PREFIX obo:
PREFIX rdf:
PREFIX rdfs:
PREFIX xsd:
obo:OBI_0002467 a rdfs:Class ;
rdfs:label "alignment counting application"@en ;
rdfs:comment "A software application that implements an alignment counting algorithm, used to count the overlap of aligned sequencing reads with genes."@en ;
rdfs:subClassOf obo:IAO_0000594 .
obo:OBI_0000094 a rdfs:Class ;
rdfs:label "material processing"@en ;
rdfs:comment "A planned process which results in physical changes in a specified input material"@en ;
rdfs:subClassOf obo:OBI_0000011 .
obo:UBERON_0000465 a rdfs:Class ;
rdfs:label "material anatomical entity" ;
rdfs:comment "Anatomical entity that has mass." ;
rdfs:subClassOf obo:BFO_0000040 .
obo:OBI_0000198 a rdfs:Class ;
rdfs:label "biological replicate role"@en ;
rdfs:comment "a reference participant role realized by equivalent treatment of participants" ;
rdfs:subClassOf obo:OBI_0000220 .
obo:OBI_0002465 a rdfs:Class ;
rdfs:label "age since culture seeding measurement datum" ;
rdfs:comment "An age measurement datum that is the result of the measurement of the age of a cell since cultured (the process of seeding cells onto a culture dish)." ;
rdfs:subClassOf obo:OBI_0001167 .
obo:OBI_0000102 a rdfs:Class ;
rdfs:label "responsible party role"@en ;
rdfs:comment "a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study"@en ;
rdfs:subClassOf obo:OBI_0000202 .
obo:OBI_0000947 a rdfs:Class ;
rdfs:label "service provider role" ;
rdfs:comment "is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person" ;
rdfs:subClassOf obo:BFO_0000023 .
obo:BFO_0000017 a rdfs:Class ;
rdfs:label "realizable entity"@en ;
rdfs:subClassOf obo:BFO_0000020 .
obo:TAXRANK_0000000 a rdfs:Class ;
rdfs:label "taxonomic_rank" ;
rdfs:comment "A level of depth of a taxon in a taxonomic hierarchy." ;
rdfs:subClassOf obo:GENEPIO_0001170 .
obo:OBI_0001933 a rdfs:Class ;
rdfs:label "value specification" ;
rdfs:comment "An information content entity that specifies a value within a classification scheme or on a quantitative scale." ;
rdfs:subClassOf obo:IAO_0000030 .
obo:OBI_0000832 a rdfs:Class ;
rdfs:label "measurement device" ;
rdfs:comment "A device in which a measure function inheres." ;
rdfs:subClassOf obo:OBI_0000968 .
obo:IAO_0000416 a rdfs:Class ;
rdfs:label "time measurement datum"@en ;
rdfs:comment "A scalar measurement datum that is the result of measuring a temporal interval"@en ;
rdfs:subClassOf obo:IAO_0000032 .
obo:GO_0044464 a rdfs:Class ;
rdfs:label "cell part" ;
rdfs:comment "Any constituent part of a cell, the basic structural and functional unit of all organisms." ;
rdfs:subClassOf obo:GO_0005575 .
obo:OBI_0002472 a rdfs:Class ;
rdfs:label "dbGaP study identifier"@en ;
rdfs:comment "A central registered identifier symbol that denotes a specific study in dbGaP."@en ;
rdfs:subClassOf obo:IAO_0000577 .
obo:ORNASEQ_0000006 a rdfs:Class ;
rdfs:label "Illumina TruSeq Stranded"@en ;
rdfs:subClassOf obo:GENEPIO_0000085 .
obo:OBI_0000312 a rdf:Property ;
rdfs:label "is_specified_output_of"@en ;
rdfs:comment "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en ;
rdfs:range ;
rdfs:subPropertyOf obo:RO_0000056 .
obo:ORNASEQ_0000001 a rdfs:Class ;
rdfs:label "date of specimen amplification"@en ;
rdfs:subClassOf obo:OBI_0002471 .
obo:RO_0002223 a rdf:Property ;
rdfs:label "starts"@en ;
rdfs:comment "inverse of starts with" ;
rdfs:range ;
rdfs:subPropertyOf obo:BFO_0000050 .
