to obtain 3D information on structural cellular arrangements with a high resolution." ;
rdfs:subClassOf obo:MI_0020 .
obo:MI_2237 a rdfs:Class ;
rdfs:label "up-regulates quantity" ;
rdfs:comment "The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B." ;
rdfs:subClassOf obo:MI_2235 .
obo:MI_0570 a rdfs:Class ;
rdfs:label "protein cleavage" ;
rdfs:comment "Covalent modification of a polypeptide occuring during its maturation or its proteolytic degradation." ;
rdfs:subClassOf obo:MI_0194 .
obo:MI_0326 a rdfs:Class ;
rdfs:label "protein" ;
rdfs:comment "A linear polymer of amino acids joined by peptide bonds in a specific sequence." ;
rdfs:subClassOf obo:MI_0383 .
obo:MI_0247 a rdfs:Class ;
rdfs:label "newt" ;
rdfs:comment """New EBI Web Taxonomy.
http://www.ebi.ac.uk/newt OBSOLETE: Consider remapping to uniprot taxonomy MI:0942""" .
obo:MI_0399 a rdfs:Class ;
rdfs:label "two hybrid fragment pooling approach" ;
rdfs:comment "Individual baits are mated against pools of random fragmented preys. The usage of degenerated fragment allows identification of the minimal protein region required for the interaction. Since multiple clones that encode overlapping regions of protein are often identified, the minimal domain for interaction may be readily apparent from the initial screen." ;
rdfs:subClassOf obo:MI_1112 .
obo:MI_0500 a rdfs:Class ;
rdfs:label "biological role" ;
rdfs:comment "Physiological role of an interactor in a cell or in vivo environment, which is reproduced in the current experiment." ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_2099 a rdfs:Class ;
rdfs:label "fda approved drug" ;
rdfs:comment "A drug licensed for sale in the USA by the FDA." ;
rdfs:subClassOf obo:MI_2040 .
obo:MI_0130 a rdfs:Class ;
rdfs:label "n-acetyl-histidine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00781.""" .
obo:MI_1319 a rdfs:Class ;
rdfs:label "sulfate acceptor" ;
rdfs:comment "Molecule to which a sulphate group may be transferred from a sulphate donor." ;
rdfs:subClassOf obo:MI_0919 .
obo:MI_1071 a rdfs:Class ;
rdfs:label "literature-based confidence" ;
rdfs:comment "Confidence in an interaction is based on co-occurrence of an interacting pair or molecules in the same article, or sentence within an article, usually identified by text-mining." ;
rdfs:subClassOf obo:MI_1064 .
obo:MI_0026 a rdfs:Class ;
rdfs:label "correlated mutations" ;
rdfs:comment "Pairs of multiple alignments of orthologous sequences are used to identify potential interacting partners as proteins that show covariation of their residue identities between different species. Proteins displaying inter-protein correlated mutations during evolution are likely to be interacting proteins due to co-adapted evolution of their protein interacting interfaces." ;
rdfs:subClassOf obo:MI_0101 , obo:MI_0660 .
obo:MI_0063 a rdfs:Class ;
rdfs:label "interaction prediction" ;
rdfs:comment "Computational methods to predict an interaction." ;
rdfs:subClassOf obo:MI_0001 .
obo:MI_0090 a rdfs:Class ;
rdfs:label "protein complementation assay" ;
rdfs:comment "In the protein-fragment complementation assay, the proteins of interest (\"Bait\" and \"Prey\") are covalently linked at the genetic level to incomplete fragments of a third protein (known as the \"reporter\") and are expressed in vivo, Interaction between the \"bait\" and the \"prey\" proteins brings the fragments of the \"reporter\" protein in close enough proximity to allow them to reform and become the functional reporter protein. Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode." ;
rdfs:subClassOf obo:MI_0045 .
obo:MI_1157 a rdfs:Class ;
rdfs:label "allostery" ;
rdfs:comment "Reciprocal energetic coupling between two binding events at distinct sites on the same molecule. The first binding event alters the binding or catalytic properties of the molecule for the second binding event." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_1156 .
obo:MI_1233 a rdfs:Class ;
rdfs:label "resulting-cleavage" ;
rdfs:comment "The cleavage which results due to the action of a proteolytic enzyme on its substrate." ;
rdfs:subClassOf obo:MI_0639 .
obo:MI_0157 a rdfs:Class ;
rdfs:label "methylated residue" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00427.""" .
obo:MI_0077 a rdfs:Class ;
rdfs:label "nuclear magnetic resonance" ;
rdfs:comment "Nuclear magnetic resonance (NMR) is an effect whereby magnetic nuclei in a magnetic field absorb and re-emit electromagnetic (EM) energy. Certain atomic nuclei, and in particular hydrogen, have a magnetic moment or spin; i.e., they have an intrinsic magnetisation, like a bar magnet. The spin aligns along the strong magnetic field, but can be changed to a misaligned excited state in response to applied radio frequency (RF) pulses of electromagnetic radiation. When the excited hydrogen nuclei relax to their aligned state, they emit RF radiation, which can be measured and displayed as a spectrum. The nature of the emitted radiation depends on the environment of each hydrogen nucleus, and if one nucleus is excited, it will influence the absorption and emission of radiation by other nuclei that lie close to it. It is consequently possible, by an ingenious elaboration of the basic NMR technique known as two-dimensional NMR, to distinguish the signals from hydrogen nuclei in different amino acid residues and to identify and measure the small shifts in these signals that occur when these hydrogen nuclei lie close enough to interact: the size of such a shift reveals the distance between the interacting pair of hydrogen atoms. In this way NMR can give information about the distances between the parts of the interacting molecule. NMR provides information about interacting atoms thereby permitting to obtain information about macromolecular structure and molecular interactions." ;
rdfs:subClassOf obo:MI_0013 , obo:MI_0659 .
obo:MI_1033 a rdfs:Class ;
rdfs:label "atto 550" ;
rdfs:comment "Fluorescent tag - maleimide couples to thiols." ;
rdfs:subClassOf obo:MI_1092 .
obo:MI_0854 a rdfs:Class ;
rdfs:label "3 prime overhang" ;
rdfs:comment "An overhang is a stretch of unpaired nucleotides in the end of a 3' strand of a DNA molecule." ;
rdfs:subClassOf obo:MI_0853 .
obo:MI_1269 a rdfs:Class ;
rdfs:label "duplicated protein" ;
rdfs:comment "An identical protein sequence is coded for by the multiple genes within the same organism. These proteins may previously be merged into a single entry by UniProt and subsequently demerged." ;
rdfs:subClassOf obo:MI_1341 .
obo:MI_0498 a rdfs:Class ;
rdfs:label "prey" ;
rdfs:comment "Molecule experimentally identified as being captured by a given bait." ;
rdfs:subClassOf obo:MI_0495 .
obo:MI_0636 a rdfs:Class ;
rdfs:label "author-list" ;
rdfs:comment "List of authors associated to a publication. This attribute is generally associated to an experiment." ;
rdfs:subClassOf obo:MI_1093 .
obo:MI_2049 a rdfs:Class ;
rdfs:label "elimination half life" ;
rdfs:comment "Rate The time it takes for the body to eliminate or breakdown half of a dose of a pharmacologic agent, in practice the time taken for plasma concentration to reduce by 50%." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0088 a rdfs:Class ;
rdfs:label "primer specific pcr" ;
rdfs:comment "Sequences can be identified in a DNA mixture by launching a PCR (Polymerase Chain Reaction) controlled by sequence specific primers. Such reaction starts only when the hybridization of the primer with a complementary sequence occurs." ;
rdfs:subClassOf obo:MI_0080 .
obo:MI_2409 a rdfs:Class ;
rdfs:label "Plant Ontology" ;
rdfs:comment """The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.
https://www.ebi.ac.uk/ols/ontologies/po""" ;
rdfs:subClassOf obo:MI_0473 .
obo:MI_1179 a rdfs:Class ;
rdfs:label "partial nucleotide sequence identification" ;
rdfs:comment "Identification of a part of a nucleotide sequence, usually then related to the full length sequence by alignment. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clone.s" ;
rdfs:subClassOf obo:MI_0078 .
obo:MI_0406 a rdfs:Class ;
rdfs:label "deacetylase assay" ;
rdfs:comment "Measures the catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0048 a rdfs:Class ;
rdfs:label "filamentous phage display" ;
rdfs:comment "Filamentous phages (M13, f1, fd) have been extensively used to develop and implement the technology of phage display. Repertoires of relatively short peptides of random amino acid sequences or cDNA libraries have been constructed and searched successfully. Most experiments have taken advantage of the ability to assemble phages decorated with hybrid versions of the receptor protein pIII or of the major coat protein pVIII. Both systems allow the display of foreign peptides by fusion to the amino-terminus of the capsid protein but differ in the number of peptide copies that can be displayed on each phage particle. Display libraries of very diverse protein fragments have been constructed by fusing either genomic or cDNA fragments to gene III or gene VIII." ;
rdfs:subClassOf obo:MI_0084 .
obo:MI_0066 a rdfs:Class ;
rdfs:label "lambda phage display" ;
rdfs:comment "Morphologically classified as one of the siphoviridae, lambda is a temperate bacteriophage of E.coli, with a double-stranded DNA genome. It has an icosahedral head attached to a flexible helical tail. Both the tail protein pV and the head protein pD have been used for displaying (C or N terminally) foreign peptides on the viral capsid." ;
rdfs:subClassOf obo:MI_0084 .
obo:MI_2207 a rdfs:Class ;
rdfs:label "resulting nucleic acid chemical modification" ;
rdfs:comment "Chemical modification observed on an RNA molecule resulting subsequently of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition." ;
rdfs:subClassOf obo:MI_2206 .
obo:MI_2283 a rdfs:Class ;
rdfs:label "southwestern blotting" ;
rdfs:comment "Southwestern blotting, is a lab technique which involves identifying and characterizing DNA-binding proteins by their ability to bind to specific oligonucleotide probes, generally radioactively labeled. The proteins are separated by gel electrophoresis and are subsequently transferred to nitrocellulose membranes similar to other types of blotting." ;
rdfs:subClassOf obo:MI_0047 .
obo:MI_0669 a rdfs:Class ;
rdfs:label "organism attribute name" ;
rdfs:comment "Attribute name of annotation associated to an organism element." ;
rdfs:subClassOf obo:MI_0590 .
obo:MI_0337 a rdfs:Class ;
rdfs:label "less-than" ;
rdfs:comment "Partially determined sequence position known to be in a position lower than a given position." ;
rdfs:subClassOf obo:MI_0333 .
obo:MI_0388 a rdfs:Class ;
rdfs:label "alexa 532 label" ;
rdfs:comment "Alexa fluorescent dye analogue to Rhodamine 6G with an approximate excitation wavelength maximum of 532nm." ;
rdfs:subClassOf obo:MI_0384 .
obo:MI_2218 a rdfs:Class ;
rdfs:label "luciferase-n" ;
rdfs:comment "The n-terminus of a luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay." ;
rdfs:subClassOf obo:MI_1205 .
obo:MI_0364 a rdfs:Class ;
rdfs:label "inferred by curator" ;
rdfs:comment "Evidence based on a curator assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences." ;
rdfs:subClassOf obo:MI_0362 .
obo:MI_0269 a rdfs:Class ;
rdfs:label "synthetic phenotype" ;
rdfs:comment """Two silent mutations show an altered phenotype when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794.""" .
obo:MI_0625 a rdfs:Class ;
rdfs:label "agonist" ;
rdfs:comment "Any chemical applied externally to cells or any type of environmental condition, such as hypoxia, that stimulates an interaction, potentially by causing modification of one or more of the interactors." ;
rdfs:subClassOf obo:MI_0664 .
obo:MI_0664 a rdfs:Class ;
rdfs:label "interaction attribute name" ;
rdfs:comment "Attribute name of annotation associated to an interaction element." ;
rdfs:subClassOf obo:MI_0590 .
obo:MI_0258 a rdfs:Class ;
rdfs:label "inhibitor antibodies" ;
rdfs:comment """Intracellular or extracellular expression of antibodies is used to target specific gene products in order to inactivate them. Most of the times the antibody scaffold need s to reengineered for efficient expression and solubility in the cytoplasm.
OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).""" .
obo:MI_0124 a rdfs:Class ;
rdfs:label "n-acetyl-asparagine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00780.""" .
obo:MI_1189 a rdfs:Class ;
rdfs:label "methylation interference assay" ;
rdfs:comment "In interference assays, the DNA will be methylated before the binding assay. Protein binding to DNA protects DNA from methylation by dimethylsulphate. If the contact points are methylated, the protein binding is prevented. After isolating the protein-DNA complex, the methylation sites are cleaved by chemical method. As a result, only those regions out of the binding sites will be cleaved. The protein binding region is not methylated; hence, this region is not cleaved. Although the pattern looks like a footprint, the blank region means \"contact points\"." ;
rdfs:subClassOf obo:MI_0605 .
obo:MI_0736 a rdfs:Class ;
rdfs:label "protein passive uptake" ;
rdfs:comment "Proteins entrance into cells that does not involved specific treatments but rely on natural cellular processes." ;
rdfs:subClassOf obo:MI_0716 , obo:MI_0721 .
obo:MI_2309 a rdfs:Class ;
rdfs:label "attached carbohydrate causing an interaction" ;
rdfs:comment "Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that enables an interaction when compared with the non-glycosylated molecule, which does not interact." ;
rdfs:subClassOf obo:MI_2308 .
obo:MI_0533 a rdfs:Class ;
rdfs:label "glycosylated residue" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00693.""" .
obo:MI_0994 a rdfs:Class ;
rdfs:label "demyristoylase assay" ;
rdfs:comment "measures the removal of N6-myristoyl-L-lysine, which is cleaved and returns a K residue." ;
rdfs:subClassOf obo:MI_0991 .
obo:MI_2125 a rdfs:Class ;
rdfs:label "maximum absorbable dose" ;
rdfs:comment "The Maximum Absorbable Dose (MAD) represents the amount of drug that can permeate across a barrier." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0725 a rdfs:Class ;
rdfs:label "protein delivery by infection" ;
rdfs:comment "Protein introduced into a cell via an external organism, usually a virus or bacteria." ;
rdfs:subClassOf obo:MI_0310 , obo:MI_0721 .
obo:MI_1076 a rdfs:Class ;
rdfs:label "einecs" ;
rdfs:comment "The EINECS database provides general information such as CAS number, EINECS number, Substance Name and Chemical Formula for 100,204 chemical substances. Where available each compound entry is linked to risk and safety phrases and IUCLID and OECD chemical data sheets." ;
rdfs:subClassOf obo:MI_2054 .
obo:MI_2213 a rdfs:Class ;
rdfs:label "super-resolution microscopy" ;
rdfs:comment "Super-resolution microscopy is a form of light microscopy that allows images to be taken with a higher resolution than the diffraction limit. Several different methods can be used to achieve beyond-diffraction limit resolution and these can be broadly divided in two categories: \"true\" super-resolution techniques, which capture information contained in evanescent waves, and \"functional\" super-resolution techniques, which use clever experimental techniques and known limitations on the matter being imaged to reconstruct a super-resolution image." ;
rdfs:subClassOf obo:MI_0428 .
obo:MI_1258 a rdfs:Class ;
rdfs:label "tetramethyl rhodamine label" ;
rdfs:comment "Tetramethyl rhodamine - a derivative of rhodamine." ;
rdfs:subClassOf obo:MI_1257 .
obo:MI_2319 a rdfs:Class ;
rdfs:label "surface force measurement" ;
rdfs:comment "A technique that measures interaction force between two surfaces as they are brought together and retracted." ;
rdfs:subClassOf obo:MI_2318 .
obo:MI_0438 a rdfs:Class ;
rdfs:label "rna three hybrid" ;
rdfs:comment "In vivo reconstruction of specific RNA-proteins interactions. The DNA binding and transcription activator domains of GAL4 are brought together via the interaction of recombinant RNA. The first hybrid protein contains the DNA binding domain of GAL4 fused to RevM10 (a mutated RNA binding protein of HIV-1 that binds specifically to the Rev responsive element RRE of the env gene). A recombinant RNA contains the RRE sequence and a target RNA sequence X. The second hybrid protein contains the activation domain of GAL4 fused to protein Y tested for its ability to bind the target RNA X. If this interaction occurs the three hybrid reconstructs GAL4 and the transcription of a reporter gene is activated." ;
rdfs:subClassOf obo:MI_0588 .
obo:MI_0848 a rdfs:Class ;
rdfs:label "125i radiolabel" ;
rdfs:comment "Molecule labelled with 125 radio isotope of iodine atoms." ;
rdfs:subClassOf obo:MI_0517 .
obo:MI_0985 a rdfs:Class ;
rdfs:label "deamination reaction" ;
rdfs:comment "The removal of an amine group from a molecule." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_2253 a rdfs:Class ;
rdfs:label "gtpase-activating protein reaction" ;
rdfs:comment "A family of cellular proteins able to increases the activity of a GTPase." .
obo:MI_0934 a rdfs:Class ;
rdfs:label "obsolete neutral genetic interaction" ;
rdfs:comment """OBSOLETE: An effect in which the observed phenotype of individual perturbations and/or the double perturbation collectively exhibit values both greater than AND less than wild type (on the same scale). Alternatively, this could describe a scenario in which individual perturbations result in qualitatively different phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a < wt < b [ab != E]
OR
With respect to two qualitatively different phenotypes, this may be expressed as an inequality as:
(a != wt AND b != wt AND a != b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively different phenotypes.""" .
obo:MI_0866 a rdfs:Class ;
rdfs:label "tag visualisation" ;
rdfs:comment "Molecule whose sequence identity is not checked after the interaction but its presence is detected through its tag." ;
rdfs:subClassOf obo:MI_0396 .
obo:MI_2259 a rdfs:Class ;
rdfs:label "causal interactor type" ;
rdfs:comment "Entity involved in a causative relationship. These terms have to be used as interactor types only if associated with causal statements." ;
rdfs:subClassOf obo:MI_2233 .
obo:MI_0557 a rdfs:Class ;
rdfs:label "adp ribosylation reaction" ;
rdfs:comment "Involves the addition of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_2439 a rdfs:Class ;
rdfs:label "abcd" ;
rdfs:comment "The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies(https://web.expasy.org/abcd/), developed by the Geneva Antibody Facility at the University of Geneva, in collaboration with the CALIPHO and Swiss-Prot groups at SIB Swiss Institute of Bioinformatics." ;
rdfs:subClassOf obo:MI_0473 .
obo:MI_1080 a rdfs:Class ;
rdfs:label "tair" ;
rdfs:comment "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community." ;
rdfs:subClassOf obo:MI_1094 .
obo:MI_2178 a rdfs:Class ;
rdfs:label "agi_locuscode" ;
rdfs:comment "The Arabidopsis Genome Initiative comprises TAIR, TIGR and MIPS." ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_1121 a rdfs:Class ;
rdfs:label "ceYFP" ;
rdfs:comment "c-terminal fragment of enhanced yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC)." ;
rdfs:subClassOf obo:MI_1118 .
obo:MI_0912 a rdfs:Class ;
rdfs:label "spdp cross linker" ;
rdfs:comment """N -Succinimidyl 3-(2-pyridyldithio)-propionate, is heterobifunctional, thiol-cleavable
and membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester
that will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond.""" ;
rdfs:subClassOf obo:MI_0911 .
obo:MI_0231 a rdfs:Class ;
rdfs:label "mammalian protein protein interaction trap" ;
rdfs:comment "The MAPPIT(mammalian protein-protein interaction Trap) is a screening method for protein-protein interaction in mammalian cells, based on the reconstitution of a membrane STAT (signal transducers and activators of transcription) receptor. The bait protein is fused to a STAT recruitment-deficient receptor and the prey protein to a functional STAT recruitment sites. In such a configuration, a given baitprey interaction restores a STAT-dependent responses leading to the expression of a reporter gene. This system, enable to demonstrate not only protein interaction but also modification-independent and tyrosine phosphorylation- dependent interactions." ;
rdfs:subClassOf obo:MI_0090 .
obo:MI_0315 a rdfs:Class ;
rdfs:label "protein complex" ;
rdfs:comment "A stable set of interacting proteins that can be copurified and operate as a functional unit." ;
rdfs:subClassOf obo:MI_1299 .
obo:MI_0591 a rdfs:Class ;
rdfs:label "experiment description" ;
rdfs:comment "The experimental condition text description, should contain information about the organisms hosting the interaction." ;
rdfs:subClassOf obo:MI_0665 .
obo:MI_0102 a rdfs:Class ;
rdfs:label "sequence tag identification" ;
rdfs:comment "This approach leads to protein identification by combining mass measurement and short amino acid sequence information obtained by tandem mass spectrometry. This information is then used to automatically find the best match in a sequence database. A mixture of peptides derived from a protease digestion is analysed by nanoelectrospray LC-MS/MS (Liquid Chromatography Tandem Mass Spectrometer or nanoESI MS/MS) mass spectrometry. Electrospray mass spectrometry cannot be applied to dilute samples and is affected by high salt. As a consequence peptides, normally extracted from acrylamide gels by in situ proteolysis, are desalted and concentrated on a microcolumn followed by elution into a capillary used for nanoelectrospray tandem mass spectrometry. A first mass spectrum (Normal mass spectrum or Q1 mass spectrum) gives information about the masses of all the peptides. Peptides observed in the normal mass spectrum are isolated in turn and dissociated into fragments by collision with gas molecules within the mass spectrometer. Some of the fragments obtained from a peptide constitute a nested set, differing by one amino acid, and the mass difference between them allows assignment of a partial sequence. The masses of the fragments define the position of the partial sequence in the peptide. Together with the cleavage specificity of the protease used to cleave the protein, and mass information such sequence tag provides much higher search specificity to match the a database entry. The procedure is repeated with several peptides from the digest, resulting in multiple identifications of the same protein or identification of several proteins from the peptide mixture. Unknown proteins can easily be identified by using the high specificity of the peptide sequence tag for searches in most sequence databases including EST or genome databases." ;
rdfs:subClassOf obo:MI_0427 , obo:MI_0433 .