obo:ORNASEQ_0000017 a rdfs:Class ;
rdfs:label "verse"@en ;
rdfs:subClassOf obo:OBI_0002467 .
obo:NCIT_C19498 a rdfs:Class ;
rdfs:label "Document" ;
rdfs:comment "A physical object, or electronic counterpart, that is characterized by containing writing which is meant to be human-readable." ;
rdfs:subClassOf obo:NCIT_C25198 .
obo:OBI_0001167 a rdfs:Class ;
rdfs:label "age measurement datum"@en ;
rdfs:comment "A time measurement datum that is the result of measurement of age of an organism" ;
rdfs:subClassOf obo:IAO_0000416 .
obo:OBI_0002476 a rdfs:Class ;
rdfs:label "number of rounds of amplification"@en ;
rdfs:comment "A data item that is the number of times an amplification reaction happened."@en ;
rdfs:subClassOf obo:IAO_0000027 .
obo:OBI_0002461 a rdfs:Class ;
rdfs:label "BCL format"@en ;
rdfs:comment "A data format specification that is a binary file containing base calling data. These files are created by sequencing machines during the act of sequencing, and contain data about each of the nucleotide clusters on a sequencing flow cell."@en ;
rdfs:subClassOf obo:IAO_0000098 .
obo:OBI_0000047 a rdfs:Class ;
rdfs:label "processed material"@en ;
rdfs:comment "Is a material entity that is created or changed during material processing."@en ;
rdfs:subClassOf obo:BFO_0000040 .
obo:OBI_0000835 a rdfs:Class ;
rdfs:label "manufacturer" ;
rdfs:comment "A person or organization that has a manufacturer role" ;
rdfs:subClassOf obo:BFO_0000040 .
obo:IAO_0000017 a rdfs:Class ;
rdfs:label "model number"@en ;
rdfs:comment "A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots."@en ;
rdfs:subClassOf obo:IAO_0000028 .
obo:ORNASEQ_0000012 a rdfs:Class ;
rdfs:label "RNA harvest compound"@en ;
rdfs:subClassOf obo:CHEBI_23367 .
obo:RO_0000087 a rdf:Property ;
rdfs:label "has role"@en ;
rdfs:comment "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en ;
rdfs:range ;
rdfs:subPropertyOf obo:RO_0000053 .
obo:OBI_0000968 a rdfs:Class ;
rdfs:label "device" ;
rdfs:comment "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." ;
rdfs:subClassOf obo:OBI_0000047 .
obo:OBI_0002479 a rdfs:Class ;
rdfs:label "sequence read length measurement datum"@en ;
rdfs:comment "A measurement datum that is the result of the measurement of the number of bases in a DNA or RNA sequence."@en ;
rdfs:subClassOf obo:IAO_0000109 .
obo:OBI_0002483 a rdfs:Class ;
rdfs:label "spike-in dilution factor"@en ;
rdfs:comment "A data item that indicates the dilution of spike-in added to a specimen."@en ;
rdfs:subClassOf obo:IAO_0000027 .
obo:OBI_0002484 a rdfs:Class ;
rdfs:label "star algorithm"@en ;
rdfs:comment "A reference genome transcriptome alignment algorithm that is a standalone RNA-seq alignment algorithm that uses uncompressed suffix arrays and a mapping algorithm similar to those used in large-scale genome alignment tools to align RNA-seq reads to a genomic reference."@en ;
rdfs:subClassOf obo:OBI_0002478 .
obo:OBI_0001468 a rdfs:Class ;
rdfs:label "cell specimen"@en ;
rdfs:comment "A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture." ;
rdfs:subClassOf obo:OBI_0100051 .
obo:IAO_0000098 a rdfs:Class ;
rdfs:label "data format specification"@en ;
rdfs:comment """A data format specification is the information content borne by the document published defining the specification.
Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"""@en ;
rdfs:subClassOf obo:IAO_0000033 .
obo:OBI_0002468 a rdfs:Class ;
rdfs:label "base calling algorithm"@en ;
rdfs:comment "An algorithm that assigns nucleotides to temporal or spatial peaks generated by a detector, such as peaks of light intensities generated by a DNA sequencer"@en ;
rdfs:subClassOf obo:IAO_0000064 .
obo:GENEPIO_0000081 a rdfs:Class ;
rdfs:label "sequencing kit"@en ;
rdfs:comment "Pre-filled, ready-to-use reagent cartridges. Used to produce improved chemistry, cluster density and read length as well as improve quality (Q) scores. Reagent components are encoded to interact with the sequencing system to validate compatibility with user-defined applications." ;
rdfs:subClassOf obo:OBI_0000047 .
obo:NCIT_C70663 a rdfs:Class ;
rdfs:label "Unique Identifier" ;
rdfs:comment "A set of characters used as a code that is unique in the context or the system for which it is created. It serves as a means of identification and reference (often instead of a name) for an entity, person, thing, function, procedure, activity, variable, or body of data." ;
rdfs:subClassOf obo:NCIT_C25364 .
obo:IAO_0000028 a rdfs:Class ;
rdfs:label "symbol"@en ;
rdfs:comment "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity."@en ;
rdfs:subClassOf obo:IAO_0000030 .
obo:BFO_0000040 a rdfs:Class ;
rdfs:label "material entity"@en ;
rdfs:subClassOf obo:BFO_0000004 .
obo:OBI_0002464 a rdfs:Class ;
rdfs:label "SRS identifier"@en ;
rdfs:comment "An accession number that applies to a database record for an individual sample object in an NCBI Sequence Read Archive (SRA) submission. These records are imported from the NCBI BioSample database."@en ;
rdfs:subClassOf obo:NCIT_C25402 .
obo:OBIws_0000088 a rdfs:Class ;
rdfs:label "BLAST algorithm" ;
rdfs:comment "BLAST (Basic Local Alignment Search Tool), a pairwise sequence alignment algorithm is a heuristic search algorithm for comparing primary biological sequence information, such as the amino-acid or nucleotides sequences with a database of sequences, and identify sequences that resemble the query sequence above a certain threshold." ;
rdfs:subClassOf obo:OBIws_0000015 .
obo:OBI_0000973 a rdfs:Class ;
rdfs:label "sequence data"@en ;
rdfs:comment """A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
""" ;
rdfs:subClassOf obo:IAO_0000109 .
obo:OBI_0000932 a rdfs:Class ;
rdfs:label "material separation device" ;
rdfs:comment "A device with a separation function realized in a planed process" ;
rdfs:subClassOf obo:OBI_0000968 .
obo:IAO_0000577 a rdfs:Class ;
rdfs:label "centrally registered identifier symbol"@en ;
rdfs:comment "A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry."@en ;
rdfs:subClassOf obo:IAO_0000028 .
a rdfs:Class ;
rdfs:label "taxonomic rank" ;
rdfs:subClassOf obo:IAO_0000109 .
obo:OBI_0001852 a rdfs:Class ;
rdfs:label "paired-end library preparation"@en ;
rdfs:comment "A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process. " ;
rdfs:subClassOf obo:OBI_0000711 .
obo:OBI_0000070 a rdfs:Class ;
rdfs:label "assay"@en ;
rdfs:comment "A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies."@en ;
rdfs:subClassOf obo:OBI_0000011 .
obo:CL_0000000 a rdfs:Class ;
rdfs:label "cell" ;
rdfs:comment "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." ;
rdfs:subClassOf obo:BFO_0000040 .
obo:CL_0000127 a rdfs:Class ;
rdfs:label "astrocyte" ;
rdfs:comment "A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from 'star' cells) are irregularly shaped with many long processes, including those with 'end feet' which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and 'reactive astrocytes' (along with microglia) respond to injury." ;
rdfs:subClassOf obo:CL_0000000 .
a rdfs:Class ;
rdfs:label "transcriptome" ;
rdfs:comment "The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells." ;
rdfs:subClassOf obo:BFO_0000040 .
obo:OBI_0001185 a rdfs:Class ;
rdfs:label "selectively maintained organism"@en ;
rdfs:comment "An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms" ;
rdfs:subClassOf obo:OBI_0100026 .