obo:MI_0966 a rdfs:Class ;
rdfs:label "ultraviolet-visible spectroscopy" ;
rdfs:comment "Ultraviolet-visible spectroscopy or ultraviolet-visible spectrophotometry (UV-Vis or UV/Vis) involves the spectroscopy of photons in the UV-visible region. This means it uses light in the visible and adjacent (near ultraviolet (UV) and near infrared (NIR)) ranges." ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_0252 a rdfs:Class ;
rdfs:label "biological feature" ;
rdfs:comment "Property of a subsequence that may be involved with or interfere with the binding of a molecule and are supported by experimental evidences." ;
rdfs:subClassOf obo:MI_0116 .
obo:MI_1146 a rdfs:Class ;
rdfs:label "phospholipase reaction" ;
rdfs:comment "Measurement of the hydrolysis of phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_2325 a rdfs:Class ;
rdfs:label "nanoluc luciferase protein tag" ;
rdfs:comment "NanoLuc luciferase (Nluc) is a small (19 kDa), highly stable, ATP independent, bioluminescent protein derived from the luciferase complex of the deep-sea shrimp O. gracilirostris." ;
rdfs:subClassOf obo:MI_1205 .
obo:MI_0893 a rdfs:Class ;
rdfs:label "neutron diffraction" ;
rdfs:comment "Analysis of diffraction pattern using neutron beam" ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_2365 a rdfs:Class ;
rdfs:label "fluorescent protein-protein interaction-visualization" ;
rdfs:comment "FluoPPI system (Fluorescent Protein-Protein Interaction-visualization):-FLUOPPI utilises the formation of fluorescence foci whereby the interacting proteins of interest are genetically fused with either a tetramerizing fluorescent protein (FP-tag) or an assembly helper tag (Ash-tag). The incorporation of these tags onto a pair of interacting proteins enables the formation of intensely bright foci when co-expressed in mammalian cells. In these foci the FP-tag induces the fused protein to form a tetramer that can now interact with up to 4 copies of the Ash-tagged partner protein. The cognate interacting protein also forms an oligomer through the Ash tag, which in turn can interact with multiple copies of the FP-fused partner protein. The potential of both constructs to interact with multiple copies of each other enable large foci incorporating the fluorescent protein to form, which can be clearly observed when imaging the cell." ;
rdfs:subClassOf obo:MI_0428 .
obo:MI_0648 a rdfs:Class ;
rdfs:label "molar" ;
rdfs:comment "Molarity is the number of moles of solute dissolved in one liter of solution. The units, therefore are moles per liter, specifically it's moles of solute per liter of solution. These units are abbreviated as M and it means moles per liter (not just moles)." ;
rdfs:subClassOf obo:MI_0647 .
obo:MI_1022 a rdfs:Class ;
rdfs:label "field flow fractionation" ;
rdfs:comment "A separation technique where a field is applied to a mixture perpendicular to the mixtures flow. The filed can be graviational, centrifugal, magnetic or a cross flow of fluids." ;
rdfs:subClassOf obo:MI_0027 .
obo:MI_0179 a rdfs:Class ;
rdfs:label "other modification" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00032.""" .
obo:MI_0888 a rdfs:Class ;
rdfs:label "small angle neutron scattering" ;
rdfs:comment "During a SANS experiment a beam of neutrons is directed at a sample. The neutrons are elastically scattered by a sample and the resulting scattering pattern is analyzed to provide information about the size, shape and orientation of some component of the sample." ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_2248 a rdfs:Class ;
rdfs:label "translation regulation" ;
rdfs:comment "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA." ;
rdfs:subClassOf obo:MI_2245 .
obo:MI_0740 a rdfs:Class ;
rdfs:label "cell penetrating peptide tag" ;
rdfs:comment "The peptides named CPPs vary greatly in size, amino acid sequence, and charge, but share the common feature that they have the ability to rapidly translocate the plasma membrane and enable delivery to the cytoplasm or nucleus." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_0574 a rdfs:Class ;
rdfs:label "digital object identifier" ;
rdfs:comment "Identifier of a publication prior to pubmed indexing." ;
rdfs:subClassOf obo:MI_0445 .
obo:MI_1055 a rdfs:Class ;
rdfs:label "internally-curated" ;
rdfs:comment "Data has been directly curated into this database from the paper describing the experimental evidence" ;
rdfs:subClassOf obo:MI_1053 .
obo:MI_0142 a rdfs:Class ;
rdfs:label "n-acetyl-valine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00063.""" .
obo:MI_0445 a rdfs:Class ;
rdfs:label "literature database" ;
rdfs:comment "Databases acting as a source of literature information." ;
rdfs:subClassOf obo:MI_0444 .
obo:MI_0816 a rdfs:Class ;
rdfs:label "molecular weight estimation by staining" ;
rdfs:comment "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker." ;
rdfs:subClassOf obo:MI_0815 .
obo:MI_2258 a rdfs:Class ;
rdfs:label "xenobiotic" ;
rdfs:comment "Molecule that encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity, which is not physiologically part of a cell, tissue, organ, or organism." ;
rdfs:subClassOf obo:MI_0328 .
obo:MI_0579 a rdfs:Class ;
rdfs:label "electron donor" ;
rdfs:comment "Any molecule that is able to transfer an electron to another chemical species." ;
rdfs:subClassOf obo:MI_0918 .
obo:MI_2273 a rdfs:Class ;
rdfs:label "tyrosination" ;
rdfs:comment "Reversible reaction that add a tyrosine residues to the c-terminal end of alpha-tubulin." ;
rdfs:subClassOf obo:MI_2272 .
obo:MI_0608 a rdfs:Class ;
rdfs:label "ribosomal rna" ;
rdfs:comment "RNA that is transcribed from the DNA of the nucleolus and is found, together with characteristic proteins, in the ribosomes." ;
rdfs:subClassOf obo:MI_0320 .
obo:MI_0703 a rdfs:Class ;
rdfs:label "gene3d" ;
rdfs:comment """The Gene3D database provides a combined structural, functional and evolutionary view of the protein world. It is focused on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species.
http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/""" ;
rdfs:subClassOf obo:MI_0449 .
obo:MI_2020 a rdfs:Class ;
rdfs:label "canadian drug identification number" ;
rdfs:comment "Drug Identification Number (Canadian Drug ID system)" ;
rdfs:subClassOf obo:MI_2054 .
obo:MI_2192 a rdfs:Class ;
rdfs:label "clip-seq" ;
rdfs:comment """This method combines UV cross-linking and immunoprecipitation with high-throughput sequencing to identify binding sites of RNA-binding proteins.
https://en.wikipedia.org/wiki/HITS-CLIP""" ;
rdfs:subClassOf obo:MI_2191 .
obo:MI_1135 a rdfs:Class ;
rdfs:label "venus fluorescent protein tag" ;
rdfs:comment "Introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L), produced Venus. This mutation dramatically accelerates oxidation of the chromophore, the rate-limiting step in fluorescent protein maturation. Additional mutations were also introduced in order to increase the tolerance of Venus to acidic environments and to reduce the sensitivity to chloride. The absorption and emission spectral peaks are 515 and 528 nanometers, respectively." ;
rdfs:subClassOf obo:MI_0368 .
obo:MI_2286 a rdfs:Class ;
rdfs:label "functional association" ;
rdfs:comment "Binary relationship between biological entities when one of them modulates the other in terms of function, expression, degradation or stability of the other and the relationship between the partners cannot be ascertained as direct, so intermediate steps are implicitly present. This relation specifically does not imply a physical interaction between the entities involved." ;
rdfs:subClassOf obo:MI_0190 .
obo:MI_1175 a rdfs:Class ;
rdfs:label "allosteric post-translational modification" ;
rdfs:comment "A post-translational modification that elicits an allosteric response upon addition to a target molecule. An allosteric post-translational modification is identified by referring to its feature id." ;
rdfs:subClassOf obo:MI_0252 , obo:MI_0664 , obo:MI_1149 .
obo:MI_0907 a rdfs:Class ;
rdfs:label "conformational status" ;
rdfs:comment "Statement about the native/denatured conformation of the protein." ;
rdfs:subClassOf obo:MI_0346 .
obo:MI_2167 a rdfs:Class ;
rdfs:label "kinetic exclusion assay" ;
rdfs:comment "In the kinetic exclusion assay one of the interaction components (bait) is immobilized to a solid phase (beads) and is used to capture the prey from a solution containing free molecules of both the prey and the bait that has reached kinetic equilibrium. This mixture of free components is only allowed to contact the immobilized bait for a very short time, so bait-prey complexes do not dissociate. The immobilized bait captures a small percentage of the prey, which is proportional to the free prey concentration, and the captured prey is detected usually via a fluorescent tag." ;
rdfs:subClassOf obo:MI_0892 .
obo:MI_1011 a rdfs:Class ;
rdfs:label "deneddylase assay" ;
rdfs:comment "Measurement of the reaction that breaks a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_1345 a rdfs:Class ;
rdfs:label "rho tag" ;
rdfs:comment "A 9-amino acid peptide representing C terminus of bovine rhodopsin widely used as an epitope tag. A number of anti-rhodopsin antibodies recognize this epitope." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_2147 a rdfs:Class ;
rdfs:label "chemical stability at pH 7.4" ;
rdfs:comment "Chemical stabilityat at pH 7.4" ;
rdfs:subClassOf obo:MI_2055 .
obo:MI_2229 a rdfs:Class ;
rdfs:label "nucleicacid-gene" ;
rdfs:comment "Interaction between a nucleic acid and a gene region." ;
rdfs:subClassOf obo:MI_1046 .
obo:MI_0253 a rdfs:Class ;
rdfs:label "isotope label" ;
rdfs:comment "One of several nuclides having the same number of protons in their nuclei and hence having the same atomic number, but differing in the number of neutrons and therefore, in the mass number." ;
rdfs:subClassOf obo:MI_0505 .
obo:MI_0383 a rdfs:Class ;
rdfs:label "biopolymer" ;
rdfs:comment "Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds." ;
rdfs:subClassOf obo:MI_0313 .
obo:MI_0236 a rdfs:Class ;
rdfs:label "32p radiolabel" ;
rdfs:comment "Molecule labelled with the radio isotope 32 of phosphorus atoms." ;
rdfs:subClassOf obo:MI_0517 .
obo:MI_0242 a rdfs:Class ;
rdfs:label "gene ontology definition reference" ;
rdfs:comment "This qualifier is used when the crossreference is imported from the Gene Ontology tag definition_reference." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_0860 a rdfs:Class ;
rdfs:label "genbank identifier" ;
rdfs:comment " edit" ;
rdfs:subClassOf obo:MI_0683 .
obo:MI_0647 a rdfs:Class ;
rdfs:label "parameter unit" ;
rdfs:comment "Controlled vocabulary for kinetic constant units." ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_0882 a rdfs:Class ;
rdfs:label "atpase reaction" ;
rdfs:comment "Catalysis of the hydrolisis of ATP+ H2O = ADP + phosphate." ;
rdfs:subClassOf obo:MI_0881 .
obo:MI_0128 a rdfs:Class ;
rdfs:label "n-acetyl-glutamic acid" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00053.""" .
obo:MI_0896 a rdfs:Class ;
rdfs:label "renilla luciferase protein tag" ;
rdfs:comment "Renilla luciferase, is an enzyme of the sea pansy catalyzing the oxidation of the coelenterazine pigment) that produces light. Renilla luciferase produces a blue light of 480nm." ;
rdfs:subClassOf obo:MI_1205 .
obo:MI_1110 a rdfs:Class ;
rdfs:label "predicted interaction" ;
rdfs:comment "Interaction has been predicted by either interologue mapping, by an algorithm or by a computational method." ;
rdfs:subClassOf obo:MI_0190 .
obo:MI_0189 a rdfs:Class ;
rdfs:label "ubiquitinated lysine" ;
rdfs:comment """Residue modification due to a cross-link between a lysine and a glycine from the ubiquitine protein.
OBSOLETE remap to MOD:00134.""" .
obo:MI_0901 a rdfs:Class ;
rdfs:label "isotope label footprinting" ;
rdfs:comment "Exposed amino acid residues undergo a rapid exchange of a specific radio-isotope e.g. hydrogen/deuterium. Residues involved in a molecular interaction are protected from this exchange and exhibit a much slower rate of exchange. This method of binding range identification must be coupled to NMR or mass spectrometry technologies in order to detect the radio-isotope exchange." ;
rdfs:subClassOf obo:MI_0605 .
obo:MI_2113 a rdfs:Class ;
rdfs:label "dissolution profile" ;
rdfs:comment "The rate of dissolution is a key target for controlling the duration of a drug's effect, and as such, several dosage forms that contain the same active ingredient may be available, differing only in the rate of dissolution. If a drug is supplied in a form that is not readily dissolved, the drug may be released more gradually over time with a longer duration of action. Having a longer duration of action may improve compliance since the medication will not have to be taken as often. Additionally, slow-release dosage forms may maintain concentrations within an acceptable therapeutic range over a long period of time, as opposed to quick-release dosage forms which may result in sharper peaks and troughs in serum concentrations." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0191 a rdfs:Class ;
rdfs:label "aggregation" ;
rdfs:comment """Physical association among molecules.
OBSOLETE since too non-specific. Consider using physical interaction (MI:0218) instead.""" .
obo:MI_0899 a rdfs:Class ;
rdfs:label "p3 filamentous phage display" ;
rdfs:comment "pIII is one of the minor coat proteins that decorates in five copies the emerging tip of filamentous phage. Similarly to pVIII pIII also tolerates peptide insertions at the amino-terminus. The sequences to be displayed can either be encoded in the phage copy of the coat gene or in an extra pIII gene copy carried on a phagemid. In the first case 5 copies o the hybrid proteins are displayed while in the latter only a few capsid display one copy and the majority display none. Because of the low copy number pIII display is often referred to as low valency display." ;
rdfs:subClassOf obo:MI_0048 .
obo:MI_0659 a rdfs:Class ;
rdfs:label "experimental feature detection" ;
rdfs:comment "Experimental method by which a feature is detected or identified." ;
rdfs:subClassOf obo:MI_0003 .
obo:MI_0977 a rdfs:Class ;
rdfs:label "no-imex-export" ;
rdfs:comment "Prevents export of experiment and associated interactions to IMEx" ;
rdfs:subClassOf obo:MI_0665 .
obo:MI_1037 a rdfs:Class ;
rdfs:label "Split renilla luciferase complementation" ;
rdfs:comment "The N-terminal portion of synthetic renilla luciferase (hrluc) is attached to one protein through the linker peptide (GGGS)2 and C-terminal portion of synthetic renilla luciferase is connected to the second protein through the linker (GGGGS)2. Interaction of the 2 proteins recovers hrluc activity and produces light." ;
rdfs:subClassOf obo:MI_1203 .
obo:MI_2443 a rdfs:Class ;
rdfs:label "qsproteome" ;
rdfs:comment """QSProteome is a centralized, community-driven structural biology resource that hosts over 35,000 predicted oligomeric protein complex models, covering more than 42,000 genes across multiple species. It prevents redundant modeling by allowing researchers to track existing predictions and provides clear quality metrics (pLDDT, ipTM, PAE) to assess model reliability. Each entry includes interactive 3D visualization, functional annotations, and links to databases such as BioCyc, ComplexPortal, PDB, and UniProt, integrating computational predictions with experimental data. The platform also supports community curation, enabling users to refine models and contribute to the expanding structural proteome.
https://qsproteome.org/""" ;
rdfs:subClassOf obo:MI_0489 .
obo:MI_0004 a rdfs:Class ;
rdfs:label "affinity chromatography technology" ;
rdfs:comment "This class of approaches is characterised by the use of affinity resins as tools to purify molecule of interest (baits) and their binding partners. The baits can be captured by a variety of high affinity ligands linked to a resin - for example, antibodies specific for the bait itself, antibodies for specific tags engineered to be expressed as part of the bait or other high affinity binders such as glutathione resins for GST fusion proteins, metal resins for histidine-tagged proteins." ;
rdfs:subClassOf obo:MI_0091 , obo:MI_0400 .
obo:MI_0359 a rdfs:Class ;
rdfs:label "biological process" ;
rdfs:comment "Cross reference pointing to a Gene Ontology -'cellular process' term." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_1095 a rdfs:Class ;
rdfs:label "hgnc" ;
rdfs:comment "HGNC is the nomenclature committee responsible for the naming of human genes." ;
rdfs:subClassOf obo:MI_1109 .
obo:MI_0563 a rdfs:Class ;
rdfs:label "methylated arginine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00658.""" .
obo:MI_0619 a rdfs:Class ;
rdfs:label "pathway" ;
rdfs:comment "Refers to the metabolic or signalling pathway involving an interaction or a complex." ;
rdfs:subClassOf obo:MI_0664 .
obo:MI_0805 a rdfs:Class ;
rdfs:label "wwpdb" ;
rdfs:comment """The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community.
http://www.wwpdb.org/""" ;
rdfs:subClassOf obo:MI_0447 , obo:MI_0461 , obo:MI_0489 .
obo:MI_0509 a rdfs:Class ;
rdfs:label "phosphatase homogeneous time resolved fluorescence" ;
rdfs:comment "Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being removed from close proximity on the phosphorylated substrate due to the action of the phosphatase." ;
rdfs:subClassOf obo:MI_0434 , obo:MI_0510 .
obo:MI_0225 a rdfs:Class ;
rdfs:label "chromatin immunoprecipitation array" ;
rdfs:comment "The method combines a modified chromatin immunoprecipitation (ChIP) procedure, with DNA microarray analysis. Cells are fixed with formaldehyde, harvested, and disrupted by sonication. The DNA fragments cross-linked to a protein of interest are enriched by immunoprecipitation with a specific antibody. After reversal of the cross-links, the enriched DNA is amplified and labeled with a fluorescent dye (Cy5) by using a ligation-mediatedpolymerase chain reaction (LM-PCR). In parallel a sample of DNA that is not enriched by immunoprecipitation is subjected to LM-PCR in the presence of a different fluorophore (Cy3), and both immunoprecipitation (IP)-enriched and unenriched pools of labeled DNA were hybridized to a single DNA microarray containing a set of intergenic sequences. The ratio of the Cy5 to Cy3 fluorescence intensities measured at each DNA element in the microarray provided a measure of the extent of binding of the transcription factor to the corresponding genomic locus." ;
rdfs:subClassOf obo:MI_0008 , obo:MI_0402 .
obo:MI_1334 a rdfs:Class ;
rdfs:label "rigid" ;
rdfs:comment "A global unique identifier to identify interactions that are identical. A RIG identifier (RIGID) is constructed by concatenating ROGID MI:1335 (after sorting them in ascending lexicographical order ), applying the SHA-1 algorithm to the resulting string, converting the digest to its base64 representation and removing all trailing \"=\" characters used for padding." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_1212 .
obo:MI_2036 a rdfs:Class ;
rdfs:label "boiling point" ;
rdfs:comment "The boiling point of a liquid is the temperature at which the vapor pressure of the liquid equals the environmental pressure surrounding the liquid. A liquid in a vacuum environment has a lower boiling point than when the liquid is at atmospheric pressure. A liquid in a high pressure environment has a higher boiling point than when the liquid is at atmospheric pressure. In other words, the boiling point of liquids varies with and depends upon the surrounding environmental pressure." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0885 a rdfs:Class ;
rdfs:label "journal" ;
rdfs:comment "Name and details of a journal from which paper has been taken." ;
rdfs:subClassOf obo:MI_1093 .
obo:MI_0311 a rdfs:Class ;
rdfs:label "microinjection" ;
rdfs:comment "The insertion of a substance into a cell through a microneedle. To extrude the substances through the very fine needle tip, either hydrostatic pressure (pressure injection) or electric currents (ionophoresis) is employed." ;
rdfs:subClassOf obo:MI_0307 .
obo:MI_0304 a rdfs:Class ;
rdfs:label "isoform synonym" ;
rdfs:comment "Isoform synonym." ;
rdfs:subClassOf obo:MI_1041 .
obo:MI_0529 a rdfs:Class ;
rdfs:label "s-(adp-ribosyl)-cysteine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00178.""" .
obo:MI_1304 a rdfs:Class ;
rdfs:label "molecule set" ;
rdfs:comment "A group of molecules linked by a high degree of similarity of sequence and/or function and not easily separated by participant identification methods." ;
rdfs:subClassOf obo:MI_0313 .
obo:MI_0580 a rdfs:Class ;
rdfs:label "electron acceptor" ;
rdfs:comment "Molecule to which an electron may be transferred from an electron donor." ;
rdfs:subClassOf obo:MI_0919 .
obo:MI_1060 a rdfs:Class ;
rdfs:label "spoke expansion" ;
rdfs:comment "Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with a single designated molecule, usually the bait." ;
rdfs:subClassOf obo:MI_1059 .
obo:MI_0541 a rdfs:Class ;
rdfs:label "gpi-anchor amidated asparagine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00167.""" .
obo:MI_0220 a rdfs:Class ;
rdfs:label "ubiquitination reaction" ;
rdfs:comment "Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0241 a rdfs:Class ;
rdfs:label "horseradish peroxidase tag" ;
rdfs:comment "Protein is fused to horseradish peroxidase, and the measure of this enzyme activity can be taken as indicative of presence of protein." ;
rdfs:subClassOf obo:MI_0365 .
obo:MI_0168 a rdfs:Class ;
rdfs:label "n-methyl-methionine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00073.""" .
obo:MI_0449 a rdfs:Class ;
rdfs:label "interpro" ;
rdfs:comment """InterPro combines a number of databases (referred to as member databases) that use different methodologies and a varying degree of biological information on well-characterised proteins to derive protein signatures that predict family membership and domain composition of naive protein sequences.
https://www.ebi.ac.uk/interpro/""" ;
rdfs:subClassOf obo:MI_0447 .
obo:MI_0568 a rdfs:Class ;
rdfs:label "desumoylation reaction" ;
rdfs:comment "Cleavage of the G-K bond and release of the SUMO ubiquitin like proteins." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_1298 a rdfs:Class ;
rdfs:label "complex type" ;
rdfs:comment "A classification of the structural characteristics of a macromolecular complex." ;
rdfs:subClassOf obo:MI_0314 .
obo:MI_0972 a rdfs:Class ;
rdfs:label "phosphopantetheinylase assay" ;
rdfs:comment "Assay of the posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0510 a rdfs:Class ;
rdfs:label "homogeneous time resolved fluorescence" ;
rdfs:comment "Methods based on the exceptionally long fluorescence lifetime characteristics of certain fluorophores, which allows the elimination of the effects of background fluorescence. Uses nonradiative energy transfer or quenching between fluorescent lanthanide chelates and different acceptors to measure reaction rates." ;
rdfs:subClassOf obo:MI_0051 .
obo:MI_0161 a rdfs:Class ;
rdfs:label "beta-methylthioaspartic acid" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00237.""" .
obo:MI_0871 a rdfs:Class ;
rdfs:label "demethylation reaction" ;
rdfs:comment "The cleavage of a methyl group from a polypeptide. Methylation is generally an irreversible reaction except in mamalian." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0153 a rdfs:Class ;
rdfs:label "n-palmitoyl-cysteine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00069.""" .
obo:MI_0859 a rdfs:Class ;
rdfs:label "force spectroscopy" ;
rdfs:comment "A single-molecule technique that measures the behavior of a molecular complex under stretching or torsional mechanical force." ;
rdfs:subClassOf obo:MI_0013 , obo:MI_2318 .
obo:MI_0918 a rdfs:Class ;
rdfs:label "donor" ;
rdfs:comment "Molecule which emits active chemical groups, electrons or ions that are transfered to an acceptor molecule." ;
rdfs:subClassOf obo:MI_0500 .
obo:MI_1320 a rdfs:Class ;
rdfs:label "membrane yeast two hybrid" ;
rdfs:comment "Traditional yeast two hybrid assays are not suitable for the analysis of membrane proteins, as they require the interactions to occur in the nucleus. Methods have been specifically developed to assay for interactions of membrane proteins with both cytosolic or membrane-bound partners." ;
rdfs:subClassOf obo:MI_2412 .
obo:MI_1044 a rdfs:Class ;
rdfs:label "rice genome annotation project" ;
rdfs:comment "NSF funded annotation project." ;
rdfs:subClassOf obo:MI_1094 .
obo:MI_0113 a rdfs:Class ;
rdfs:label "western blot" ;
rdfs:comment "Western blot is a procedure to identify and quantify proteins. A mixture of protein is first submitted to an electrophoresis in denaturing condition and then electro-transferred from the gel to a membrane. The membrane is then incubated with a primary antibody specific for a given protein or a specific residue modification in the sample under analysis. A secondary antibody, radiolabelled or fused to fluorophore or to a chromogenic enzyme, targets the first antibody and allows the visualisation of the protein band on the membrane." ;
rdfs:subClassOf obo:MI_0421 , obo:MI_0659 .
obo:MI_2336 a rdfs:Class ;
rdfs:label "luminescence acceptor donor pair" ;
rdfs:comment "Pair of luminescence donor-fluorophore or fluorophores attached to the same molecule used in a bret or fret experiment to observe the details of conformational changes." ;
rdfs:subClassOf obo:MI_0495 .
obo:MI_0552 a rdfs:Class ;
rdfs:label "s-nitrosyl-cysteine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00235.""" .
obo:MI_2269 a rdfs:Class ;
rdfs:label "de-ubiquitinylated residue" ;
rdfs:comment "A protein modification that effectively cleaves the G-K bond and releases ubiquitin or ubiquitin like proteins." ;
rdfs:subClassOf obo:MI_2262 .
obo:MI_0522 a rdfs:Class ;
rdfs:label "myc tag" ;
rdfs:comment "The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_1107 a rdfs:Class ;
rdfs:label "pid" ;
rdfs:comment "Curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. It is a collaborative project between the US National Cancer Institute (NCI) and Nature Publishing Group (NPG), and is an open access online resource (http://pid.nci.nih.gov/)." ;
rdfs:subClassOf obo:MI_1106 .
obo:MI_0329 a rdfs:Class ;
rdfs:label "unknown participant" ;
rdfs:comment "Any type of molecule, including complexes, that may be observed but not identified. This term should be use only at PARTICIPANT level." ;
rdfs:subClassOf obo:MI_0313 .
obo:MI_0961 a rdfs:Class ;
rdfs:label "rapid curation" ;
rdfs:comment "Minimal interaction data has been extracted from the paper" ;
rdfs:subClassOf obo:MI_0955 .
obo:MI_0181 a rdfs:Class ;
rdfs:label "selenomethionine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00530.""" .
obo:MI_0059 a rdfs:Class ;
rdfs:label "gst pull down" ;
rdfs:comment """The bait protein is expressed and purified as a fusion to the glutathione S-tranferase protein. The bait protein is normally attached to a glutathione sepharose resin or alternatively to a support containing an anti-GST antibody.
OBSOLETE redundant term. Map to feature type : gst-tagged (MI:0519) and Interaction detection method: pull down (MI:0096).""" .
obo:MI_2376 a rdfs:Class ;
rdfs:label "dosage rescue (sensu BioGRID)" ;
rdfs:comment "Increased dosage of one gene rescues lethality or a growth defect associated with perturbation of another gene." ;
rdfs:subClassOf obo:MI_2379 , obo:MI_2395 .
obo:MI_0172 a rdfs:Class ;
rdfs:label "aspartic 4-phosphoric anhydride" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00042.""" .
obo:MI_2297 a rdfs:Class ;
rdfs:label "carbohydrate chemical modification causing an interaction" ;
rdfs:comment "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that enables an interaction when compared with the unaltered carbohydrate, which does not interact." ;
rdfs:subClassOf obo:MI_2276 .
obo:MI_1186 a rdfs:Class ;
rdfs:label "dna methyltransferase tag" ;
rdfs:comment "The protein of interest is fused to Escherichia coli DNA adenine methyltransferase (dam). Expression of this fusion protein in vivo leads to preferential methylation of adenines in DNA surrounding the native binding sites of the dam fusion partner. Because adenine methylation does not occur endogenously in most eukaryotes, it provides a unique tag to mark protein interaction sites." ;
rdfs:subClassOf obo:MI_0365 .
obo:MI_0958 a rdfs:Class ;
rdfs:label "partial coverage" ;
rdfs:comment "Not all interactions which can be ascribed to an unambiguous identified in this paper have been captured." ;
rdfs:subClassOf obo:MI_0956 .
obo:MI_0922 a rdfs:Class ;
rdfs:label "imex evidence" ;
rdfs:comment "Experimental evidence supporting an interaction curated and released under the IMEx agreement." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_2275 a rdfs:Class ;
rdfs:label "regulator target" ;
rdfs:comment "Entity whose concentration, frequency, rate or extent are regulated by the regulator entity." ;
rdfs:subClassOf obo:MI_0500 .
obo:MI_1066 a rdfs:Class ;
rdfs:label "structure-based confidence" ;
rdfs:comment "Confidence score based on similarity to interacting molecules of known structure, presence of known interacting domains etc." ;
rdfs:subClassOf obo:MI_1064 .
obo:MI_2097 a rdfs:Class ;
rdfs:label "anti-convulsant" ;
rdfs:comment "Therapeutic category or general category of drug -anti-convulsant" ;
rdfs:subClassOf obo:MI_2041 .
obo:MI_0846 a rdfs:Class ;
rdfs:label "r1 spin label" ;
rdfs:comment """Paramagnetic molecule (1-oxyl-2,2,5,5-tetramethylpyrroline-
3-methyl)-methanethiosulfonate. that can be covalently attached to any cysteine aminoacid producing a nitroxide
side chain designated R1.""" ;
rdfs:subClassOf obo:MI_0845 .
obo:MI_0686 a rdfs:Class ;
rdfs:label "unspecified method" ;
rdfs:comment "Yet to be identified interaction detection method associated with interaction data imported from a third party database. This database may have potentially different standards of curation." ;
rdfs:subClassOf obo:MI_0001 .
obo:MI_0620 a rdfs:Class ;
rdfs:label "search-url-ascii" ;
rdfs:comment "Search URL to retrieve an external entry in ASCII format. Generally associated to Cv Database terms." ;
rdfs:subClassOf obo:MI_0667 .
obo:MI_0911 a rdfs:Class ;
rdfs:label "cross linker" ;
rdfs:comment "A variety of crosslinkers are used to analyze subunit structure of proteins, protein interactions and various parameters of protein function. Subunit structure is deduced since crosslinkers only bind surface amino residues in relatively close proximity in the native state. Protein interactions are often too weak or transient to be easily detected, but by crosslinking, the interactions can be captured and analyzed." ;
rdfs:subClassOf obo:MI_0505 .
obo:MI_1125 a rdfs:Class ;
rdfs:label "direct binding region" ;
rdfs:comment "The defined region of protein which makes physical contact with the interacting partner." ;
rdfs:subClassOf obo:MI_0442 .
obo:MI_0962 a rdfs:Class ;
rdfs:label "strep ii tag" ;
rdfs:comment "The protein of interest is expressed with a StrepII fusion peptide Ser-Ala-Trp-Ser-His-Pro-Gln-Phe-Glu-Lys (SAWSHPQFEK)." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_2240 a rdfs:Class ;
rdfs:label "down-regulates" ;
rdfs:comment "The effect of a modulator entity A on a modulated entity B that decreases the concentration and/or frequency and/or ate and/or extent of molecular function of B." ;
rdfs:subClassOf obo:MI_2234 .
obo:MI_1301 a rdfs:Class ;
rdfs:label "non-obligate complex" ;
rdfs:comment "Protein chains present in the complex may also be found as independent stable proteins in vivo." ;
rdfs:subClassOf obo:MI_1298 .
obo:MI_0098 a rdfs:Class ;
rdfs:label "ribosome display" ;
rdfs:comment "This method permits the coupling of phenotype to genotype via the formation of a non-covalent ternary complex between mRNAs and their encoded polypeptides while they are translated in an in vitro system. As a first step a cDNA library is constructed that encodes chimeric proteins in which the natural proteins or protein domains are fused to a C-terminal tether. As a consequence when the mRNA is translated in vitro the domain can fold while the tether is still in the ribosomal tunnel. Furthermore this chimeric mRNAs lack a stop codon, thus preventing release of the mRNA and the polypeptide from the ribosome. High concentrations of magnesium and low temperature further stabilise the ternary complex. Similarly to phage display, these complexes can be used directly to select for nucleic acids encoding proteins with desired properties." ;
rdfs:subClassOf obo:MI_0034 .
obo:MI_0250 a rdfs:Class ;
rdfs:label "gene" ;
rdfs:comment "A genomic region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." ;
rdfs:subClassOf obo:MI_0313 .
obo:MI_0612 a rdfs:Class ;
rdfs:label "comment" ;
rdfs:comment "Comment for public view. This attribute can be associated to interaction, experiment, CV term, an organism and any participant." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_0665 , obo:MI_0666 , obo:MI_0667 , obo:MI_0668 , obo:MI_0669 .
obo:MI_0046 a rdfs:Class ;
rdfs:label "experimental knowledge based" ;
rdfs:comment "Predictive algorithms that rely on the information obtained by experimental results." ;
rdfs:subClassOf obo:MI_0063 .
obo:MI_1079 a rdfs:Class ;
rdfs:label "ratmap" ;
rdfs:comment "The rat genome database RatMap (http://ratmap.org or http://ratmap.gen.gu.se) has been one of the main resources for rat genome information since 1994. The database is maintained by CMB Genetics at Gothenburg University in Sweden and provides information on rat genes, polymorphic rat DNA-markers and rat quantitative trait loci (QTLs), all curated at RatMap." ;
rdfs:subClassOf obo:MI_1094 .
obo:MI_0870 a rdfs:Class ;
rdfs:label "demethylase assay" ;
rdfs:comment "Measures the catalysis of the hydrolysis of an methyl group from a substrate molecule." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0467 a rdfs:Class ;
rdfs:label "reactome" ;
rdfs:comment """The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology.
http://www.reactome.org/""" ;
rdfs:subClassOf obo:MI_1106 .
obo:MI_0403 a rdfs:Class ;
rdfs:label "colocalization" ;
rdfs:comment "Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred." ;
rdfs:subClassOf obo:MI_0190 .
obo:MI_0138 a rdfs:Class ;
rdfs:label "n-acetyl-serine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00060.""" .
obo:MI_2128 a rdfs:Class ;
rdfs:label "ABCB1 transporter substrate" ;
rdfs:comment "Substrate for the representitive member of the ABC transprorter family ABCB1 (MDR1, pgy1, P08183). ABC transporters preventing uptake or facilitating clearance of toxic substances, playing an important role in drug excretion through the bile." ;
rdfs:subClassOf obo:MI_2121 .
obo:MI_0158 a rdfs:Class ;
rdfs:label "n-methyl-alanine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00070.""" .
obo:MI_0900 a rdfs:Class ;
rdfs:label "p8 filamentous phage display" ;
rdfs:comment "pVIII is the major coat protein of filamentous phage. Its amino-terminus is exposed to solvent and tolerates the insertion of relatively large peptide fragments. By inserting the peptide coding sequence into the phage copy of the pVIII gene up to 3000 copies of the hybrid proteins can be displayed along the phage capsid. Alternatively the hybrid protein can be encoded on a phagemid that is incorporated in a virus like particle by infection with a helper phage. In this latter case one obtains a chimeric capsid where hybrid proteins are interspersed at different density in an otherwise wild type coat. Because of the high copy number pVIII display is also referred to as high valency display." ;
rdfs:subClassOf obo:MI_0048 .
obo:MI_2314 a rdfs:Class ;
rdfs:label "attached carbohydrate increasing interaction rate" ;
rdfs:comment "Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule." ;
rdfs:subClassOf obo:MI_2312 .
obo:MI_1072 a rdfs:Class ;
rdfs:label "method-based confidence" ;
rdfs:comment "The confidence of an interaction is assessed on the number of different methods by which it is observed." ;
rdfs:subClassOf obo:MI_1064 .
obo:MI_0634 a rdfs:Class ;
rdfs:label "contact-email" ;
rdfs:comment "E-mail address to contact the author or organisation which has produced the data. This attribute is generally associated to an experiment." ;
rdfs:subClassOf obo:MI_1093 .
obo:MI_0207 a rdfs:Class ;
rdfs:label "formylation reaction" ;
rdfs:comment "Reaction that can affect K or G residues. Reside is functionalised with a formyl group." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_1041 a rdfs:Class ;
rdfs:label "synonym" ;
rdfs:comment "Alternative name or descriptor for an entity." ;
rdfs:subClassOf obo:MI_0300 .
obo:MI_1159 a rdfs:Class ;
rdfs:label "allosteric molecule" ;
rdfs:comment "A molecule whose binding or catalytic properties at one site are altered by allosteric post-translational modification or binding of an allosteric effector at a distinct site. An allosteric molecule is identified by referring to its participant id." ;
rdfs:subClassOf obo:MI_0500 , obo:MI_0664 , obo:MI_1149 .
obo:MI_0489 a rdfs:Class ;
rdfs:label "source database" ;
rdfs:comment "Database that originally provided the interaction record for exchange purposes." ;
rdfs:subClassOf obo:MI_0444 .
obo:MI_2064 a rdfs:Class ;
rdfs:label "solubility" ;
rdfs:comment "Potential ability of a substance to dissolve in a liquid." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0857 a rdfs:Class ;
rdfs:label "fluorescent dye label" ;
rdfs:comment "Dye label containing a fluorophore which absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength." ;
rdfs:subClassOf obo:MI_0373 , obo:MI_0856 .
obo:MI_0016 a rdfs:Class ;
rdfs:label "circular dichroism" ;
rdfs:comment "Circular dichroism (CD) is observed when optically active molecules absorb left and right hand circularly polarized light slightly differently. Linearly polarized light can be viewed as a superposition of two components of circularly polarized light of equal amplitude and phase but opposite handness. When this light passes through an optically active sample the two polarized components are absorbed differently. The difference in left and right handed absorbance A(l)- A(r) is the signal registered in CD spectra. This signal displays distinct features corresponding to different secondary structures present in peptides, proteins and nucleic acids. The analysis of CD spectra can therefore yield valuable information about the secondary structure of biological macromolecules and the interactions among molecules that influence their structure." ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_0892 a rdfs:Class ;
rdfs:label "solid phase assay" ;
rdfs:comment "Assay where at least one molecule under analysis is bound to a solid surface, such as a microplate wall or the sides of a tube, the other reactants being free in solution." ;
rdfs:subClassOf obo:MI_0400 .
obo:MI_1130 a rdfs:Class ;
rdfs:label "mutation decreasing interaction rate" ;
rdfs:comment "Region of a molecule whose mutation or deletion decreases significantly interaction rate (in the case of interactions inferred from enzymatic reaction)." ;
rdfs:subClassOf obo:MI_0119 .
obo:MI_1291 a rdfs:Class ;
rdfs:label "genetic suppression (partial)" ;
rdfs:comment """An effect in which the perturbation of one gene results in the amelioration or lessening of the severity/penetrance of a mutant phenotype caused by perturbation of another gene, in effect making the organism more, but not completely, \"wild type\" in character with regards to the phenotype in question. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* < ab < wt [E = a*]
OR
wt < ab < a* [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_2379 .
obo:MI_2235 a rdfs:Class ;
rdfs:label "up-regulates" ;
rdfs:comment "The effect of a modulator entity A on a modulated entity B that increases the concentration and/or frequency and/or rate and/or extent of the molecular function of B." ;
rdfs:subClassOf obo:MI_2234 .
obo:MI_0697 a rdfs:Class ;
rdfs:label "dna directed dna polymerase assay" ;
rdfs:comment "Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template or primer." ;
rdfs:subClassOf obo:MI_0696 .
obo:MI_0366 a rdfs:Class ;
rdfs:label "alkaline phosphatase tag" ;
rdfs:comment "Protein is fused to alkaline phosphatase, and the measure of this enzyme activity can be taken as indicative of presence of protein." ;
rdfs:subClassOf obo:MI_0365 .
obo:MI_1312 a rdfs:Class ;
rdfs:label "aut-page" ;
rdfs:comment "Method allowing the detection of interactions between two or more molecules by their very close proximity or the overlap of their respective bands in a SDS gel containing urea as an additional denaturing agent." ;
rdfs:subClassOf obo:MI_0807 .
obo:MI_0617 a rdfs:Class ;
rdfs:label "disease" ;
rdfs:comment "The interaction has a known or demonstrated disease association." ;
rdfs:subClassOf obo:MI_0664 .
obo:MI_0723 a rdfs:Class ;
rdfs:label "protein microinjection" ;
rdfs:comment "Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases proteins." ;
rdfs:subClassOf obo:MI_0311 , obo:MI_0721 .
obo:MI_0951 a rdfs:Class ;
rdfs:label "chain parent sequence reference" ;
rdfs:comment "Reference to the master sequence from which this chain has been derived." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_0456 a rdfs:Class ;
rdfs:label "scop superfamily" ;
rdfs:comment """SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain.
http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/""" ;
rdfs:subClassOf obo:MI_0449 .
obo:MI_0057 a rdfs:Class ;
rdfs:label "gene neighbourhood" ;
rdfs:comment "Gene pairs that show a conserved topological neighbourhood in many prokaryotic genomes are considered by this approach to encode interacting or functionally related proteins. By measuring the physical distance of any given gene pair in different genomes, interacting partners are inferred." ;
rdfs:subClassOf obo:MI_0058 .
obo:MI_1199 a rdfs:Class ;
rdfs:label "anti-tag immunohistochemistry" ;
rdfs:comment "Method using an antibody coupled with some colouring agent to detect a tag fused to a specific protein within a tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody." ;
rdfs:subClassOf obo:MI_1198 .
obo:MI_2234 a rdfs:Class ;
rdfs:label "causal statement" ;
rdfs:comment "The effect of modulator entity A on a modulated entity B." ;
rdfs:subClassOf obo:MI_2233 .