obo:OBI_0002477 a rdfs:Class ;
rdfs:label "reference genome role"@en ;
rdfs:comment "A reference substance role that is played by a reference genome when used during sequence alignment."@en ;
rdfs:subClassOf obo:OBI_0000025 .
obo:OBI_0002486 a rdfs:Class ;
rdfs:label "verse algorithm"@en ;
rdfs:comment "An alignment counting algorithm that assigns gene features to genomic alignments using a hierarchical assignment scheme, which allows simultaneous quantification of multiple feature types or annotation levels without repeatedly assigning reads."@en ;
rdfs:subClassOf obo:OBI_0002466 .
obo:OMIABIS_0001039 a rdfs:Class ;
rdfs:label "date of specimen collection"@en ;
rdfs:comment "A data item that indicates the time when the collection of a specimen occurred."@en ;
rdfs:subClassOf obo:IAO_0000027 .
obo:BFO_0000023 a rdfs:Class ;
rdfs:label "role"@en ;
rdfs:subClassOf obo:BFO_0000017 .
obo:NCIT_C20181 a rdfs:Class ;
rdfs:label "Conceptual Entity" ;
rdfs:comment "An organizational header for concepts representing mostly abstract entities." .
a rdfs:Class ;
rdfs:label "replicate" ;
rdfs:comment "A role played by a a biological sample in the context of an experiment where the intent is that biological or technical variation is measured." ;
rdfs:subClassOf obo:BFO_0000023 .
obo:OBI_0002475 a rdfs:Class ;
rdfs:label "number of PCR cycles during library construction"@en ;
rdfs:comment "A data item that is the number of PCR cycles used during the construction of a sequencing library."@en ;
rdfs:subClassOf obo:IAO_0000027 .
obo:OBI_0002488 a rdfs:Class ;
rdfs:label "pipette"@en ;
rdfs:comment "A device that is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser."@en ;
rdfs:subClassOf obo:OBI_0000968 .
obo:OBI_0001271 a rdfs:Class ;
rdfs:label "RNA-seq assay"@en ;
rdfs:comment "An assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance"@en ;
rdfs:subClassOf obo:OBI_0600047 .
a rdfs:Class ;
rdfs:label "CEL data file format" ;
rdfs:comment "CEL data file format describes the format used in a CEL file for storing the results of the intensity calculations on the pixel values of a DAT file. This includes an intensity value, standard deviation of the intensity, the number of pixels used to calculate the intensity value, a flag to indicate an outlier as calculated by the algorithm and a user defined flag indicating the feature should be excluded from future analysis. The file stores the previously stated data for each feature on the probe array." ;
rdfs:subClassOf obo:IAO_0000098 .
obo:IAO_0000030 a rdfs:Class ;
rdfs:label "information content entity"@en ;
rdfs:comment "A generically dependent continuant that is about some thing."@en ;
rdfs:subClassOf obo:BFO_0000031 .
obo:ORNASEQ_0000007 a rdfs:Class ;
rdfs:label "library preparation protocol"@en ;
rdfs:subClassOf obo:OBI_0000272 .
obo:OBI_0000103 a rdfs:Class ;
rdfs:label "principal investigator role"@en ;
rdfs:comment "a responsible party role played by a person responsible for the overall conduct of a study"@en ;
rdfs:subClassOf obo:OBI_0000102 .
obo:OBI_0002471 a rdfs:Class ;
rdfs:label "date process started"@en ;
rdfs:comment "A data item that is the date when a process was initiated."@en ;
rdfs:subClassOf obo:IAO_0000027 .
obo:OBI_0000272 a rdfs:Class ;
rdfs:label "protocol"@en ;
rdfs:comment "A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process."@en ;
rdfs:subClassOf obo:IAO_0000104 .
obo:ORNASEQ_0000002 a rdfs:Class ;
rdfs:label "date of specimen library preparation"@en ;
rdfs:subClassOf obo:OBI_0002471 .
a rdfs:Class ;
rdfs:label "BAM format" ;
rdfs:comment "BAM is the compressed binary version of the Sequence Alignment/Map (SAM) format" ;
rdfs:subClassOf obo:IAO_0000098 .