obo:MI_0087 a rdfs:Class ;
rdfs:label "predictive text mining" ;
rdfs:comment "Methods based on natural language processing to detect possible interactions between proteins (direct physical interactions or indirect genetic interactions). This includes the detection of non ambiguous protein or gene names and analysis of the relation expressed in a sentence among them." ;
rdfs:subClassOf obo:MI_0110 .
obo:MI_1292 a rdfs:Class ;
rdfs:label "monophenotypic genetic suppression" ;
rdfs:comment """An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more \"wild type\" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a < ab <= b = wt [E = a]
OR
wt = b <= ab < a [E = a]
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0796 , obo:MI_2382 .
obo:MI_0606 a rdfs:Class ;
rdfs:label "DNase I footprinting" ;
rdfs:comment "Deoxyribonuclease I (DNase I) does not have high specificity for given sequences or residues, thus footprinting with DNase I permits the exact delineation of the protein-DNA binding site. Moreover DNase I, can be used for in vivo footprinting by treating intact cells with permeabilising drugs. In this latter case DNase I in vivo footprinting allow studies of the chromatin structure in genomic DNA." ;
rdfs:subClassOf obo:MI_1183 .
obo:MI_1061 a rdfs:Class ;
rdfs:label "matrix expansion" ;
rdfs:comment "Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with each other." ;
rdfs:subClassOf obo:MI_1059 .
obo:MI_1252 a rdfs:Class ;
rdfs:label "methylmalonyl-CoA isomerase asf say" ;
rdfs:comment "The catalysis othe conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2" ;
rdfs:subClassOf obo:MI_1249 .
obo:MI_1190 a rdfs:Class ;
rdfs:label "hydroxy radical footprinting" ;
rdfs:comment "Hydroxyl radicals are created from the Fenton reaction, which involves reducing Fe2+ with H2O2 to form free hydroxyl molecules. These hydroxyl molecules react with the DNA backbone, resulting in a break. Protein bound regions of the DNA are protected." ;
rdfs:subClassOf obo:MI_0602 .
obo:MI_2011 a rdfs:Class ;
rdfs:label "cas registry number" ;
rdfs:comment "Chemical Abstract Service identification number" ;
rdfs:subClassOf obo:MI_2054 .
obo:MI_2291 a rdfs:Class ;
rdfs:label "atomic force microscopy cantilevers" ;
rdfs:comment "Molecules adsorbed on a solid surface are picked up by a microscopic tip (nanometers wide) that is located at the end of an elastic cantilever. Piezoelectric controller is used to measure forces generated by single molecules or molecular complexes stretched between the substrate and the cantilever tip." ;
rdfs:subClassOf obo:MI_0859 .
obo:MI_1230 a rdfs:Class ;
rdfs:label "uridylation reaction" ;
rdfs:comment "The formation of a phosphodiester or phosphoramide ester of UMP and amino acid (MOD:01166)." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_1323 a rdfs:Class ;
rdfs:label "tag visualisation by alkaline phosphatase activity" ;
rdfs:comment "The protein is expressed as a hybrid protein fused to a tag containing an alkaline phosphatase activity. Subsequent observation or measurement of alkaline phosphatase activity is used to identify the presence of the molecule in an interaction." ;
rdfs:subClassOf obo:MI_0980 .
obo:MI_2016 a rdfs:Class ;
rdfs:label "bind smid" ;
rdfs:comment "BIND database Small Molecule Identification number (if molecule is in BIND)" ;
rdfs:subClassOf obo:MI_2054 .
obo:MI_0428 a rdfs:Class ;
rdfs:label "imaging technique" ;
rdfs:comment "Methods that provide images of molecules at various resolution depending on the technology used." ;
rdfs:subClassOf obo:MI_0045 .
obo:MI_1114 a rdfs:Class ;
rdfs:label "virhostnet" ;
rdfs:comment "A database of viral-host interactions." ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_1241 a rdfs:Class ;
rdfs:label "variant" ;
rdfs:comment "A natural change in a sequence or structure in comparison to a reference entity." ;
rdfs:subClassOf obo:MI_0252 .
obo:MI_0973 a rdfs:Class ;
rdfs:label "imex source" ;
rdfs:comment "Databases that contain curated experimental interaction data and exchanging it with other IMEx databases." ;
rdfs:subClassOf obo:MI_0489 .
obo:MI_0895 a rdfs:Class ;
rdfs:label "protein kinase A complementation" ;
rdfs:comment "This method uses Renilla luciferase (Rluc)-based protein fragment complementation assay (PCA) that is designed specifically to investigate dynamic protein complexes (association and dissociation). It is chose to generate a PCA based on the Rluc, which is, because of its simplicity and sensitivity, a widely used bioluminescence reporter. The general scheme for construction and detection of the Rluc-PCA PKA sensor consists of fusing complementary fragments of Rluc to the regulatory (Reg) and catalytic (Cat) PKA subunits of PKA." ;
rdfs:subClassOf obo:MI_0090 .
obo:MI_0218 a rdfs:Class ;
rdfs:label "physical interaction" ;
rdfs:comment """Interaction among molecules that can be direct or indirect.
OBSOLETE: splitted to 'association' MI:0914 and 'physical association' MI:0915. For remapping consider the experimental setting of an interaction. For bulk remapping a possible criteria is to whatever physical interaction that has among its participant a bait should become 'association' MI:0914 the others can become 'physical association' MI:0915. Two hybrid interactions are an expection and can be 'physical association' MI:0915.""" .
obo:MI_0355 a rdfs:Class ;
rdfs:label "molecular function" ;
rdfs:comment "Cross reference pointing to a Gene Ontology -'molecular function' term." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_1282 a rdfs:Class ;
rdfs:label "cisphenotypic genetic suppression (partial)" ;
rdfs:comment """An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected, but not wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a* <= b < wt) AND (a* < ab < wt) [E = a*]
OR
(wt < b <= a*) AND (wt < ab < a*) [E = a*]
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1280 , obo:MI_1291 .
obo:MI_0815 a rdfs:Class ;
rdfs:label "confirmation by molecular weight" ;
rdfs:comment "Molecule whose sequence identity is derived from their molecular weight" ;
rdfs:subClassOf obo:MI_0396 .
obo:MI_0881 a rdfs:Class ;
rdfs:label "nucleoside triphosphatase reaction" ;
rdfs:comment "Catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0596 a rdfs:Class ;
rdfs:label "experimental form description" ;
rdfs:comment "Free text description of all the tags and artificial process undergone by a molecule during an experiment." ;
rdfs:subClassOf obo:MI_0666 .
obo:MI_2382 a rdfs:Class ;
rdfs:label "monophenotypic phenotype result" ;
rdfs:comment "A phenotype result in which only one of multiple perturbations results in the phenotype in question." ;
rdfs:subClassOf obo:MI_2384 .
obo:MI_2342 a rdfs:Class ;
rdfs:label "partial identity match" ;
rdfs:comment "Reference to the corresponding object in another database. Correspondence is partial, so the objects are similar but explicitly not identical." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_2027 a rdfs:Class ;
rdfs:label "water solubility" ;
rdfs:comment "Water solubility in mg/mL or g/L" ;
rdfs:subClassOf obo:MI_2160 .
obo:MI_2163 a rdfs:Class ;
rdfs:label "by homology" ;
rdfs:comment "Reference assigned to a molecule by sequence homology with another similar sequence." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_0377 a rdfs:Class ;
rdfs:label "fluorescein isothiocyanate label" ;
rdfs:comment "Fluorescein isothiocyanate is a yellow-green coloured low molecular weight dye which couples to proteins via reaction with primary amine groups at high pH. FITC is excitable at 488nm, close to its absorption maximum at 494nm, and produces maximum fluorescence emission around 520nm." ;
rdfs:subClassOf obo:MI_0939 .
obo:MI_2436 a rdfs:Class ;
rdfs:label "initiator methionine" ;
rdfs:comment "Cleaved initiator methionine." ;
rdfs:subClassOf obo:MI_0252 .
obo:MI_0601 a rdfs:Class ;
rdfs:label "sequence ontology" ;
rdfs:comment "The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data." ;
rdfs:subClassOf obo:MI_0447 , obo:MI_0473 .
obo:MI_1195 a rdfs:Class ;
rdfs:label "quantitative pcr" ;
rdfs:comment "Quantitative PCR (Q-PCR) is used to measure the quantity of a PCR product (commonly in real-time). It quantitatively measures starting amounts of DNA, cDNA, or RNA." ;
rdfs:subClassOf obo:MI_0088 .
obo:MI_1003 a rdfs:Class ;
rdfs:label "geranylgeranylase assay" ;
rdfs:comment "Measurement of the attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s)." ;
rdfs:subClassOf obo:MI_1001 .
obo:MI_0585 a rdfs:Class ;
rdfs:label "intenz" ;
rdfs:comment """IntEnz is the name for the Integrated relational Enzyme database and is the official version of the Enzyme Nomenclature. The Enzyme Nomenclature comprises recommendations of the Nomenclature Committee of the International Union of Bio chemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. IntEnz is supported by NC-IUBMB and contains enzyme data curated and approved by this committee. The database IntEnz is available at.
http://www.ebi.ac.uk/intenz""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_2425 a rdfs:Class ;
rdfs:label "ProteomeHD" ;
rdfs:comment """A web-resource (https://www.proteomehd.net) that provides a co-regulation map of the human proteome built from ProteomeHD data (5,288 individual mass spectrometry experiments) and datasets from the Proteomics Identifications dataset using the machine learning algorithm treeClust to identify functional associations between co-regulated human proteins.
https://www.proteomehd.net""" ;
rdfs:subClassOf obo:MI_1336 .
obo:MI_2033 a rdfs:Class ;
rdfs:label "hydrophobicity" ;
rdfs:comment "Physical property of a molecule (known as a hydrophobe) that is repelled from a mass of water. Gravy score." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_2118 a rdfs:Class ;
rdfs:label "volume of distribution" ;
rdfs:comment "The Volume of Distribution is the amount of drug in the body divided by the concentration in the blood. Drugs that are highly lipid soluble have a very high volume of distribution (500 litres). Drugs which are lipid insoluble remain in the blood, and have a low Vd." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0933 a rdfs:Class ;
rdfs:label "diverging genetic interaction" ;
rdfs:comment """An effect in which two genetic perturbations, when combined, result in a phenotype that is more severe/penetrant than expected given the phenotypes of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab < E <= wt
OR
wt <= E < ab
where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0208 .
obo:MI_0005 a rdfs:Class ;
rdfs:label "alanine scanning" ;
rdfs:comment "This approach is used to identify the residues that are involved in an interaction. Several variants of the native protein are prepared by sequentially mutating each residue of interest to an alanine. The mutated proteins are expressed and probed in the binding assay." ;
rdfs:subClassOf obo:MI_0810 .
obo:MI_2303 a rdfs:Class ;
rdfs:label "carbohydrate chemical modification disrupting interaction strength" ;
rdfs:comment "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction strength when compared with the unaltered carbohydrate." ;
rdfs:subClassOf obo:MI_2302 .
obo:MI_1030 a rdfs:Class ;
rdfs:label "excimer fluorescence" ;
rdfs:comment "Excimer (excited-dimer) fluorescence is produced by complexes formed by two molecules, at least one of which is in an excited state. It is characterized by a lower energy (i.e. red shift) than fluorescence of a single, non-interacting molecule." ;
rdfs:subClassOf obo:MI_0051 .
obo:MI_0631 a rdfs:Class ;
rdfs:label "3d-r-factors" ;
rdfs:comment "Free R-Factor and working R-Factor for the quality of the crystallographic model. This attribute is generally associated to an interaction." ;
rdfs:subClassOf obo:MI_0664 .
obo:MI_1141 a rdfs:Class ;
rdfs:label "s tag" ;
rdfs:comment "S-tag is the name of an oligopeptide derived from pancreatic ribonuclease A (RNase A). The amino acid sequence of the S-tag is: Lys-Glu-Thr-Ala-Ala-Ala-Lys-Phe-Glu-Arg-Gln-His-Met-Asp-Ser." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_1050 a rdfs:Class ;
rdfs:label "interaction representation" ;
rdfs:comment "Provides an indication of the level of post-processing of experimental data relating to specific binary pairs" ;
rdfs:subClassOf obo:MI_1045 .
obo:MI_2264 a rdfs:Class ;
rdfs:label "tyrosinated residue" ;
rdfs:comment "A protein modification that effectively add a tyrosine residues to the c-terminal end of alpha-tubulin." ;
rdfs:subClassOf obo:MI_2262 .
obo:MI_2262 a rdfs:Class ;
rdfs:label "causal regulatory modification" ;
rdfs:comment "The modification of a subsequence that regulates the concentration and/or frequency and/or rate and/or extent of the molecular function of an entity." ;
rdfs:subClassOf obo:MI_2233 .
obo:MI_2224 a rdfs:Class ;
rdfs:label "chemical rna modification plus base pairing prediction" ;
rdfs:comment "In this method predicted RNA-RNA pairings are tested by knocking down one of the two interacting RNAs and then experimentally determine if its presence is required for the other to be chemically modified." ;
rdfs:subClassOf obo:MI_0254 .
obo:MI_0070 a rdfs:Class ;
rdfs:label "mobility shift" ;
rdfs:comment "Protein modifications can be identified by gel electrophoresis since any change in the mass and/or the charge of the protein can alter its mobility in PAGE. Although this method does not allow the unequivocal identification of the type of modification that has caused the shift, it is possible, by combining this approach with more direct methods, to correlate the extent of the shift to a specific modification." ;
rdfs:subClassOf obo:MI_0659 .
obo:MI_1103 a rdfs:Class ;
rdfs:label "solution state nmr" ;
rdfs:comment """NMR solution state analysis provides useful data regarding the type, quantity and arrangement of different atoms in chemical systems, liquids and solids. Samples are dissolved in deuterated solvents and spectra consist of a series of very sharp
transitions, due to averaging of anisotropic NMR interactions
by rapid random tumbling. Solution-state NMR only requires that the molecule be soluble at sufficient concentration for data collection, but becomes increasingly difficult for biomolecules over 30 kDa so that a practical size limitation is placed on full structure determinations.""" ;
rdfs:subClassOf obo:MI_0077 .
obo:MI_0300 a rdfs:Class ;
rdfs:label "alias type" ;
rdfs:comment "Descriptor of type of nomenclature used to describe interactor." ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_1184 a rdfs:Class ;
rdfs:label "dna adenine methyltransferase identification" ;
rdfs:comment "DNA adenine methyltransferase identification is used to map the binding sites of DNA- and chromatin-binding proteins in eukaryotes. DamID identifies binding sites by expressing the proposed DNA-binding protein as a fusion protein with DNA methyltransferase. Binding of the protein of interest to DNA localizes the methyltransferase in the region of the binding site. Adenosine methylation does not occur naturally in eukaryotes and therefore adenine methylation in any region can be concluded to have been caused by the fusion protein, implying the region is located near a binding site." ;
rdfs:subClassOf obo:MI_1313 .
obo:MI_0389 a rdfs:Class ;
rdfs:label "alexa 546 label" ;
rdfs:comment "Alexa fluorescent dye analogue to Cy3 with an approximate excitation wavelength maximum of 546nm." ;
rdfs:subClassOf obo:MI_0384 .
obo:MI_0940 a rdfs:Class ;
rdfs:label "fluorescein-5-maleimide label" ;
rdfs:comment "Fluorescein-5-maleimide is one of the most popular fluorescent dyes for thiol modifications of proteins at cysteine residues that either are intrinsically present or result from reduction of cystines. Unlike iodoacetamides, maleimides do not react with histidines and methionines under physiological conditions." ;
rdfs:subClassOf obo:MI_0939 .
obo:MI_0709 a rdfs:Class ;
rdfs:label "polyclonal antibody immunostaining" ;
rdfs:comment "Immunostaining assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest. These antibodies are used to detect the protein within a cell or tissue sample." ;
rdfs:subClassOf obo:MI_0422 .
obo:MI_0348 a rdfs:Class ;
rdfs:label "fixed cell" ;
rdfs:comment "Cells has been fixed by treatment with organic solvent, staining and inclusion in a resin for microscopic analysis." ;
rdfs:subClassOf obo:MI_0342 .
obo:MI_0127 a rdfs:Class ;
rdfs:label "n-acetyl-glutamine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00054.""" .
obo:MI_0478 a rdfs:Class ;
rdfs:label "flybase" ;
rdfs:comment """FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila.
http://flybase.org""" ;
rdfs:subClassOf obo:MI_1094 .
obo:MI_0735 a rdfs:Class ;
rdfs:label "transactivating tag" ;
rdfs:comment "Tag derived from the transactivating (Tat) protein of human immunodeficiency virus 1 (HIV-1) that can enter cells efficiently when added exogenously in tissue culture. The Tat tag can carry other molecules into cells, by fusion of Tat peptides (residues 1-72 or 37-72,) to any molecule under study. Tat-mediated uptake may allow the delivery of macromolecules previously thought to be impermeable to living cells." ;
rdfs:subClassOf obo:MI_0740 .
obo:MI_2106 a rdfs:Class ;
rdfs:label "degree of ionisation ph 7.4" ;
rdfs:comment "The degree of ionization refers to the proportion of neutral particles such as those in a gas or aqueous solution, that are ionized into charged particles. A low degree of ionization is sometimes called partially ionized, and a very high degree of ionization as fully ionized. This measurment is performed at pH 7.4" ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_2100 a rdfs:Class ;
rdfs:label "experimental drug" ;
rdfs:comment "A drug which has yet to be formally approved for the indication which it is currently being used to treat." ;
rdfs:subClassOf obo:MI_2040 .
obo:MI_1203 a rdfs:Class ;
rdfs:label "split luciferase complementation" ;
rdfs:comment "Two proteins of interest, a bait and prey, which are genetically fused to amino- and carboxy-terminal fragments of luciferase, are transiently expressed. Physical interactions of these bait and prey proteins reconstitute some of the luciferase activity and result in light emission in the presence of the luciferase substrate." ;
rdfs:subClassOf obo:MI_0090 .
obo:MI_0192 a rdfs:Class ;
rdfs:label "acetylation reaction" ;
rdfs:comment "Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0322 a rdfs:Class ;
rdfs:label "guide rna" ;
rdfs:comment "Small RNA molecules that hybridize to specific mRNAs and direct their RNA editing." ;
rdfs:subClassOf obo:MI_0320 .
obo:MI_1260 a rdfs:Class ;
rdfs:label "pyrene label" ;
rdfs:comment "Pyrene is a polycyclic aromatic hydrocarbon (PAH) consisting of four fused benzene rings, resulting in a flat aromatic system. The chemical formula is C16H10. Its derivatives are valuable molecular probes via fluorescence spectroscopy, having a high quantum yield and lifetime." ;
rdfs:subClassOf obo:MI_0857 .
obo:MI_0081 a rdfs:Class ;
rdfs:label "peptide array" ;
rdfs:comment "The peptide synthesis methods offer numerous opportunities to synthesise and subsequently screen large arrays of synthetic peptides on planar cellulose supports. Discrete spots are arranged as arrays on membrane sheets where each spot is individually accessed by manual or automated delivery of the appropriate reagent solutions. Over the past few years protein-protein recognition, peptide-metal ion interactions, peptide-nucleic acid binding, enzymatic modification of peptides experiments, have been explored using synthetic peptide arrays on planar support." ;
rdfs:subClassOf obo:MI_0008 .
obo:MI_0350 a rdfs:Class ;
rdfs:label "purified" ;
rdfs:comment "Molecule has undergone one or more purification steps to isolate it from the cellular environment." ;
rdfs:subClassOf obo:MI_0342 .
obo:MI_2111 a rdfs:Class ;
rdfs:label "diffusion coefficient" ;
rdfs:comment "Diffusion coefficient D is proportional to the velocity of the diffusing particles, which depends on the temperature, viscosity of the fluid and the size of the particles according to the Stokes-Einstein relation. In dilute aqueous solutions the diffusion coefficients of most ions are similar and have values that at room temperature are in the range of 0.6x10-9 to 2x10-9 m2/s. For biological molecules the diffusion coefficients normally range from 10-11 to 10-10 m2/s." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0092 a rdfs:Class ;
rdfs:label "protein in situ array" ;
rdfs:comment "Protein In Situ Array is a method by which protein arrays are rapidly generated in one step directly from DNA, by cell-free protein expression and simultaneous in situ immobilisation at a surface. Individual genes or fragments are produce by PCR or RT-PCR depending on the source of genetic material using properly designed primers. The PISA is generated by cell-free protein synthesis using coupled transcription and translation to produce a tagged protein, the reaction being carried out on a surface to which the protein adheres as soon as it is synthesised." ;
rdfs:subClassOf obo:MI_0089 .
obo:MI_0653 a rdfs:Class ;
rdfs:label "picomolar" ;
rdfs:comment """10E-12 moles per liter of solution.
OBSOLETE: term redundant with the schema exponent attribute of the parameter.""" .
obo:MI_0331 a rdfs:Class ;
rdfs:label "engineered" ;
rdfs:comment "Molecule has been added into system from an external source or altered within the cell." ;
rdfs:subClassOf obo:MI_0330 .
obo:MI_0423 a rdfs:Class ;
rdfs:label "in-gel kinase assay" ;
rdfs:comment "Substrate protein radio-labelled by kinase transferring an isotope of phosphate from the nucleotide. Substrate isolated by gel electrophoresis and radio-labelling confirmed by autoradiography." ;
rdfs:subClassOf obo:MI_0424 .
obo:MI_0798 a rdfs:Class ;
rdfs:label "conditional genetic interaction defined by inequality" ;
rdfs:comment "The phenotype resulting from genetic perturbation of A has an effect only in the b background, or the b mutant has an effect only in the a background. a has an effect only in the b background, or the b mutant has an effect only in the a background. E. g., WT = a > ab > b or WT > a > b > ab." .
obo:MI_1215 a rdfs:Class ;
rdfs:label "bifc tag" ;
rdfs:comment "Fusion protein which consists of either the N- or C-terminal sequence of a fluorescent or luciferase protein. Binding of the proteins of interest enable the reassembly of the molecule, indicating that an interaction has occured." ;
rdfs:subClassOf obo:MI_0240 .
obo:MI_2414 a rdfs:Class ;
rdfs:label "Cellosaurus" ;
rdfs:comment "The Cellosaurus is a knowledge resource on cell lines. It aims to describe all cell lines used in biomedical research." ;
rdfs:subClassOf obo:MI_0473 .
obo:MI_2005 a rdfs:Class ;
rdfs:label "drug mixture brand name" ;
rdfs:comment "Brand names and composition of mixtures that include the drug described in this DrugCard file." ;
rdfs:subClassOf obo:MI_1041 .
obo:MI_2358 a rdfs:Class ;
rdfs:label "mirbase" ;
rdfs:comment """A searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download.
Homepage: http://www.mirbase.org/""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0495 a rdfs:Class ;
rdfs:label "experimental role" ;
rdfs:comment "Role played by the participant within the experiment." ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_1129 a rdfs:Class ;
rdfs:label "mutation disrupting interaction rate" ;
rdfs:comment "Region of a molecule whose mutation or deletion totally disrupts an interaction rate (in the case of interactions inferred from enzymatic reaction).." ;
rdfs:subClassOf obo:MI_0573 .
obo:MI_1316 a rdfs:Class ;
rdfs:label "complex systematic name" ;
rdfs:comment "A name for a complex built of the component parts of that complex." ;
rdfs:subClassOf obo:MI_1041 .
obo:MI_2045 a rdfs:Class ;
rdfs:label "drug absorption" ;
rdfs:comment "Determination of how quickly and how much of a drug reaches its intended target (site) of action." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_2150 a rdfs:Class ;
rdfs:label "illicit drug" ;
rdfs:comment "A drug which has not been approved for sale, a drug taken for recreational purposes or a licensed drug sold without a prescription." ;
rdfs:subClassOf obo:MI_2040 .
obo:MI_1208 a rdfs:Class ;
rdfs:label "firefly luciferase protein tag" ;
rdfs:comment "Firefly luciferase, is an enzyme from beetles (Photinus pyralis) catalyzing the oxidation of the lucifering pigment (reaction with ATP or oxygen) that produces light. Firefly luciferase produces a greenish yellow light in the 550-570nm range." ;
rdfs:subClassOf obo:MI_1205 .
obo:MI_2331 a rdfs:Class ;
rdfs:label "phage library" ;
rdfs:comment "A bacteriophage library of genes encoding proteins or peptides fused to a phage coat protein that are expressed on the surface of the phage virion." ;
rdfs:subClassOf obo:MI_0342 .
obo:MI_1248 a rdfs:Class ;
rdfs:label "bodipy label" ;
rdfs:comment "Composed of dipyrromethene complexed with a disubstituted boron atom, typically a BF2 unit. Notable for their uniquely small Stokes shift, high, environment-independent fluorescence quantum yields." ;
rdfs:subClassOf obo:MI_0857 .
obo:MI_1342 a rdfs:Class ;
rdfs:label "qcmd" ;
rdfs:comment "The quartz crystal microbalance is a physical technique that detects changes in the resonance frequency of an electrically driven quartz crystal with changes in mass. It provides qualitative and quantitative information about biomolecular interactions by translating changes in mass at the probe-immobilized surface of the crystal sensor into measurable changes in the resonant frequency of the quartz crystal. QCM-D enables real-time, label free measurements of molecular adsorption and/or interactions on various surfaces and is able to monitor conformational changes upon interactions." ;
rdfs:subClassOf obo:MI_0968 .
obo:MI_2371 a rdfs:Class ;
rdfs:label "positive genetic interaction (sensu BioGRID)" ;
rdfs:comment "Genetic perturbation of multiple genes in combination that results in a less severe phenotype than from individual perturbations. This term is reserved for high throughput studies with scores." ;
rdfs:subClassOf obo:MI_2379 .
obo:MI_2417 a rdfs:Class ;
rdfs:label "ensemblfungi" ;
rdfs:comment "Ensembl Fungi is a browser for fungal genomes. https://fungi.ensembl.org/" ;
rdfs:subClassOf obo:MI_1013 .
obo:MI_2320 a rdfs:Class ;
rdfs:label "aruk-ucl" ;
rdfs:comment """The Alzheimer's Research UK Gene Ontology Project represents a collaboration between University College London, the European Bioinformatics Institute (EBI) and the University of Manchester, funded by Alzheimer's Research UK. This annotation group is a member of the IMEx Consortium.
www.ucl.ac.uk/functional-gene-annotation/neurological""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_2406 a rdfs:Class ;
rdfs:label "ribozyme" ;
rdfs:comment "Ribozymes (ribonucleic acid enzymes) are folded catalytic RNA molecules that perform important biological functions." ;
rdfs:subClassOf obo:MI_0500 .
obo:MI_0873 a rdfs:Class ;
rdfs:label "curation request" ;
rdfs:comment "Annotation of a published paper which has been externally requested." ;
rdfs:subClassOf obo:MI_1093 .
obo:MI_0551 a rdfs:Class ;
rdfs:label "nitro-tyrosine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00461.""" .
obo:MI_0239 a rdfs:Class ;
rdfs:label "biotin tag" ;
rdfs:comment "Biotin, a 244 Dalton vitamin found in tissue and blood, binds with high affinity to avidin and streptavidin protein. Since biotin is a relatively small molecule, it can be conjugated to many proteins or nucleic acids without significantly altering their biological activity. Biotinylation reagents are available for targeting a variety of specific functional groups, including primary amines, sulfhydryls, carboxyls and carbohydrates that lead to nucleotides or amino acid biotinilation." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_1173 a rdfs:Class ;
rdfs:label "binding site hiding" ;
rdfs:comment "The occurrence of overlapping or adjacent, mutually exclusive binding sites promotes competitive binding. When there is a large difference in affinity of the different sites or in local abundance of competitors, binding at one site results in hiding of the second site, thereby precluding it from interacting when the hiding molecule is present." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_1170 .
obo:MI_1348 a rdfs:Class ;
rdfs:label "chembl target" ;
rdfs:comment "ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets." ;
rdfs:subClassOf obo:MI_0683 , obo:MI_1349 .
obo:MI_2360 a rdfs:Class ;
rdfs:label "beta gal tag" ;
rdfs:comment "Protein is fused to beta-galactosidase, and the measure of this enzyme activity can be taken as indicative of presence of protein." ;
rdfs:subClassOf obo:MI_0365 .
obo:MI_1331 a rdfs:Class ;
rdfs:label "evidence ontology" ;
rdfs:comment "The Evidence Ontology (ECO) describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means." ;
rdfs:subClassOf obo:MI_1336 .
obo:MI_2145 a rdfs:Class ;
rdfs:label "solubility ph 6.5" ;
rdfs:comment "Solubility pH 6.5." ;
rdfs:subClassOf obo:MI_2064 .
obo:MI_0702 a rdfs:Class ;
rdfs:label "panther" ;
rdfs:comment """The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.
www.pantherdb.org/""" ;
rdfs:subClassOf obo:MI_0449 .
obo:MI_1271 a rdfs:Class ;
rdfs:label "genetic enhancement (sensu unexpected)" ;
rdfs:comment """An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation to a severity/penetrance beyond (further from wild type) that expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
ab < E < wt
OR
wt < E < ab
where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0933 , obo:MI_2380 .
obo:MI_0266 a rdfs:Class ;
rdfs:label "suppression overexpression" ;
rdfs:comment """Overexpression is the suppressor of a phenotype.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'over expressed' MI:0506. """ .
obo:MI_2053 a rdfs:Class ;
rdfs:label "contraindications" ;
rdfs:comment "Cautions or conditions indicating why or when the drug should not be taken or prescribed." ;
rdfs:subClassOf obo:MI_2089 .
obo:MI_0637 a rdfs:Class ;
rdfs:label "isoform-comment" ;
rdfs:comment "Participant isoform's comment. This attribute can be attached to interactions or participants." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_0666 .
obo:MI_0828 a rdfs:Class ;
rdfs:label "polyprotein fragment" ;
rdfs:comment "Subpart of a polyprotein that is naturally cleaved in vivo." ;
rdfs:subClassOf obo:MI_0252 .
obo:MI_2428 a rdfs:Class ;
rdfs:label "Kilodalton" ;
rdfs:comment "A unit of mass used to express molecular mass, especially for large molecules, such as proteins and polysaccharides. It is equal to 1000 daltons. A dalton is equal to one twelfth of the mass of an atom of carbon-12, or 1.660 33 × 10−27 kg." ;
rdfs:subClassOf obo:MI_0647 .
obo:MI_0997 a rdfs:Class ;
rdfs:label "ubiquitinase assay" ;
rdfs:comment "Measures the reversible reaction that creates a covalent bond between a C-terminus G of ubiquitin and a K residue of the target." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0169 a rdfs:Class ;
rdfs:label "n-methyl-phenylalanine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00074.""" .
obo:MI_0675 a rdfs:Class ;
rdfs:label "international protein index" ;
rdfs:comment "IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI effectively maintains a database of cross references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) and maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources." ;
rdfs:subClassOf obo:MI_1096 .
obo:MI_0076 a rdfs:Class ;
rdfs:label "neural network on interface properties" ;
rdfs:comment "Neural networks are trained on the properties of residues belonging to a cluster of residues that are neighbours in space on protein surface. The predictor permits the inference of the residues that are likely to be on an interaction interface." ;
rdfs:subClassOf obo:MI_0577 .
obo:MI_1087 a rdfs:Class ;
rdfs:label "monoclonal antibody blockade" ;
rdfs:comment "Method to block a binding site on a molecule, such as a protein, using a monoclonal antibody to test that the binding site is involved in an interaction with another molecule." ;
rdfs:subClassOf obo:MI_0400 , obo:MI_2197 .
obo:MI_0540 a rdfs:Class ;
rdfs:label "gpi-anchor amidated alanine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00172.""" .
obo:MI_0069 a rdfs:Class ;
rdfs:label "mass spectrometry studies of complexes" ;
rdfs:comment "Mass spectrometric approaches to the study of macromolecular complexes permits the identification of subunit stoichiometry and transient associations. By preserving complexes intact in the mass spectrometer, mass measurement can be used for monitoring changes in different experimental conditions, or to investigate how variations of collision energy affect their dissociation." ;
rdfs:subClassOf obo:MI_0943 .
obo:MI_0537 a rdfs:Class ;
rdfs:label "omega-n-glycosyl-arginine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00332.""" .
obo:MI_2353 a rdfs:Class ;
rdfs:label "epistatic gene" ;
rdfs:comment "A gene whose genetic perturbation masks the phenotype resulting from a different genetic perturbation." ;
rdfs:subClassOf obo:MI_0495 .
obo:MI_0484 a rdfs:Class ;
rdfs:label "sgd" ;
rdfs:comment """SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae.
http://www.yeastgenome.org/""" ;
rdfs:subClassOf obo:MI_1094 .
obo:MI_1327 a rdfs:Class ;
rdfs:label "sulfurtransfer reaction" ;
rdfs:comment "Reaction where a sulfate group is transferred between two proteins" ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_1148 a rdfs:Class ;
rdfs:label "ampylation reaction" ;
rdfs:comment """AMPylation, previously known as adenylylation, is formation of a
phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys
(RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino
acids.""" ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_2123 a rdfs:Class ;
rdfs:label "renal clearance" ;
rdfs:comment "The renal clearance ratio or fractional excretion is a measure of the speed at which a constituent of urine passes through the kidneys, in this context the rate at which a pharmacological agent is lost from the body via urine." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_1353 a rdfs:Class ;
rdfs:label "au5 tag" ;
rdfs:comment "Epitope tag engineered onto the N- or C- terminus of a protein of interest so that the tagged protein can be analyzed and visualized by immunochemical methods. The recognized AU5 epitope represents the amino acid sequence TDFYLK." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_0344 a rdfs:Class ;
rdfs:label "cell lysate" ;
rdfs:comment "Cell has been physically or chemically broken open and molecule present in resulting mixture of cellular components." ;
rdfs:subClassOf obo:MI_0342 .
obo:MI_1092 a rdfs:Class ;
rdfs:label "atto label" ;
rdfs:comment "Fluorescent dyes - spectral range 500 to 700 nm." ;
rdfs:subClassOf obo:MI_0857 .
obo:MI_0642 a rdfs:Class ;
rdfs:label "ec50" ;
rdfs:comment "Molar concentration of an agonist which produces 50% of the maximum possible response for that agonist. Note this measure depends on the specific agonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ec50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0611 a rdfs:Class ;
rdfs:label "signal recognition particle rna" ;
rdfs:comment "Small (300 nucleotides) stable RNAs transcribed by RNA pol III that are part of the signal-recognition particle (SRP). This particle comprises one RNA and six proteins bound to the RNA. SRP function is to assist secretory proteins sorting in the endoplasmic reticulum (ER). SRP is a cytosolic particle that transiently binds to the ER signal sequence of a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane." ;
rdfs:subClassOf obo:MI_0320 .
obo:MI_1274 a rdfs:Class ;
rdfs:label "minimal genetic epistasis" ;
rdfs:comment """An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the least severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
a* < ab = b < wt
OR
wt < b = ab < a*
where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_1272 , obo:MI_1282 .
obo:MI_0333 a rdfs:Class ;
rdfs:label "feature range status" ;
rdfs:comment "Describes sequence positions resolution of a given participant feature. In PSI schema this CV is associated with the start and end position of a feature range." ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_2212 a rdfs:Class ;
rdfs:label "proteomexchange" ;
rdfs:comment """The ProteomeXchange consortium was set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination. The data is actually hosted by consortium member databases like PeptideAtlas or PRIDE.
http://www.proteomexchange.org""" ;
rdfs:subClassOf obo:MI_0737 .
obo:MI_0320 a rdfs:Class ;
rdfs:label "ribonucleic acid" ;
rdfs:comment "Polymer formed by ribose sugar group, and the bases of the nucleotides adenine, guanine, uracil and cytosine." ;
rdfs:subClassOf obo:MI_0318 .
obo:MI_0199 a rdfs:Class ;
rdfs:label "deformylation reaction" ;
rdfs:comment "N6-formyl-L-lysine is cleaved and returns a K residue." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0724 a rdfs:Class ;
rdfs:label "protein delivery by cationic lipid treatment" ;
rdfs:comment "Proteins are delivered into cells by treatment with cationic lipids." ;
rdfs:subClassOf obo:MI_0721 .
obo:MI_0824 a rdfs:Class ;
rdfs:label "x-ray powder diffraction" ;
rdfs:comment "Analysis of a diffraction pattern generated by an isotropic sample composed of many randomly oriented crystals." ;
rdfs:subClassOf obo:MI_0114 .
obo:MI_0214 a rdfs:Class ;
rdfs:label "myristoylation reaction" ;
rdfs:comment "Irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid. Reaction that can affect K or G residues." ;
rdfs:subClassOf obo:MI_0211 .
obo:MI_0228 a rdfs:Class ;
rdfs:label "cytoplasmic complementation assay" ;
rdfs:comment "Protein complementation assay performed by dissecting a cytoplasmic protein activity and restoring it through the two hybrid proteins interaction. OBSOLETE remap to MI:0090 protein complementation assay" .
obo:MI_2308 a rdfs:Class ;
rdfs:label "attached carbohydrate" ;
rdfs:comment "Carbohydrate species chemically attached to proteins, or other organic molecules." ;
rdfs:subClassOf obo:MI_0252 .
obo:MI_1337 a rdfs:Class ;
rdfs:label "efo" ;
rdfs:comment "The Experimental Factor Ontology provides a systematic description of many experimental variables, combining parts of several biological ontologies to additional new terms." ;
rdfs:subClassOf obo:MI_1336 .
obo:MI_2156 a rdfs:Class ;
rdfs:label "monoisotopic molecular weight" ;
rdfs:comment "Molecular weight in g/mol, determined from molecular formula or sequence." ;
rdfs:subClassOf obo:MI_2025 .
obo:MI_0203 a rdfs:Class ;
rdfs:label "dephosphorylation reaction" ;
rdfs:comment "Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0188 a rdfs:Class ;
rdfs:label "n6-retinal-lysine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00129.""" .
obo:MI_1191 a rdfs:Class ;
rdfs:label "ultraviolet (uv) footprinting" ;
rdfs:comment "Ultraviolet irradiation excites nucleic acids and creates photoreactions, which results in damaged bases in the DNA strand. Protein bound regions of the DNA are protected. UV footprinting technique can detect sequence-specific protein-DNA interactions in vivo. Protein contacts can inhibit of enhance UV photoproduct formation by affecting the ability of DNA to adopt a geometry necessary for the formation of a UV photoproduct. Thus, differences in the strand-breakage patterns of protein-free and protein-bound DNA can be used to detect protein-DNA contacts." ;
rdfs:subClassOf obo:MI_0417 .
obo:MI_0581 a rdfs:Class ;
rdfs:label "suppressor gene" ;
rdfs:comment "A gene whose genetic perturbation suppresses the phenotype resulting from a different genetic perturbation." ;
rdfs:subClassOf obo:MI_0495 .
obo:MI_0439 a rdfs:Class ;
rdfs:label "random spore analysis" ;
rdfs:comment "A technique used to detect genetic interactions between 2 (or more) genes in a sporulating organism by scoring a large population of haploid spores for a phenotype and correlating the phenotype with the presence of single vs double (multiple) mutations. A diploid heterozygous organism harbouring mutations in two (or more) genes is induced to sporulate. Resulting spores are meiotic segregants that are haploid and are either wild type or mutant at each locus. Spores are scored for a phenotype, such as loss of viability." ;
rdfs:subClassOf obo:MI_0254 .
obo:MI_1085 a rdfs:Class ;
rdfs:label "photon acceptor" ;
rdfs:comment "Molecule to which a photon may be transferred from an photon donor." ;
rdfs:subClassOf obo:MI_0919 .
obo:MI_0109 a rdfs:Class ;
rdfs:label "tap tag coimmunoprecipitation" ;
rdfs:comment """The TAP method involves the fusion of the TAP tag (encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A) to the target protein and the introduction of the construct into the host cell or organism, maintaining the expression of the fusion protein at, or close to, its natural level. The fusion protein and associated components are recovered from cell extracts by affinity selection on an IgG matrix. After washing, the TEV protease is added to release the bound material. The eluate is incubated with calmodulin-coated beads in the presence of calcium. This second affinity step is required to remove the TEV protease as well as traces of contaminants remaining after the first affinity selection. After washing, the bound material is released with EGTA. This two steps purification steps ensures a highly selective complex purification of the tapped protein (first round of selection on the protein A, a high affinity tag) under mild condition (non denaturant pH or conditions required to remove the tag).