obo:GENEPIO_0000085 a rdfs:Class ;
rdfs:label "library preparation kit" ;
rdfs:comment "Packaged kits (containing adapters, indexes, enzymes, buffers etc), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids." ;
rdfs:subClassOf obo:OBI_0000047 .
obo:BFO_0000001 a rdfs:Class ;
rdfs:label "entity"@en .
obo:NCBITaxon_9606 a rdfs:Class ;
rdfs:label "Homo sapiens" ;
rdfs:subClassOf obo:OBI_0100026 .
obo:ORNASEQ_0000013 a rdfs:Class ;
rdfs:label "specimen harvest source type"@en ;
rdfs:subClassOf obo:BFO_0000040 .
obo:BFO_0000004 a rdfs:Class ;
rdfs:label "independent continuant"@en ;
rdfs:comment "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en ;
rdfs:subClassOf obo:BFO_0000002 .
obo:BFO_0000015 a rdfs:Class ;
rdfs:label "process"@en ;
rdfs:comment "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en ;
rdfs:subClassOf obo:BFO_0000003 .
obo:OBI_0400099 a rdfs:Class ;
rdfs:label "flow cytometer sorter"@en ;
rdfs:comment "A flow_cytometer_sorter is a flow_cytometer that analyzes and separates or sorts particles passing through (based on properties measured during analysis) to collect cells of interest."@en ;
rdfs:subClassOf obo:OBI_0000932 .
obo:ORNASEQ_0000008 a rdfs:Class ;
rdfs:label "number of flow cell lanes"@en ;
rdfs:subClassOf obo:IAO_0000027 .
obo:TAXRANK_0000006 a rdfs:Class ;
rdfs:label "species" ;
rdfs:subClassOf obo:TAXRANK_0000000 .
obo:GENEPIO_0000069 a rdfs:Class ;
rdfs:label "sequencing run date"@en ;
rdfs:comment "date the sequencing run was performed"@en ;
rdfs:subClassOf obo:IAO_0000027 .
obo:OBI_0002482 a rdfs:Class ;
rdfs:label "specimen harvest quantity"@en ;
rdfs:comment "A scalar measurement datum that indicates the amount of specimen collected."@en ;
rdfs:subClassOf obo:IAO_0000032 .
obo:OBI_0002469 a rdfs:Class ;
rdfs:label "base calling application"@en ;
rdfs:comment "A base-calling application that implments a base-calling algorithm to convert BCL (binary base call) files, (e.g., those generated by Illumina sequencing systems) to standard FASTQ file formats for downstream analysis."@en ;
rdfs:subClassOf obo:IAO_0000594 .
obo:CHEBI_23367 a rdfs:Class ;
rdfs:label "molecular entity" ;
rdfs:comment "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:BFO_0000040 .
obo:OBI_0000722 a rdfs:Class ;
rdfs:label "paired-end library" ;
rdfs:comment "is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs" ;
rdfs:subClassOf obo:OBI_0000047 .
obo:OBI_0002127 a rdfs:Class ;
rdfs:label "single cell specimen"@en ;
rdfs:comment "A cell specimen that contains only one cell." ;
rdfs:subClassOf obo:OBI_0001468 .
obo:OBI_0002487 a rdfs:Class ;
rdfs:label "microraft"@en ;
rdfs:comment "A material separation device also commerically known as Isoraft, that is used to isolate single cells."@en ;
rdfs:subClassOf obo:OBI_0000932 .
obo:IAO_0000104 a rdfs:Class ;
rdfs:label "plan specification"@en ;
rdfs:comment "A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified."@en ;
rdfs:subClassOf obo:IAO_0000033 .
obo:OBI_0000011 a rdfs:Class ;
rdfs:label "planned process"@en ;
rdfs:comment "A processual entity that realizes a plan which is the concretization of a plan specification."@en ;
rdfs:subClassOf obo:BFO_0000015 .
obo:OBI_0002478 a rdfs:Class ;
rdfs:label "reference genome-transcriptome alignment algorithm"@en ;
rdfs:comment "An algorithm that attempts to align a nucleic acid sequence to a reference genome and transcriptome."@en ;
rdfs:subClassOf obo:IAO_0000064 .