OBSOLETE redundant term. Map to feature type: tap tagged (MI:0524) and as interaction detection method tandem affinity purification (MI:0676).""" .
obo:MI_2201 a rdfs:Class ;
rdfs:label "DNA chemical modification" ;
rdfs:comment "Chemical alterations occurring at the nucleotide level in the specific DNA molecule involved in an interaction. The process can involve covalent modifications (i.e. methylations) or other forms of chemical modification." ;
rdfs:subClassOf obo:MI_0252 .
obo:MI_0810 a rdfs:Class ;
rdfs:label "substitution analysis" ;
rdfs:comment "In this approach, once a molecule is demonstrated to participate in an interaction, several substitution mutants are produced and tested in the binding assay to identify the residues which identity is crucial for the interaction." ;
rdfs:subClassOf obo:MI_0074 .
obo:MI_1118 a rdfs:Class ;
rdfs:label "enhanced yellow fluorescent protein tag" ;
rdfs:comment "A variation of yellow fluorescent protein derived from eGFP." ;
rdfs:subClassOf obo:MI_0368 .
obo:MI_2398 a rdfs:Class ;
rdfs:label "aphenotypic neutral multigenic phenotype result" ;
rdfs:comment """A genetic aphenotypic phenotype result (both genetic perturbations result in a wild type (or control) phenotype) in which case the double genetic perturbation also results in the wild type (or control) phenotype, thus resulting in the expected phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
wt = a = b = ab [E = wt]
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" ;
rdfs:subClassOf obo:MI_0932 , obo:MI_2381 .
obo:MI_0024 a rdfs:Class ;
rdfs:label "confirmational text mining" ;
rdfs:comment "Text mining is used to support interactions which have been determined by other methods." ;
rdfs:subClassOf obo:MI_0110 .
obo:MI_0656 a rdfs:Class ;
rdfs:label "identified peptide" ;
rdfs:comment "Peptide whose sequence is experimentally identified and can lead to a full protein identification." ;
rdfs:subClassOf obo:MI_0505 .
obo:MI_1285 a rdfs:Class ;
rdfs:label "obsolete opposing epistasis" ;
rdfs:comment """OBSOLETE: An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a < wt < b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.""" .
obo:MI_2139 a rdfs:Class ;
rdfs:label "carcinogenicity" ;
rdfs:comment "Tendency of a bioactive entity to induce a cancer." ;
rdfs:subClassOf obo:MI_2135 .
obo:MI_0839 a rdfs:Class ;
rdfs:label "per mole per second" ;
rdfs:comment "Per mole per second, unit for association rate constant." ;
rdfs:subClassOf obo:MI_0647 .
obo:MI_2190 a rdfs:Class ;
rdfs:label "long non-coding ribonucleic acid" ;
rdfs:comment "Non-protein coding transcripts longer than 200 nucleotides and that can be involved in a number of functions, like transcription, post-translational and epigenetic regulation. Most lncRNAs do not have a known function so far." ;
rdfs:subClassOf obo:MI_0320 .
obo:MI_1178 a rdfs:Class ;
rdfs:label "sequence based prediction of binding of transcription factor to transcribed gene regulatory elements" ;
rdfs:comment "Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict a transcription factor using structural and sequence features of the protein, e.g., by evaluating if the potential transcription factor protein contains a DNA-binding domain that is known to bind to some regulatory elements, or prediction of transcription factor functional domains (DNA binding, transcription factor dimerization, etc.), all based on sequence or structural features of the transcription factor." ;
rdfs:subClassOf obo:MI_0101 .
obo:MI_2387 a rdfs:Class ;
rdfs:label "transphenotypic phenotype result" ;
rdfs:comment "A phenotype result in which two perturbations result in the opposite phenotype compared to wild type. For example, one perturbation results in an increased quality phenotype and the second perturbation results in a decreased quality phenotype." ;
rdfs:subClassOf obo:MI_2384 .
obo:MI_0713 a rdfs:Class ;
rdfs:label "nucleic acid passive uptake" ;
rdfs:comment "Nucleic acid entrance into cells that does not involved specific treatments but rely on natural cellular processes." ;
rdfs:subClassOf obo:MI_0704 , obo:MI_0716 .
obo:MI_0969 a rdfs:Class ;
rdfs:label "bio-layer interferometry" ;
rdfs:comment "BLI is an optical analytical technique that analyzes the interference pattern of white light reflected from two surfaces: a layer of immobilized protein on the biosensor tip, and an internal reference layer" ;
rdfs:subClassOf obo:MI_0968 .
obo:MI_2347 a rdfs:Class ;
rdfs:label "biorxiv" ;
rdfs:comment """bioRxiv is a free online archive and distribution service for unpublished preprints in the life sciences, operated by Cold Spring Harbor Laboratory. Articles are not peer-reviewed, edited, or typeset before being posted online.
http://biorxiv.org/""" ;
rdfs:subClassOf obo:MI_0445 .
obo:MI_0592 a rdfs:Class ;
rdfs:label "ipfam" ;
rdfs:comment """Web resource that allows the investigation of protein interactions in the Protein Data Bank structures at the level of Pfam domains and amino acid residues. iPfam is available on the Web for browsing at.
http://www.sanger.ac.uk/Software/Pfam/iPfam/""" ;
rdfs:subClassOf obo:MI_0447 .
obo:MI_2393 a rdfs:Class ;
rdfs:label "transphenotypic genetic suppression (expected)" ;
rdfs:comment "A transphenotypic suppression in which the double genetic perturbation phenotype is expected, according to some chosen neutrality function." ;
rdfs:subClassOf obo:MI_0932 , obo:MI_2390 .
obo:MI_1237 a rdfs:Class ;
rdfs:label "proline isomerization reaction" ;
rdfs:comment "The conversion between cis- and trans- peptide bonds formed by the amine group of a proline." ;
rdfs:subClassOf obo:MI_1250 .
obo:MI_0850 a rdfs:Class ;
rdfs:label "encode" ;
rdfs:comment """ENCODE (the Encyclopedia Of DNA Elements) seeks to identify all protein-coding genes. The current ENCODE data set is derived from 1% of the human genome and has been selected for analysis in the pilot phase of the project.
http://www.genome.gov/10005107""" ;
rdfs:subClassOf obo:MI_1094 .
obo:MI_2251 a rdfs:Class ;
rdfs:label "transcriptional regulation by direct binding of dbTF to DNA regulatory element" ;
rdfs:comment "Direct binding of a DbTF to a DNA regulatory sequence that modulates the frequency, rate or extent of the chemical reactions resulting in the transcription of DNA to RNA and gene activity regulation." .
obo:MI_0645 a rdfs:Class ;
rdfs:label "kcat" ;
rdfs:comment "The number of substrate molecules converted to product in a given unit of time, on a single enzyme molecule when the enzyme is saturated with substrate. Unit per second, or s-1." ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0434 a rdfs:Class ;
rdfs:label "phosphatase assay" ;
rdfs:comment "Measures the catalysis of the reaction: a phosphosubstrate + H2O = a substrate + phosphate." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0862 a rdfs:Class ;
rdfs:label "zz tag" ;
rdfs:comment "The ZZ tag is a tag made out of two tandem repeats of the Protein A IgG binding domain. " ;
rdfs:subClassOf obo:MI_0861 .
obo:MI_0380 a rdfs:Class ;
rdfs:label "15n label" ;
rdfs:comment "Molecules labelled with isotope 15 of nytrogen atoms." ;
rdfs:subClassOf obo:MI_0378 .
obo:MI_0626 a rdfs:Class ;
rdfs:label "antagonist" ;
rdfs:comment "Any chemical applied externally to cells or any type of environmental condition, such as hypoxia, that inhibits an interaction, potentially by alteration of amount or binding affinity of one or more of the interactors." ;
rdfs:subClassOf obo:MI_0664 .
obo:MI_1226 a rdfs:Class ;
rdfs:label "ampylation assay" ;
rdfs:comment "Formation of phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids" .
obo:MI_0908 a rdfs:Class ;
rdfs:label "denatured" ;
rdfs:comment "Altered conformation state of the protein as a result of heat or chemical modification resulting in a changed structure of the protein." ;
rdfs:subClassOf obo:MI_0907 .
obo:MI_0943 a rdfs:Class ;
rdfs:label "detection by mass spectrometry" ;
rdfs:comment "'Study of interactions by an analytical technique based on measurements of mass-to-charge ratio of charged particles in a mass spectrometer." ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_1163 a rdfs:Class ;
rdfs:label "allosteric v-type response" ;
rdfs:comment "An allosteric response in which catalysis (kcat or Vmax) of an enzyme is altered." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_1161 .
obo:MI_2089 a rdfs:Class ;
rdfs:label "bioactive entity attribute name" ;
rdfs:comment "Properties of a chemical tested or used as a drug, herbicide, insecticide etc." ;
rdfs:subClassOf obo:MI_0590 .
obo:MI_0027 a rdfs:Class ;
rdfs:label "cosedimentation" ;
rdfs:comment "Separation of a mixture of molecules under the influence of a force such as artificial gravity. Molecules sedimenting together are assumed to interact." ;
rdfs:subClassOf obo:MI_0401 .
obo:MI_1259 a rdfs:Class ;
rdfs:label "acrylodan label" ;
rdfs:comment "The thiol reactive acrylodan (6-acryloyl-2-dimethylaminonaphthalene) generally reacts with thiols more slowly than iodoacetamides or maleimides, but does form very strong thioether bonds that are expected to remain stable under conditions required for complete amino acid analysis. The fluorescence emission peak and intensity of these adducts are particularly sensitive to conformational changes or ligand binding." ;
rdfs:subClassOf obo:MI_0857 .
obo:MI_2375 a rdfs:Class ;
rdfs:label "synthetic rescue (sensu BioGRID)" ;
rdfs:comment "Mutation of one gene rescues lethality or a growth defect associated with perturbation of another gene." ;
rdfs:subClassOf obo:MI_2379 , obo:MI_2395 .
obo:MI_1098 a rdfs:Class ;
rdfs:label "uniprot/swiss-prot" ;
rdfs:comment """UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. UniProtKB/Swiss-Prot is manually curated which means that the information in each entry is annotated and reviewed by a curator.
http://www.uniprot.org""" ;
rdfs:subClassOf obo:MI_0486 .
obo:MI_1032 a rdfs:Class ;
rdfs:label "atto 488" ;
rdfs:comment "Fluorescent tag - maleimide couples to thiols." ;
rdfs:subClassOf obo:MI_1092 .
obo:MI_0555 a rdfs:Class ;
rdfs:label "phospho-histidine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00890.""" .
obo:MI_0319 a rdfs:Class ;
rdfs:label "deoxyribonucleic acid" ;
rdfs:comment "Polymer formed by the deoxyribose sugar group, and the nucleotides bases adenine, guanine, thymine and cytosine." ;
rdfs:subClassOf obo:MI_0318 .
obo:MI_0232 a rdfs:Class ;
rdfs:label "transcriptional complementation assay" ;
rdfs:comment "Protein complementation assay performed by dissecting a transcription factor activity (DNA binding domain and transcription activation domain) its restoration through the two hybrid proteins interaction that lead to a reporter gene expression." ;
rdfs:subClassOf obo:MI_0090 .
obo:MI_0421 a rdfs:Class ;
rdfs:label "identification by antibody" ;
rdfs:comment "Antibody mediated participant identification." ;
rdfs:subClassOf obo:MI_0661 .
obo:MI_2369 a rdfs:Class ;
rdfs:label "synthetic growth defect (sensu BioGRID)" ;
rdfs:comment "Mutation of multiple genes in combination that results in a more severe growth defect than from individual mutation." ;
rdfs:subClassOf obo:MI_2402 .
obo:MI_0019 a rdfs:Class ;
rdfs:label "coimmunoprecipitation" ;
rdfs:comment "In this approach an antibody, specific for the molecule of interest (bait) or any tag expressed within a fusion protein, is used to separate the bait from a molecular mixture or a cell lysate and to capture its ligand simultaneously. The partners that bind to the bait molecule retained by the resin can then be eluted and identified. The antibody may be free or bound to a matrix during this process." ;
rdfs:subClassOf obo:MI_0004 .
obo:MI_1198 a rdfs:Class ;
rdfs:label "immunohistochemistry" ;
rdfs:comment "Method using an antibody coupled with some colouring agent to detect a specific protein within a tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody." ;
rdfs:subClassOf obo:MI_0422 .
obo:MI_2021 a rdfs:Class ;
rdfs:label "rxlist link" ;
rdfs:comment "Hyperlink to RxList entry for the given drug (if it exists)" ;
rdfs:subClassOf obo:MI_2054 .
obo:MI_0731 a rdfs:Class ;
rdfs:label "3d repertoire" ;
rdfs:comment "The aim of 3D Repertoire is to determine the structures of all amenable complexes in a cell at medium or high resolution, which will later serve to integrate in toponomic and dynamic analyses of protein complexes in a cell. Complex models, EM pictures, expression and purification protocols obtained in the project will be collected in a database connected to the PDB repository." ;
rdfs:subClassOf obo:MI_0489 .
obo:MI_2140 a rdfs:Class ;
rdfs:label "chromosome damage" ;
rdfs:comment "Tendency of a bioactive entity to induce damage at the level of the chromosome e.g. induce a change in chromosome structure and number." ;
rdfs:subClassOf obo:MI_2135 .
obo:MI_0696 a rdfs:Class ;
rdfs:label "polymerase assay" ;
rdfs:comment "Measures the catalysis of the transfer of a free nucleotidyl group to a nucleic acid chain." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0878 a rdfs:Class ;
rdfs:label "author submitted" ;
rdfs:comment "Data directly submitted by the authors to a database prior to publication." ;
rdfs:subClassOf obo:MI_0665 .
obo:MI_1309 a rdfs:Class ;
rdfs:label "de-ADP-ribosylation assay" ;
rdfs:comment "Hydrolytic reactions that release ADP-ribose." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_2335 a rdfs:Class ;
rdfs:label "luminescence acceptor" ;
rdfs:comment "Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific luminescence donor, then re-emit its own characteristic fluorescence. The luminescence donor may or may not be a fluorophore it self." ;
rdfs:subClassOf obo:MI_0495 .
obo:MI_0919 a rdfs:Class ;
rdfs:label "acceptor" ;
rdfs:comment "Molecule able to receive active chemical groups, electrons or ions from a donor molecule." ;
rdfs:subClassOf obo:MI_0500 .
obo:MI_2324 a rdfs:Class ;
rdfs:label "dbsnp" ;
rdfs:comment "dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations." ;
rdfs:subClassOf obo:MI_0447 .
obo:MI_0799 a rdfs:Class ;
rdfs:label "additive genetic interaction defined by inequality" ;
rdfs:comment "Single-mutant phenotype effects combine to give a double-mutant effect different from the wild type and different from single mutant effect. For instance, WT < a = b < ab, b < WT = ab < a, WT < a < b < ab, b < WT < ab < a, and all additional inequalities obtained by interchanging a and b, or reversing the effect of both a and b." .
obo:MI_0627 a rdfs:Class ;
rdfs:label "experiment modification" ;
rdfs:comment "Modifications of the standard experimental method described in the CV." ;
rdfs:subClassOf obo:MI_0665 .
obo:MI_0470 a rdfs:Class ;
rdfs:label "kegg" ;
rdfs:comment """KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information and also supplies information about chemical compounds, enzyme molecules and enzymatic reactions.
http://www.genome.ad.jp/kegg/""" ;
rdfs:subClassOf obo:MI_0473 , obo:MI_1106 .
obo:MI_0103 a rdfs:Class ;
rdfs:label "southern blot" ;
rdfs:comment "A standard procedure to identify DNA fragments containing specific gene sequences. In this procedure i) a genome is fragmented using a restriction enzyme ii) the generated fragments are separated by electrophoresis iii) the fragments are transferred to a membrane iv)the membrane is incubated with a radio labelled probe that hybridises any complementary subsequence." ;
rdfs:subClassOf obo:MI_0080 .
obo:MI_2413 a rdfs:Class ;
rdfs:label "mammalian membrane two hybrid" ;
rdfs:comment "A membrane bait protein is tagged with the C-terminal half of ubiquitin (Cub) and a chimeric transcription factor, and a cytosolic or membrane-bound prey is tagged with the N-terminal half of ubiquitin (Nub). Upon interaction of bait and prey, the split halves form pseudoubiquitin, which is recognized by cytosolic deubiquitinating enzymes, resulting in cleavage of the transcription factor and expression of a reporter gene." ;
rdfs:subClassOf obo:MI_0112 .
obo:MI_0566 a rdfs:Class ;
rdfs:label "sumoylation reaction" ;
rdfs:comment "Reversible reaction that create a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_2364 a rdfs:Class ;
rdfs:label "proximity" ;
rdfs:comment "Coincident occurrence of molecules within very close proximity (in the nanometer range), detected through molecule-level resolution methodology, but from which a physical interaction among those molecules cannot be inferred." ;
rdfs:subClassOf obo:MI_0403 .
obo:MI_0959 a rdfs:Class ;
rdfs:label "imex curation" ;
rdfs:comment "Paper has been curated to full IMEx specifications" ;
rdfs:subClassOf obo:MI_0955 .
obo:MI_2282 a rdfs:Class ;
rdfs:label "complex-primary" ;
rdfs:comment "Complex object unique primary identifier that is assigned to a complex in the Complex Portal." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_2410 a rdfs:Class ;
rdfs:label "mondo" ;
rdfs:comment """A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology.
https://www.ebi.ac.uk/ols/ontologies/mondo""" ;
rdfs:subClassOf obo:MI_0473 .
obo:MI_0663 a rdfs:Class ;
rdfs:label "confocal microscopy" ;
rdfs:comment "A confocal is a standard epifluorescence microscope with improvement essentially coming from the rejection of out-of-focus light interference. Confocal imaging system achieves this by two strategies: a) by illuminating a single point of the specimen at any one time with a focused beam, so that illumination intensity drops off rapidly and b) by the use of blocking a pinhole aperture in a conjugate focal plane to the specimen so that light emitted away from the point in the specimen being illuminated is blocked from reaching the detector. Only the light from the single point illuminated of the specimen passing through the image pinhole is detected by a photodetector. Usually a computer is used to control the sequential scanning of the sample and to assemble the image for display onto a video screen." ;
rdfs:subClassOf obo:MI_0428 .
obo:MI_1025 a rdfs:Class ;
rdfs:label "unimod" ;
rdfs:comment "A database of protein modifications for mass spectrometry. www.unimod.org" ;
rdfs:subClassOf obo:MI_0447 .
obo:MI_0193 a rdfs:Class ;
rdfs:label "amidation reaction" ;
rdfs:comment "Irreversible reaction that can affect A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y or V residues. It involves the addition of an amide group from a glycine to the target residue." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0706 a rdfs:Class ;
rdfs:label "nucleic acid transformation" ;
rdfs:comment "Transformation is the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material incorporated into the cell's genome (DNA or RNA)." ;
rdfs:subClassOf obo:MI_0704 .
obo:MI_1188 a rdfs:Class ;
rdfs:label "tag visualisation by mutated dna adenine methyltransferase" ;
rdfs:comment "A mutant form of DNA adenine methyltransferase (DamK9A) from E. coli is fused to the protein of interest and expressed. The fusion protein will bind to target binding sites and introduce N-6-adenine methylation in nearby sites in the genomic DNA." ;
rdfs:subClassOf obo:MI_1185 .
obo:MI_0577 a rdfs:Class ;
rdfs:label "feature prediction from structure" ;
rdfs:comment "Group of method taking advantage of 3D structure to calculate and infer the feature of interacting molecules." ;
rdfs:subClassOf obo:MI_0660 .
obo:MI_0143 a rdfs:Class ;
rdfs:label "amidated residue" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00674.""" .
obo:MI_0818 a rdfs:Class ;
rdfs:label "molecular weight estimation by coomasie staining" ;
rdfs:comment "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with comassie dye." ;
rdfs:subClassOf obo:MI_0816 .
obo:MI_0338 a rdfs:Class ;
rdfs:label "range" ;
rdfs:comment "Describes a sequence position known to be in a certain range, where the exact position is unclear." ;
rdfs:subClassOf obo:MI_0333 .
obo:MI_0308 a rdfs:Class ;
rdfs:label "electroporation" ;
rdfs:comment "Method for temporarily permeabilising cell membranes so as to facilitate the entry of large or hydrophilic molecules (as in transfection). A brief (ca 1 msec) electric pulse is given with potential gradients of about 700V/cm." ;
rdfs:subClassOf obo:MI_0307 .
obo:MI_1218 a rdfs:Class ;
rdfs:label "chromosome conformation capture assay" ;
rdfs:comment "Chromosome conformation capture,[1] or 3C, is a high-throughput molecular biology technique used to analyze the organization of chromosomes in a cell's natural state. The basic 3C technique consists of cross-linking by addition of formaldehyde followed by addition of a restriction enzyme in excess to the cross-linked DNA, separating the non-cross-linked DNA from the cross-linked chromatin. A intramolecular ligation step using very low concentrations of DNA favors the ligation of relevant DNA fragments with the corresponding junctions instead of the ligation of random fragments. There are two major types of ligation junctions that are over-represented. One is the junction that forms between neighboring DNA fragments due to incomplete digestion, which represents about 20-30% of all junctions. This number is decreased by reducing the cross-linking stringency in the first step. The other type of junctions over-represented in this technique is the junction that forms when one end of the fragment ligates with the other end of the same fragment, and contributes up to 30% of all junctions formed. High temperature then results in the reversal of the previously formed cross-links. The resulting linear DNA fragment has specific restriction ends as well as a central restriction site corresponding to the site of ligation. The pool of these fragments is collectively referred to as the 3C library." ;
rdfs:subClassOf obo:MI_0030 .
obo:MI_0717 a rdfs:Class ;
rdfs:label "nucleic acid transfection with liposome" ;
rdfs:comment "Lipofection (or liposome transfection) is a technique used to inject genetic material into a cell by means of liposomes which are vesicles that can easily merge with the cell membrane since they are both made of a phospholipid bilayer." ;
rdfs:subClassOf obo:MI_0312 .
obo:MI_0065 a rdfs:Class ;
rdfs:label "isothermal titration calorimetry" ;
rdfs:comment "Isothermal titration calorimetry (ITC) measures directly the energy associated with a chemical reaction triggered by the mixing of two components. A typical ITC experiment is carried out by the stepwise addition of one of the reactants (~10-6 L per injection) into the reaction cell (~1mL) containing the second reactant. The chemical reaction occurring after each injection either releases or absorbs heat (qi) proportional to the amount of ligand that binds to the protein with a characteristic binding enthalpy (DH). As modern ITC instruments operate on the heat compensation principle, the instrumental response (measured signal) is the amount of power (microcalories per second) necessary to maintain constant the temperature difference between the reaction and the reference cells. Because the amount of uncomplexed protein available progressively decreases after each successive injection, the magnitude of the peaks becomes progressively smaller until complete saturation is achieved. The difference between the concentration of bound ligand in the ith and (i-1)th injections depends on the binding constant Ka and the total ligand injected. The calculations depend on the binding model (number of substrates). Analysis of the data yields DH and DG = -RTlnKa. The entropy change is obtained by using the standard thermodynamic expression DG = DH-TDS." ;
rdfs:subClassOf obo:MI_0013 .
obo:MI_0136 a rdfs:Class ;
rdfs:label "n-acetyl-phenylalanine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00784.""" .
obo:MI_1117 a rdfs:Class ;
rdfs:label "topfind" ;
rdfs:comment "TopFIND provides information on protein N- and C-termini. Information of proteases and their substrates is provided." ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0820 a rdfs:Class ;
rdfs:label "molecular weight estimation by sybr staining" ;
rdfs:comment "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with sybr dyes." ;
rdfs:subClassOf obo:MI_0816 .
obo:MI_0450 a rdfs:Class ;
rdfs:label "cdd" ;
rdfs:comment """The Conserved Domain Database may be used to identify the conserved domains present in a protein sequence.