obo:IAO_0000033 a rdfs:Class ;
rdfs:label "directive information entity"@en ;
rdfs:comment "An information content entity whose concretizations indicate to their bearer how to realize them in a process."@en ;
rdfs:subClassOf obo:IAO_0000027 .
obo:BFO_0000002 a rdfs:Class ;
rdfs:label "continuant"@en ;
rdfs:subClassOf obo:BFO_0000001 .
obo:OBI_0000181 a rdfs:Class ;
rdfs:label "population"@en ;
rdfs:comment "a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area"@en ;
rdfs:subClassOf obo:BFO_0000040 .
obo:CL_0000540 a rdfs:Class ;
rdfs:label "neuron" ;
rdfs:comment "The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." ;
rdfs:subClassOf obo:CL_0000000 .
obo:CL_0000449 a rdfs:Class ;
rdfs:label "brown fat cell" ;
rdfs:comment "A cell from the thermogenic form of adipose tissue found in many species, particularly in newborns and hibernating mammals, but also in lesser amounts in adults of other mammals including humans. Brown fat is capable of rapid liberation of energy and seems to be important in the maintenance of body temperature immediately after birth and upon waking from hibernation." ;
rdfs:subClassOf obo:CL_0000000 .
obo:OBI_0000711 a rdfs:Class ;
rdfs:label "library preparation" ;
rdfs:comment "is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors." ;
rdfs:subClassOf obo:OBI_0000094 .
obo:IAO_0000064 a rdfs:Class ;
rdfs:label "algorithm"@en ;
rdfs:comment "A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata."@en ;
rdfs:subClassOf obo:IAO_0000104 .
obo:OBI_0002463 a rdfs:Class ;
rdfs:label "SIRV RNA spike-in"@en ;
rdfs:comment "A processed material that consists of transcript isoforms of 7 spike-in RNA variant (SIRV) genes and possibly the 92 External RNA Controls Consortium (ERCC) RNA spike-in genes."@en ;
rdfs:subClassOf obo:OBI_0000047 .
obo:ORNASEQ_0000014 a rdfs:Class ;
rdfs:label "specimen harvest source unit"@en ;
rdfs:subClassOf obo:BFO_0000040 .
a rdfs:Class ;
rdfs:label "genome" ;
rdfs:comment "A genome is the full genetic content of an organism, contained in either DNA or RNA (such as for viruses)." ;
rdfs:subClassOf obo:BFO_0000040 .
obo:OBI_0100026 a rdfs:Class ;
rdfs:label "organism"@en ;
rdfs:comment "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs."@en ;
rdfs:subClassOf obo:BFO_0000040 .
obo:NCIT_C25198 a rdfs:Class ;
rdfs:label "Record" ;
rdfs:comment "Anything (e.g., a document) providing permanent evidence of or information about past events." ;
rdfs:subClassOf obo:NCIT_C20181 .
obo:OBI_0002474 a rdfs:Class ;
rdfs:label "material sequencing library preparation role"@en ;
rdfs:comment "A worker role played by the person who performs the library preparation process to generate a sequencing library for a sample to be sequenced."@en ;
rdfs:subClassOf obo:OBI_0000116 .
obo:NCIT_C25402 a rdfs:Class ;
rdfs:label "Accession Number" ;
rdfs:comment "A control number unique to an object. It is used to identify the object among other objects in a collection." ;
rdfs:subClassOf obo:NCIT_C70663 .
obo:OBI_0000018 a rdfs:Class ;
rdfs:label "material supplier role"@en ;
rdfs:comment "a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation."@en ;
rdfs:subClassOf obo:OBI_0000947 .
obo:OBI_0002466 a rdfs:Class ;
rdfs:label "alignment counting algorithm" ;
rdfs:comment "An algorithm used to assign aligned sequence reads, resulting from a reference genome transcriptome alignment algorithm, to sequence features (e.g. genes or transcripts)."@en ;
rdfs:subClassOf obo:IAO_0000064 .
obo:ORNASEQ_0000003 a rdfs:Class ;
rdfs:label "enzymatic amplification protocol"@en ;
rdfs:subClassOf obo:OBI_0000272 .
obo:OBI_0000249 a rdfs:Class ;
rdfs:label "technical replicate role"@en ;
rdfs:comment "technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay" ;
rdfs:subClassOf obo:OBI_0000220 .
obo:BFO_0000020 a rdfs:Class ;
rdfs:label "specifically dependent continuant"@en ;
rdfs:comment "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en ;
rdfs:subClassOf obo:BFO_0000002 .
obo:OBI_0000415 a rdfs:Class ;
rdfs:label "polymerase chain reaction"@en ;
rdfs:comment "PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified."@en ;
rdfs:subClassOf obo:OBI_0600058 .
obo:OBI_0000245 a rdfs:Class ;
rdfs:label "organization"@en ;
rdfs:comment "An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members."@en ;
rdfs:subClassOf obo:BFO_0000040 .
obo:OBI_0400103 a rdfs:Class ;
rdfs:label "DNA sequencer"@en ;
rdfs:comment "A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences."@en ;
rdfs:subClassOf obo:OBI_0000832 .
obo:OBI_0002470 a rdfs:Class ;
rdfs:label "bcl2fastq software application"@en ;
rdfs:comment "A base calling application that implments a base calling algorithm to convert BCL (binary base call) files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis."@en ;
rdfs:subClassOf obo:OBI_0002469 .
obo:IAO_0000109 a rdfs:Class ;
rdfs:label "measurement datum"@en ;
rdfs:comment "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device."@en ;
rdfs:subClassOf obo:IAO_0000027 .
obo:OBI_0000091 a rdfs:Class ;
rdfs:label "detector reagent role"@en ;
rdfs:comment "a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus." ;
rdfs:subClassOf obo:BFO_0000023 .
obo:ORNASEQ_0000010 a rdfs:Class ;
rdfs:label "pairwise sequence alignment application"@en ;
rdfs:subClassOf obo:IAO_0000594 .
obo:OBIws_0000106 a rdfs:Class ;
rdfs:label "sequence data format specification" ;
rdfs:comment "A data format specification for molecular sequence feature information." ;
rdfs:subClassOf obo:IAO_0000098 .
obo:OBI_0002481 a rdfs:Class ;
rdfs:label "single-end library"@en ;
rdfs:comment "A cDNA library that is a collection of short tags from only one end of DNA fragments."@en ;
rdfs:subClassOf obo:OBI_0000047 .
obo:OBIws_0000192 a rdfs:Class ;
rdfs:label "RNA sequence data"@en ;
rdfs:comment "A sequence data that is about the primary structure of RNA."@en ;
rdfs:subClassOf obo:OBI_0000973 .
obo:ORNASEQ_0000015 a rdfs:Class ;
rdfs:label "star"@en ;
rdfs:subClassOf obo:ORNASEQ_0000010 .
obo:NCIT_C25364 a rdfs:Class ;
rdfs:label "Identifier" ;
rdfs:comment "One or more characters used to identify, name, or characterize the nature, properties, or contents of a thing." ;
rdfs:subClassOf obo:NCIT_C19498 .
obo:ORNASEQ_0000009 a rdfs:Class ;
rdfs:label "number of flow cells"@en ;
rdfs:subClassOf obo:IAO_0000027 .
obo:SO_0001505 a rdfs:Class ;
rdfs:label "reference_genome" ;
rdfs:comment "A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly." ;
rdfs:subClassOf .
obo:OBIws_0000015 a rdfs:Class ;
rdfs:label "pairwise sequence alignment algorithm"@en ;
rdfs:comment "An algorithm that attempts to align two molecular sequences (nucleic acid or protein sequences)." ;
rdfs:subClassOf obo:IAO_0000064 .
obo:GO_0030425 a rdfs:Class ;
rdfs:label "dendrite" ;
rdfs:comment "A neuron projection that has a short, tapering, morphology. Dendrites receive and integrate signals from other neurons or from sensory stimuli, and conduct nerve impulses towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body." ;
rdfs:subClassOf obo:GO_0044464 .