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml""" ;
rdfs:subClassOf obo:MI_0447 .
obo:MI_0712 a rdfs:Class ;
rdfs:label "nucleic acid microinjection" ;
rdfs:comment "Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases nucleic acids." ;
rdfs:subClassOf obo:MI_0311 , obo:MI_0704 .
obo:MI_0835 a rdfs:Class ;
rdfs:label "koff" ;
rdfs:comment "Dissociation rate constant measuring the stability of a complex. Unit SECOND (s-1)" ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0993 a rdfs:Class ;
rdfs:label "degeranylase assay" ;
rdfs:comment "Measures the removal of S-geranylgeranyl-L-cysteine, which is cleaved and returns a C residue." ;
rdfs:subClassOf obo:MI_0991 .
obo:MI_1297 a rdfs:Class ;
rdfs:label "phosphoamino acid analysis" ;
rdfs:comment "The presence of amino acid residues phosphorylated as a result of post-translational modification, can be identified by amino acid analysis. Popular techniques for this include mass spectrometry or residue-specific antibodies." ;
rdfs:subClassOf obo:MI_1296 .
obo:MI_1014 a rdfs:Class ;
rdfs:label "string" ;
rdfs:comment "STRING is a database and web resource dedicated to protein interactions, including both physical and functional interactions. It weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set of genomes and proteins." ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0526 a rdfs:Class ;
rdfs:label "n-acetyl-lysine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00723.""" .
obo:MI_0649 a rdfs:Class ;
rdfs:label "second" ;
rdfs:comment "The second is the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the cesium-133 atom. The second was originally defined as 1/86 400 mean solar day until astronomers discovered that the mean solar day is actually not constant." ;
rdfs:subClassOf obo:MI_0647 .
obo:MI_0035 a rdfs:Class ;
rdfs:label "docking" ;
rdfs:comment "Predicts the structure of a molecular complex from the unbound structures of its components. The initial approach in the majority of docking procedures is based largely on the 'rigid-body' assumption, whereby the proteins are treated as solid objects. Initial scoring of a complex is based on geometric fit or surface complementarity. This generally requires some knowledge of the binding site to limit the number of solutions." ;
rdfs:subClassOf obo:MI_0105 , obo:MI_0577 .
obo:MI_0492 a rdfs:Class ;
rdfs:label "in vitro" ;
rdfs:comment """Experiments performed with participants removed from the cellular environment e.g. cell extracts, isolated proteins.
OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.""" .
obo:MI_0125 a rdfs:Class ;
rdfs:label "n-acetyl-aspartic acid" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00051.""" .
obo:MI_2349 a rdfs:Class ;
rdfs:label "clinvar" ;
rdfs:comment """ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence.
https://www.ncbi.nlm.nih.gov/clinvar""" ;
rdfs:subClassOf obo:MI_0447 .
obo:MI_1043 a rdfs:Class ;
rdfs:label "flannotator" ;
rdfs:comment "A repository for collecting, storing and and searching the annotation of gene or protein expression patterns in Drosophila melongaster. CPTI (Cambridge Protein Trap Identifier)" ;
rdfs:subClassOf obo:MI_0683 .
obo:MI_1229 a rdfs:Class ;
rdfs:label "uridylation assay" ;
rdfs:comment "Measures the formation of a phosphodiester or phosphoramide ester of UMP and an amino acid (MOD:01166)." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0210 a rdfs:Class ;
rdfs:label "hydroxylation reaction" ;
rdfs:comment "Irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues. Hydroxylation is the first step in the oxidative degeneration of organic compounds." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0435 a rdfs:Class ;
rdfs:label "protease assay" ;
rdfs:comment "Measures the enzymatic hydrolysis of a peptide bond within a peptide or protein substrate." ;
rdfs:subClassOf obo:MI_0990 .
obo:MI_0701 a rdfs:Class ;
rdfs:label "dna strand elongation" ;
rdfs:comment "The process by which a DNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand." ;
rdfs:subClassOf obo:MI_0986 .
obo:MI_0165 a rdfs:Class ;
rdfs:label "n6-methyl-lysine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00085.""" .
obo:MI_0986 a rdfs:Class ;
rdfs:label "nucleic acid strand elongation reaction" ;
rdfs:comment "The lengthening of a strand of a nucleic acid by the systematic addition of bases by a polymerase." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_0976 a rdfs:Class ;
rdfs:label "total internal reflection fluorescence spectroscopy" ;
rdfs:comment "Used to study surface-associated interactions at the molecular level. In this method, the evanescent field from an internally reflected excitation source selectively excites fluorescent molecules on or near a surface." ;
rdfs:subClassOf obo:MI_0051 .
obo:MI_0829 a rdfs:Class ;
rdfs:label "multiple parent reference" ;
rdfs:comment "This qualifier is used for hybrid or composite molecules with more than one cross-reference to parent molecules." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_0685 a rdfs:Class ;
rdfs:label "source reference" ;
rdfs:comment "Publication or document describing the originating resource where an interaction, or other curated information, was first described." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_0720 a rdfs:Class ;
rdfs:label "nucleic acid delivery by infection" ;
rdfs:comment "Nucleic acid introduced into a cell via an external organism, usually a virus or bacteria.." ;
rdfs:subClassOf obo:MI_0310 , obo:MI_0704 .
obo:MI_2298 a rdfs:Class ;
rdfs:label "carbohydrate chemical modification with no effect" ;
rdfs:comment "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that does not have any effect over an interaction when compared with the unaltered form." ;
rdfs:subClassOf obo:MI_2276 .
obo:MI_2402 a rdfs:Class ;
rdfs:label "genetic interaction" ;
rdfs:comment """A multigenic phenotype result in which (1) the phenotype of a single genetic perturbation has been modified by the introduction of one or more additional genetic perturbations AND/OR (2) an effect in which two genetic perturbations, when combined, result in a phenotype that does not appear to be merely explained by the superimposition or addition of effects of the original perturbations.
ab (not=) E""" ;
rdfs:subClassOf obo:MI_2366 .
obo:MI_0674 a rdfs:Class ;
rdfs:label "peptide parent sequence reference" ;
rdfs:comment "Describe a cross reference pointing to a peptide parent sequence." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_0105 a rdfs:Class ;
rdfs:label "structure based prediction" ;
rdfs:comment "Methods based on 3D structure information." ;
rdfs:subClassOf obo:MI_0063 .
obo:MI_0600 a rdfs:Class ;
rdfs:label "conditional synthetic lethal nutrition-sensitivity" ;
rdfs:comment """Two silent mutations show a nutrition sensitive lethal phenotype when they co-occur on the same cell.
OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description.""" .
obo:MI_1081 a rdfs:Class ;
rdfs:label "tigr/jcvi" ;
rdfs:comment "The J. Craig Venter Institute was formed in October 2006 through the merger of several affiliated and legacy organizations including The Institute for Genomic Research (TIGR)." ;
rdfs:subClassOf obo:MI_1094 .
obo:MI_0965 a rdfs:Class ;
rdfs:label "2d-infrared spectrometry" ;
rdfs:comment "Two-dimensional infrared correlation spectroscopy analysis is the application of 2D correlation analysis on infrared spectra. 2D IR spectroscopy probes molecular structures by means of vibrational frequencies, couplings, and transition dipole angles." ;
rdfs:subClassOf obo:MI_0964 .
obo:MI_0869 a rdfs:Class ;
rdfs:label "originally assigned identifier" ;
rdfs:comment "Identifier assigned when the record was created by a source database." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_0116 a rdfs:Class ;
rdfs:label "feature type" ;
rdfs:comment "Property of a subsequence that may interfere with the binding of a molecule." ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_1096 a rdfs:Class ;
rdfs:label "protein sequence databases" ;
rdfs:comment "Databases dedicated to the collection and annotation of protein sequences." ;
rdfs:subClassOf obo:MI_0683 .
obo:MI_0038 a rdfs:Class ;
rdfs:label "dynamic light scattering" ;
rdfs:comment "In dynamic light scattering, particle diffusion in solution gives rise to fluctuations in the intensity of the scattered light on the microsecond scale. The hydrodynamic radius of the particles can be easily calculated." ;
rdfs:subClassOf obo:MI_0067 .
obo:MI_0788 a rdfs:Class ;
rdfs:label "knock out" ;
rdfs:comment "The gene has been completely removed e.g. by genetic engineering " ;
rdfs:subClassOf obo:MI_0804 .
obo:MI_1200 a rdfs:Class ;
rdfs:label "immunocytochemistry" ;
rdfs:comment "Method using an antibody coupled with some colouring agent to detect a specific protein within a cell. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody." ;
rdfs:subClassOf obo:MI_0422 .
obo:MI_0889 a rdfs:Class ;
rdfs:label "acetylase assay" ;
rdfs:comment "Measures the catalysis of the addition of an acetyl group to a target molecule." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_0948 a rdfs:Class ;
rdfs:label "kinetic conditions" ;
rdfs:comment "A brief description (such as temp, pH) of the conditions under which a kinetic measurment has been performed." ;
rdfs:subClassOf obo:MI_0664 .
obo:MI_1152 a rdfs:Class ;
rdfs:label "cooperative effect value" ;
rdfs:comment "This value quantifies the cooperative effect of an interaction on a subsequent interaction. It is the fold change of the affinity or a catalytic parameter of a molecule for one ligand in the absence, versus presence, of a second ligand or a post-translational modification." ;
rdfs:subClassOf obo:MI_0664 , obo:MI_1149 .
obo:MI_2162 a rdfs:Class ;
rdfs:label "experimental CaCO2 permeability" ;
rdfs:comment "Experimentally derived value for ability of a compound to cross epithelial and endothelial cell barriers Using the CaCo2 cell line derived from a human colorectal adenocarcinoma. Used as an in vitro permeability models to predict human intestinal absorption" ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_2270 a rdfs:Class ;
rdfs:label "signalink" ;
rdfs:comment """SignaLink 2.0 is a signaling pathway resource with multi-layered regulatory networks.
http://signalink.org""" ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0176 a rdfs:Class ;
rdfs:label "o-phospho-serine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00046.""" .
obo:MI_2246 a rdfs:Class ;
rdfs:label "indirect causal regulation" ;
rdfs:comment "The effect of a modulator entity A on a modulated entity B that occurs when A is not immediately upstream of B." .
obo:MI_2219 a rdfs:Class ;
rdfs:label "gaussia luciferase protein tag" ;
rdfs:comment "Gaussia luciferase, is an enzyme from the crustacean Gaussia princeps catalyzing the oxidation of coelenterazine to coelenteramide that produces light. Gaussia luciferase produces a blue light around the 480 nm range." ;
rdfs:subClassOf obo:MI_1205 .
obo:MI_0008 a rdfs:Class ;
rdfs:label "array technology" ;
rdfs:comment "In this class of methodologies, the molecules to be tested are presented ordered in an array format (typically at high density) on planar supports. The characteristics and chemical nature of the planar support can vary. This format permits the simultaneous assay, in controlled conditions, of several thousand proteins/peptides/nucleic acids for different functions, for instance their ability to bind any given molecule." ;
rdfs:subClassOf obo:MI_0400 .
obo:MI_0020 a rdfs:Class ;
rdfs:label "transmission electron microscopy" ;
rdfs:comment "Microscopy technique in which a beam of electrons is transmitted through a sample to form an image. Samples can be purified molecules, for which no staining is required in order to detect interaction, or tissue/cells. In the latter case, during the treatment for microscope analysis a tissue section is incubated with high-specificity antibodies coupled to heavy metals (e.g. gold). Any tissue section can then be analysed by electron microscopy to localise the target proteins within the cell. This method supports very high resolution colocalisation of different molecules in a cell." ;
rdfs:subClassOf obo:MI_0040 .
obo:MI_0544 a rdfs:Class ;
rdfs:label "gpi-anchor amidated glycine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00170.""" .
obo:MI_0215 a rdfs:Class ;
rdfs:label "non covalent interaction" ;
rdfs:comment """Interaction mediated by non-covalent, weak forces rearrangement.
OBSOLETE use physical interaction (MI:0218) instead.""" .
obo:MI_2338 a rdfs:Class ;
rdfs:label "electron tomography" ;
rdfs:comment "Three-dimensional (3D) reconstruction of single, transparent objects from a series of projection images from a tilt series recorded with a transmission electron microscope." ;
rdfs:subClassOf obo:MI_0410 .
obo:MI_0515 a rdfs:Class ;
rdfs:label "methyltransferase assay" ;
rdfs:comment "Measures the catalysis of the transfer of a methyl group to an acceptor molecule." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_1136 a rdfs:Class ;
rdfs:label "kusabira-green protein tag" ;
rdfs:comment "Monomeric coral fluorescent reporter protein." ;
rdfs:subClassOf obo:MI_0367 .
obo:MI_0261 a rdfs:Class ;
rdfs:label "obsolete suppression" ;
rdfs:comment """A supressed gene mutation cause of an altered phenotype that is reverted to wild type phenotype when cell also carry a suppressor gene with a specific mutation or altered expression level.
OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793.""" .
obo:MI_2310 a rdfs:Class ;
rdfs:label "attached carbohydrate with no effect" ;
rdfs:comment "Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that has no effect over an interaction when compared with the non-glycosylated molecule, which does not interact." ;
rdfs:subClassOf obo:MI_2308 .
obo:MI_0589 a rdfs:Class ;
rdfs:label "in vitro translated protein" ;
rdfs:comment "Protein sample collected by in vitro translation of its mRNA taking advantage of purified translation machinery." ;
rdfs:subClassOf obo:MI_0342 .
obo:MI_2179 a rdfs:Class ;
rdfs:label "subset" ;
rdfs:comment "Reference to the corresponding object in another database. It implies the object is part of a cross-referenced entity (usually a complex)." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_1300 a rdfs:Class ;
rdfs:label "obligate complex" ;
rdfs:comment "The protein chains present in the complex are not found as independent stable structures in vivo." ;
rdfs:subClassOf obo:MI_1298 .
obo:MI_0310 a rdfs:Class ;
rdfs:label "infection" ;
rdfs:comment "Molecule introduced into a cell via an external organism, usually a virus or bacteria." ;
rdfs:subClassOf obo:MI_0307 .
obo:MI_1305 a rdfs:Class ;
rdfs:label "candidate set" ;
rdfs:comment "A group of interactors hypothesized to perform a specified function. Example: Two splice variants of Raptor mRNA encode closely related proteins. One (member) has been shown to participate in formation of active mTORC complex; the other (candidate) is thought to do so." ;
rdfs:subClassOf obo:MI_1304 .
obo:MI_0221 a rdfs:Class ;
rdfs:label "expression level" ;
rdfs:comment "Synthesis rate of a molecule under investigation described in comparison with its naturally occurring expression level in a cell." ;
rdfs:subClassOf obo:MI_0346 .
obo:MI_0573 a rdfs:Class ;
rdfs:label "mutation disrupting interaction" ;
rdfs:comment "Region of a molecule whose mutation or deletion totally disrupts an interaction strength or rate (in the case of interactions inferred from enzymatic reaction).." ;
rdfs:subClassOf obo:MI_0119 .
obo:MI_0154 a rdfs:Class ;
rdfs:label "s-palmitoyl-cysteine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00115.""" .
obo:MI_0790 a rdfs:Class ;
rdfs:label "hypermorph" ;
rdfs:comment "The gene function has been partially improved compared to wild-type by altering its sequence." ;
rdfs:subClassOf obo:MI_0787 .
obo:MI_0473 a rdfs:Class ;
rdfs:label "participant database" ;
rdfs:comment "Database of molecules participating in molecular interactions." ;
rdfs:subClassOf obo:MI_0444 .
obo:MI_1263 a rdfs:Class ;
rdfs:label "molecular connections" ;
rdfs:comment "Molecular Connections Private Limited is an in silico discovery Services Company with expertise in drug-discovery, informatics and information technology. They perform pro bono work for the IMEx Consortium. http://www.molecularconnections.com" ;
rdfs:subClassOf obo:MI_0461 , obo:MI_0973 .
obo:MI_2208 a rdfs:Class ;
rdfs:label "prerequisite-nucleic acid chemical modification" ;
rdfs:comment "Chemical modification observed on a nucleic acid molecule required for an interaction to occur. Modifications involving full nucleotide substitutions/deletions are excluded from this definition." ;
rdfs:subClassOf obo:MI_2206 .
obo:MI_2327 a rdfs:Class ;
rdfs:label "nanoluc-c" ;
rdfs:comment "The c-terminus of the nanoluc luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay." ;
rdfs:subClassOf obo:MI_2325 .
obo:MI_0327 a rdfs:Class ;
rdfs:label "peptide" ;
rdfs:comment "Chains of amino acids joined by peptide bonds. Distinction between peptides, oligopeptides and polypeptides is arbitrarily by length; a polypeptide is perhaps more than 15 residues." ;
rdfs:subClassOf obo:MI_0383 .
obo:MI_0002 a rdfs:Class ;
rdfs:label "participant identification method" ;
rdfs:comment "Method to determine the molecules involved in the interaction." ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_0455 a rdfs:Class ;
rdfs:label "prosite" ;
rdfs:comment """PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles.
http://us.expasy.org/prosite/""" ;
rdfs:subClassOf obo:MI_0449 .
obo:MI_0562 a rdfs:Class ;
rdfs:label "methylated alanine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00665.""" .
obo:MI_2268 a rdfs:Class ;
rdfs:label "de-methylated residue" ;
rdfs:comment "A protein modification that effectively removes one or more methyl groups from a protein." ;
rdfs:subClassOf obo:MI_2262 .
obo:MI_0734 a rdfs:Class ;
rdfs:label "enhanced green fluorescent protein tag" ;
rdfs:comment "Variation of the green fluorescent protein derived from the bioluminescent jellyfish Aequorea victoria, can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native." ;
rdfs:subClassOf obo:MI_0367 .
obo:MI_0481 a rdfs:Class ;
rdfs:label "refseq" ;
rdfs:comment """The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for a number of organisms.
http://www.ncbi.nlm.nih.gov/RefSeq/""" ;
rdfs:subClassOf obo:MI_1096 .
obo:MI_2183 a rdfs:Class ;
rdfs:label "go_central" ;
rdfs:comment """The GO Consortium coordinated an effort to maximize and optimize GO annotations for a large and representative set of key genomes, known as 'reference genomes'. The Reference Genome Annotation Project aimed to completely annotate twelve reference genomes, producing a resource that may effectively seed automatic annotation efforts of other genomes. This resource represents manual annotation from PAINT curators into the UniProt Protein2GO curation tool.
http://www.geneontology.org/GO.refgenome.shtml""" ;
rdfs:subClassOf obo:MI_0448 .
obo:MI_0114 a rdfs:Class ;
rdfs:label "x-ray crystallography" ;
rdfs:comment "Analysis of a diffraction pattern generated by a single crystal. X-rays have a wavelength, typically around 1 Angstrom (the diameter of a hydrogen atom). If a narrow parallel beam of X-rays is directed at a sample of a pure protein, most of the X-rays will pass straight through it. A small fraction, however, will be scattered by the atoms in the sample. If the sample is a well-ordered crystal, the scattered waves will reinforce one another at certain points and will appear as diffraction spots when the X-rays are recorded by a suitable detector. The position and intensity of each spot in the X-ray diffraction pattern contain information about the position and nature of the atoms in the crystal. The three-dimensional structure of a large molecule can be deduced from the electron-density map of its crystal. In recent years X-ray diffraction analysis has become increasingly automated, and now the slowest step is likely to be the production of suitable macromolecule crystals. This requires high concentration of very pure macromolecule and empirical searching for the proper crystallization conditions." ;
rdfs:subClassOf obo:MI_0013 , obo:MI_0659 .
obo:MI_1106 a rdfs:Class ;
rdfs:label "pathways database" ;
rdfs:comment "Databases which primarily exist to display biomolecular information in structured pathways. Interactions data can be inferred from the published pathways." ;
rdfs:subClassOf obo:MI_0461 .
obo:MI_0853 a rdfs:Class ;
rdfs:label "dna overhang" ;
rdfs:comment "An overhang is a stretch of unpaired nucleotides in the end of a DNA molecule. These unpaired nucleotides can be in either strand, creating either 3' or 5' overhangs. Longer overhangs are called cohessive ends or sticky ends. They are most often created by restriction endonucleases when they cut DNA. Very often they cut the two DNA strands four base pairs from each other, creating a four-base 3' overhang in the other molecule and a complementary 5' overhang in the other. These ends are called cohessive since they are easily joined back together by a ligase" ;
rdfs:subClassOf obo:MI_0505 .
obo:MI_0947 a rdfs:Class ;
rdfs:label "bead aggregation assay" ;
rdfs:comment "Binding of proteins bound to beads leads to a measurable aggregation of the beads." ;
rdfs:subClassOf obo:MI_0892 .
obo:MI_0042 a rdfs:Class ;
rdfs:label "electron paramagnetic resonance" ;
rdfs:comment "EPR (also called ESR, Electron Spin Resonance) spectroscopy is analogous to NMR, but is based on the excitation of unpaired electrons instead of nuclei. Unpaired (single) electrons are only found in radicals and some metal ions (paramagnetic species); the EPR spectrum provides information about the environment and mobility of the paramagnetic species. The magnetic interaction of two paramagnetic centres in a protein can be used to calculate the distance between them; this allows studies of the movements and interactions of protein segments. In proteins without any intrinsic unpaired electrons it is possible to attach a radical probe (spin label). Stable nitroxide radicals can be bound to amino acid residues, in analogy with fluorescent probes. In combination with site directed mutagenesis this method is used in particular to study structure and assembly of membrane proteins, by measuring with EPR whether an amino acid is in a polar or non polar environment." ;
rdfs:subClassOf obo:MI_0043 .
obo:MI_0638 a rdfs:Class ;
rdfs:label "prerequisite-ptm" ;
rdfs:comment "Post translational modification required for an interaction to occur." ;
rdfs:subClassOf obo:MI_0925 .
obo:MI_0182 a rdfs:Class ;
rdfs:label "3-oxoalanine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:01169.""" .
obo:MI_0867 a rdfs:Class ;
rdfs:label "tag visualisation by fluorescence" ;
rdfs:comment "The molecule is produced fused to a tag containing a fluorophore, such as GFP tagged to a recombinant protein, or a fluorophore has been chemically attached to the molecule. Subsequence observation or measurement of fluorescence is used to identify the presence of the molecule in an interaction." ;
rdfs:subClassOf obo:MI_0866 .
obo:MI_0462 a rdfs:Class ;
rdfs:label "bind" ;
rdfs:comment """The Biomolecular Interaction Network Database (BIND) is a collection of records documenting molecular interactions.
http://www.blueprint.org/bind""" ;
rdfs:subClassOf obo:MI_0461 , obo:MI_0489 .
obo:MI_0847 a rdfs:Class ;
rdfs:label "dansyl label" ;
rdfs:comment "Dansyl is the acronym of 5-dimethylaminonaphthalene-1-sulfonyl radical group reacting with any NH2 groups." ;
rdfs:subClassOf obo:MI_0857 .
obo:MI_1036 a rdfs:Class ;
rdfs:label "nucleotide exchange assay" ;
rdfs:comment """Experiments monitoring
interactions of nucleotide exchange factors with their cognate nucleotidases.""" ;
rdfs:subClassOf obo:MI_0401 .
obo:MI_2279 a rdfs:Class ;
rdfs:label "complex portal" ;
rdfs:comment "The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms, entered into the IntAct molecular interaction database . Data includes protein-only complexes as well as protein-small molecule and protein-nucleic acid complexes. All complexes are derived from physical molecular interaction evidences extracted from the literature and cross-referenced in the entry, or by curator inference from information on homologs in closely related species or by inference from scientific background. All complexes are tagged with Evidence and Conclusion Ontology codes to indicate the type of evidence available for each entry." ;
rdfs:subClassOf obo:MI_0461 , obo:MI_0473 .
obo:MI_2421 a rdfs:Class ;
rdfs:label "subtilist" ;
rdfs:comment """SubtiList is the reference database dedicated to the genome of Bacillus subtilis, the paradigm of Gram-positive endospore-forming bacteria.
http://genolist.pasteur.fr/SubtiList/""" ;
rdfs:subClassOf obo:MI_1094 .
obo:MI_2444 a rdfs:Class ;
rdfs:label "YeastMap" ;
rdfs:comment "yeast.MAP is a machine-learning framework for identifying Saccharomyces cerevisiae protein complexes from mass spectrometry and other large-scale interaction datasets. Available as a searchable web resource (https://yeast.proteincomplexes.org/), yeast.MAP integrates large-scale AP-MS datasets (Michaelis et al., Nature, 2023), AP-MS evidence scored using a weighted matrix model (Hart et al., BMC Bioinformatics, 2007), and proteome-scale RoseTTAFold structure predictions (Humphreys et al., Science, 2021)." ;
rdfs:subClassOf obo:MI_0489 .
obo:MI_0053 a rdfs:Class ;
rdfs:label "fluorescence polarization spectroscopy" ;
rdfs:comment "Because of the long lifetimes of excited fluorescent molecules (nanoseconds), fluorescence can be used to monitor the rotational motion of molecules, which occurs on this timescale. This is accomplished experimentally by excitation with plane-polarized light, followed by measurement of the emission at parallel and perpendicular planes. Since rotational correlation times depend on the size of the molecule, this method can be used to measure the binding of two proteins because the observed polarization increase when a larger complex is formed. A fluorescence anisotropy experiment is normally carried out with a protein bearing a covalently added fluorescent group, which increases both the observed fluorescence lifetime of the excited state and the intensity of the fluorescent signal. Residue modification can be assessed by addition of an antibody which binds to the modified residue and alters the molecular weight of the complex. A variation of this technique has been used to show interaction of a DNA binding protein with another protein. In this case the DNA rather than protein is fluorescently labelled." ;
rdfs:subClassOf obo:MI_0051 .
obo:MI_0358 a rdfs:Class ;
rdfs:label "primary-reference" ;
rdfs:comment "Used to indicate the PMID from which the experimental data is extracted." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_2107 a rdfs:Class ;
rdfs:label "logd" ;
rdfs:comment "The LogD is the ratio of the equilibrium concentrations of all species (unionized and ionized) of a molecule in octanol to same species in the water phase at a given temperature, normally 25 C. It differs from LogP in that ionized species are considered as well as the neutral form of the molecule.pH 7.4" ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0432 a rdfs:Class ;
rdfs:label "one hybrid" ;
rdfs:comment "Protein-DNA complementation assay where a single promoter act as bait and is screened against a library of prey transcription factors." ;
rdfs:subClassOf obo:MI_0232 .
obo:MI_0842 a rdfs:Class ;
rdfs:label "phosphate donor" ;
rdfs:comment "Any molecule that is able to transfer a phosphate group to another chemical species." ;
rdfs:subClassOf obo:MI_0918 .
obo:MI_0836 a rdfs:Class ;
rdfs:label "temperature of interaction" ;
rdfs:comment "Temperature at which interaction was determined. Unit KELVIN (K)" ;
rdfs:subClassOf obo:MI_0640 .
obo:MI_0547 a rdfs:Class ;
rdfs:label "s-prenyl-cysteine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:01110.""" .
obo:MI_0807 a rdfs:Class ;
rdfs:label "comigration in gel electrophoresis" ;
rdfs:comment "The interaction of two or more molecules is determined by their very close proximity or the overlap of their respective bands in a gel." ;
rdfs:subClassOf obo:MI_0982 .
obo:MI_0954 a rdfs:Class ;
rdfs:label "curation quality" ;
rdfs:comment "An assessment of the depth and extent to which a paper has been curated" ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_0013 a rdfs:Class ;
rdfs:label "biophysical" ;
rdfs:comment "The application of physical principles and methods to biological experiments." ;
rdfs:subClassOf obo:MI_0045 .
obo:MI_0414 a rdfs:Class ;
rdfs:label "enzymatic reaction" ;
rdfs:comment "terms aiming to represent biochemical reactions referring to their resulting product modifications." ;
rdfs:subClassOf obo:MI_0407 .
obo:MI_1021 a rdfs:Class ;
rdfs:label "qx 520" ;
rdfs:comment "Nonfluorescent dye, act as a quencher in FRET assays." ;
rdfs:subClassOf obo:MI_0373 .
obo:MI_0147 a rdfs:Class ;
rdfs:label "n-formyl-methionine" ;
rdfs:comment """Residue modification.
OBSOLETE remap to MOD:00030.""" .
obo:MI_0031 a rdfs:Class ;
rdfs:label "protein cross-linking with a bifunctional reagent" ;
rdfs:comment "Cross-linking agents induce the formation of covalent bonds among proteins that are neighbours. The cross-linker may be a bifunctional molecule having two reactive ends linked by a spacer, often containing a disulfide bond. When a reducing agent is added the disulfide bridge is cleaved, the cross-linked pairs are released and can be identified. There are various classes of cross-linkers, the most common are those having photoreactive groups that become reactive fluorophores when activated by UV light thereby resulting in photolabeling the cross-linked moieties." ;
rdfs:subClassOf obo:MI_0030 .
obo:MI_2346 a rdfs:Class ;
rdfs:label "target tag" ;
rdfs:comment "Protein is fused to a 21 amino acid residues-long peptide (YPGQYPGQYPGQYPGQYPGQV) derived from human PAR-4 N-terminal peptide. The final sequence of the peptide resulted from optimization involving mutagenesis and repetition of the original reference sequence in order to maximize affinity with the P20.1 antibody." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_2432 a rdfs:Class ;
rdfs:label "bioid2 tag" ;
rdfs:comment "An engineered biotin ligase that uses ATP to convert biotin into biotin–AMP, a reactive intermediate that covalently labels proximal proteins. BioID2, derived from Aquifex aeolicus biotin ligase, is ~30% smaller than BirA" ;
rdfs:subClassOf obo:MI_2431 .
obo:MI_0254 a rdfs:Class ;
rdfs:label "genetic interference" ;
rdfs:comment "This term refers to methods that aim at interfering with the activity of a specific gene by altering the gene regulatory or coding sequences. This goal can be achieved either by a classical genetic approach (random mutagenesis followed by phenotype characterization and genetic mapping) or by a reverse genetics approach where a gene of interest is modified by directed mutagenesis." ;
rdfs:subClassOf obo:MI_0045 .
obo:MI_0384 a rdfs:Class ;
rdfs:label "alexa label" ;
rdfs:comment "All Alexa dyes are fluorescent iodoacetamide dyes that can be conjugated with the primary amines of biomolecules. All Alexa dyes and their conjugates are more fluorescent and more photostable than the commonly used dyes. The numbers in the Alexa names indicate the approximate excitation wavelength maximum in nm)." ;
rdfs:subClassOf obo:MI_0857 .
obo:MI_0982 a rdfs:Class ;
rdfs:label "electrophoretic mobility-based method" ;
rdfs:comment "Any method which relies on the motion of particles relative to a matrix under the influence of an electrical field." ;
rdfs:subClassOf obo:MI_0401 .
obo:MI_0797 a rdfs:Class ;
rdfs:label "genetic epistasis (sensu Bateson)" ;
rdfs:comment """An effect in which individual perturbations of two different genes result in different mutant phenotypes, and the resulting phenotype of their combination (the double mutant) is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:
(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)
where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively or quantitatively different phenotypes.""" ;
rdfs:subClassOf obo:MI_0208 .
obo:MI_2287 a rdfs:Class ;
rdfs:label "identification by structure determination" ;
rdfs:comment """Identity of the participant was established (or confirmed) by
fitting its molecular model to the experimentally determined
electron density.""" ;
rdfs:subClassOf obo:MI_0661 .
obo:MI_1054 a rdfs:Class ;
rdfs:label "experimentally-observed" ;
rdfs:comment "Data has been directly curated into the database from the paper describing the experimental evidence or by direct submission by the experimenter." ;
rdfs:subClassOf obo:MI_1053 .
obo:MI_2295 a rdfs:Class ;
rdfs:label "3' position" ;
rdfs:comment "Term describing the downstream end of a nucleotide sequence." ;
rdfs:subClassOf obo:MI_0333 .
obo:MI_0932 a rdfs:Class ;
rdfs:label "neutral multigenic phenotype result" ;
rdfs:comment "The observation that, when tested, no interaction was observed between two or more genes, for a given phenotype. In other words, the phenotype of the combined perturbations a and b result in the expected phenotype." ;
rdfs:subClassOf obo:MI_2366 .
obo:MI_1010 a rdfs:Class ;
rdfs:label "neddylase assay" ;
rdfs:comment "Measurement of a reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target." ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_2386 a rdfs:Class ;
rdfs:label "isophenotypic phenotype result" ;
rdfs:comment "A cisphenotypic phenotype result in which both of two perturbations result in the same phenotype, both in manner and degree, compared to wild type." ;
rdfs:subClassOf obo:MI_2385 .
obo:MI_0858 a rdfs:Class ;
rdfs:label "immunodepleted coimmunoprecipitation" ;
rdfs:comment "Method involving consecutive coimmunoimmunoprecipitations on the same sample, a control where an interaction is detected, and other CoIPs where the sample is previously treated with a specific antibody that precipitates a candidate interactor and leads to the suppression of an interaction or a change in composition of a complex." ;
rdfs:subClassOf obo:MI_0019 .
obo:MI_0204 a rdfs:Class ;
rdfs:label "deubiquitination reaction" ;
rdfs:comment "Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins." ;
rdfs:subClassOf obo:MI_0414 .
obo:MI_1047 a rdfs:Class ;
rdfs:label "protein-protein" ;
rdfs:comment "Interaction between a protein or peptide and a corresponding protein or peptide." ;
rdfs:subClassOf obo:MI_1046 .
obo:MI_0243 a rdfs:Class ;
rdfs:label "isoform parent sequence reference" ;
rdfs:comment "Reference to the master sequence from which this isoform has been derived." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_2010 a rdfs:Class ;
rdfs:label "standard inchi" ;
rdfs:comment "IUPAC International Chemical Identifier (InChI) - a machine-readable character string describing a chemical structure, developed by IUPAC and the InChI Trust as a standard to allow interoperability and linking between chemical resources. The standard InChI differs from the non-standard InChI in that it is generated with a fixed set of parameters, ensuring consistency between different resources. The current version of the standard InChI software is 1.03." ;
rdfs:subClassOf obo:MI_1212 , obo:MI_2091 .
obo:MI_0316 a rdfs:Class ;
rdfs:label "ribonucleoprotein complex" ;
rdfs:comment "A macromolecular complex containing both protein and RNA molecules." ;
rdfs:subClassOf obo:MI_1299 .
obo:MI_1147 a rdfs:Class ;
rdfs:label "ampylation assay" ;
rdfs:comment """Measurement of AMPylation, the formation of a phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino
acids.""" ;
rdfs:subClassOf obo:MI_0415 .
obo:MI_2129 a rdfs:Class ;
rdfs:label "bile transporter substrate" ;
rdfs:comment "Substrate of the bile acid carrier system in both the intestinal tract and the liver. System catalyses of the transfer of bile acid from one side of the membrane to the other. Bile acids are any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine." ;
rdfs:subClassOf obo:MI_2121 .
obo:MI_0443 a rdfs:Class ;
rdfs:label "ubiquitin binding" ;
rdfs:comment """Interaction concerning ubiquitin that is covalently attached to any Lys residue of its interaction partner.
OBSOLETE remap to ubiquitination reaction (MI:0220) or describe ubiquitine as a participant on the interaction using physical interaction (MI:0218) or covalent binding (MI:0195) as interaction type.""" .
obo:MI_0804 a rdfs:Class ;
rdfs:label "mutated gene" ;
rdfs:comment "The gene is mutated in some unknown manner" ;
rdfs:subClassOf obo:MI_0787 .
obo:MI_2086 a rdfs:Class ;
rdfs:label "physicochemical attribute name" ;
rdfs:comment "Chemical and physical properties of a molecule." ;
rdfs:subClassOf obo:MI_0590 .
obo:MI_0049 a rdfs:Class ;
rdfs:label "filter binding" ;
rdfs:comment "A method in which separation depends upon the ability of one participant to bind to a filter or membrane which the other participants do not. Molecules interacting with the bound molecule will also be retain on the filter. For example, proteins expressed by different clones of an expression library are bound to a nitrocellulose membrane, by colony (bacterial library) or plaque (phage library) blotting. A labelled protein can then be used as a probe to identify clones expressing proteins that interact with the probe. Interactions occur on the nitrocellulose filters. The method is highly general and therefore widely applicable. A variety of approaches can be used to label the ligand, alternatively the ligand can be detected by a specific antibody." ;
rdfs:subClassOf obo:MI_0892 .
obo:MI_0372 a rdfs:Class ;
rdfs:label "subcellular preparation" ;
rdfs:comment "Cell lysates are partially fractionated to isolate a specific subcellular fraction." ;
rdfs:subClassOf obo:MI_0344 .
obo:MI_1059 a rdfs:Class ;
rdfs:label "complex expansion" ;
rdfs:comment "The method by which complex n-ary data is expanded into binary data. This may be performed manually on data input, or computationally on data export." ;
rdfs:subClassOf obo:MI_1045 .
obo:MI_0305 a rdfs:Class ;
rdfs:label "ordered locus name" ;
rdfs:comment "A name used to represent an ORF in a completely sequenced genome or chromosome. It is generally based on a prefix representing the organism and a number which usually represents the sequential ordering of genes on the chromosome. Depending on the genome sequencing center, numbers are attributed only to protein-coding genes, or also to pseudogenes, or also to tRNAs and other features." ;
rdfs:subClassOf obo:MI_1041 .
obo:MI_2168 a rdfs:Class ;
rdfs:label "conditional site labelling" ;
rdfs:comment "The interaction is detected through labelling of a specific site -which can be an active site- that is only accessible once the participants are interacting. This conditional site is then marked with a chemical label for detection." ;
rdfs:subClassOf obo:MI_1313 .
obo:MI_0884 a rdfs:Class ;
rdfs:label "vsv tag" ;
rdfs:comment "Epitope tag derived from vesicular stomatitis virus (VSV) glycoprotein. The tag sequence is YTDIEMNRLGK and many antibodies against it are commercially available." ;
rdfs:subClassOf obo:MI_0507 .
obo:MI_0921 a rdfs:Class ;
rdfs:label "surface plasmon resonance array" ;
rdfs:comment "This array technology allows the screening of binding abilities of hundreds or thousands of biomolecules (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) printed onto the gold-coated chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with a non-labelled sample (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) to identify the baits that can bind to it. This is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation on each spot." ;
rdfs:subClassOf obo:MI_0008 , obo:MI_0107 .
obo:MI_0831 a rdfs:Class ;
rdfs:label "cell ontology" ;
rdfs:comment """Ontology of cell types.
http://obo.sourceforge.net/cgi-bin/detail.cgi?cell""" ;
rdfs:subClassOf obo:MI_0473 .
obo:MI_0361 a rdfs:Class ;
rdfs:label "additional information" ;
rdfs:comment "Related object within the same database or pointing to an external database." ;
rdfs:subClassOf obo:MI_0353 .
obo:MI_0454 a rdfs:Class ;
rdfs:label "prodom" ;
rdfs:comment """The ProDom protein domain database consists of an automatic compilation of homologous domains.
http://protein.toulouse.inra.fr/prodom.html""" ;
rdfs:subClassOf obo:MI_0449 .
obo:MI_1180 a rdfs:Class ;
rdfs:label "partial DNA sequence identification" ;
rdfs:comment "Identification of a part of a DNA sequence, usually then related to the full length sequence by alignment. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones." ;
rdfs:subClassOf obo:MI_1179 .
obo:MI_0444 a rdfs:Class ;
rdfs:label "database citation" ;
rdfs:comment "Database citation list names of databases commonly used to cross reference interaction data. http://purl.obolibrary.org/obo/clo.owl" ;
rdfs:subClassOf obo:MI_0000 .
obo:MI_2437 a rdfs:Class ;
rdfs:label "holdup assay" ;
rdfs:comment "A method for high-throughput measurement of protein-ligand binding affinities. A resin is saturated at high concentration with either a control or a bait molecule. The loaded resins are incubated with a prey solution containing either individual purified proteins/domains or complex mixtures. The bait is present in substantial molar excess relative to all potential preys, ensuring non-saturating binding conditions. Each significantly interacting prey is depleted from the solution by the resin, in a proportion related to its own affinity constant for the bait. After incubation, the liquid phases containing the unbound fractions are recovered, without any washing step to maintain thermodynamic equilibrium. For each prey, its amount in the unbound fraction of the bait sample is quantified relatively to its amount in the unbound fraction of the control sample. This relative quantification enables calculation of dissociation constants (Kd), with rigorously validated accuracy and precision. Prey that are well-quantified but not significantly depleted (their affinity for the bait is lower than the assay’s known detection threshold) may be regarded as a negative interaction." ;
rdfs:subClassOf obo:MI_0004 .
obo:MI_2274 a rdfs:Class ;
rdfs:label "regulator" ;
rdfs:comment "Entity whose activity exerts an effect on the concentration, frequency, rate or extent of the target entity." ;
rdfs:subClassOf obo:MI_0500 .
obo:MI_2257 a rdfs:Class ;
rdfs:label "small molecule catalysis reaction" ;
rdfs:comment "The chemical reactions and pathways resulting in the formation, breakdown, modification of small molecules." .
obo:MI_0825 a rdfs:Class ;
rdfs:label "x-ray fiber diffraction" ;
rdfs:comment "Analysis of the diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using X-ray." ;
rdfs:subClassOf obo:MI_0114 .
obo:IAO_0000115 a rdf:Property ;
rdfs:label "definition" ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:label "Label from MS DeltaMass" ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:comment "Drugable Genome Project" ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:label "Alternate label curated by PSI-MI" ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:label "Unique short label curated by PSI-MI" ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:comment "Subset of PSI-MI" ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:label "Alternate label curated by PSI-MOD" ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:label "Unique short label curated by PSI-MOD" ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:comment "subset of protein modifications" ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:label "Agreed label from MS community" ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:label "Alternate name from RESID" ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:label "Misnomer label from RESID" ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:label "Name from RESID" ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:label "Systematic name from RESID" ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:label "Alternate name from UniMod" ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:label "Description (full_name) from UniMod" ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:label "Interim label from UniMod" ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:label "Label (title) from UniMod" ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:label "Protein feature description from UniProtKB" ;
rdfs:range xsd:string .