obo:OBI_0001895 a rdfs:Class ;
rdfs:label "specimen collector"@en ;
rdfs:comment "A person who collects the specimen" ;
rdfs:subClassOf obo:NCBITaxon_9606 .
obo:IAO_0000010 a rdfs:Class ;
rdfs:label "software"@en ;
rdfs:comment """Software is a plan specification composed of a series of instructions that can be
interpreted by or directly executed by a processing unit."""@en ;
rdfs:subClassOf obo:IAO_0000104 .
obo:OBI_0000626 a rdfs:Class ;
rdfs:label "DNA sequencing" ;
rdfs:comment "DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument." ;
rdfs:subClassOf obo:OBI_0600047 .
obo:ORNASEQ_0000011 a rdfs:Class ;
rdfs:label "region of material anatomical entity"@en ;
rdfs:subClassOf obo:UBERON_0000465 .
obo:IAO_0000032 a rdfs:Class ;
rdfs:label "scalar measurement datum"@en ;
rdfs:comment "a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label."@en ;
rdfs:subClassOf obo:IAO_0000109 .
obo:OBI_0000202 a rdfs:Class ;
rdfs:label "investigation agent role" ;
rdfs:comment "A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing."@en ;
rdfs:subClassOf obo:BFO_0000023 .
obo:GO_0005739 a rdfs:Class ;
rdfs:label "mitochondrion" ;
rdfs:comment "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." ;
rdfs:subClassOf obo:GO_0044464 .
a rdfs:Class ;
rdfs:label "FASTQ format" ;
rdfs:comment "FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores." ;
rdfs:subClassOf obo:IAO_0000098 .
obo:OBI_0600058 a rdfs:Class ;
rdfs:label "enzymatic amplification"@en ;
rdfs:comment "the use of enzymes to increase the number of molecules of a biomaterial"@en ;
rdfs:subClassOf obo:OBI_0000094 .
obo:OBI_0000220 a rdfs:Class ;
rdfs:label "reference subject role"@en ;
rdfs:comment "a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference"@en ;
rdfs:subClassOf obo:OBI_0000097 .
obo:OBI_0001891 a rdfs:Class ;
rdfs:label "sequencing facility organization"@en ;
rdfs:comment "An organization that provides sequence determination service" ;
rdfs:subClassOf obo:OBI_0000245 .
obo:OBI_0600047 a rdfs:Class ;
rdfs:label "sequencing assay"@en ;
rdfs:comment "the use of a chemical or biochemical means to infer the sequence of a biomaterial"@en ;
rdfs:subClassOf obo:OBI_0000070 .
obo:CHEBI_16991 a rdfs:Class ;
rdfs:label "deoxyribonucleic acid" ;
rdfs:comment "High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms." ;
rdfs:subClassOf obo:CHEBI_23367 .
obo:OBI_0000116 a rdfs:Class ;
rdfs:label "worker role"@en ;
rdfs:comment "a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline"@en ;
rdfs:subClassOf obo:OBI_0000202 .
obo:OBIws_0000140 a rdfs:Class ;
rdfs:label "BLASTn" ;
rdfs:comment "A BLAST algorithm that searches/aligns a nucleotide query sequence against a nucleotide database at a nucleotide level." ;
rdfs:subClassOf obo:OBIws_0000088 .
obo:ORNASEQ_0000016 a rdfs:Class ;
rdfs:label "TIVA tag"@en ;
rdfs:subClassOf obo:ORNASEQ_0000012 .
obo:CL_2000029 a rdfs:Class ;
rdfs:label "central nervous system neuron" ;
rdfs:comment "Any neuron that is part of a central nervous system." ;
rdfs:subClassOf obo:CL_0000540 .
obo:OBI_0001850 a rdfs:Class ;
rdfs:label "transcript analysis by paired-end tag sequencing"@en ;
rdfs:comment "An assay that incorporates Paired-End Tags and sequencing technology to determine transcripts, gene structures, and gene expressions." ;
rdfs:subClassOf obo:OBI_0600047 .
obo:ORNASEQ_0000005 a rdfs:Class ;
rdfs:label "Illumina TruSeq Rapid SBS Kit v2"@en ;
rdfs:subClassOf obo:GENEPIO_0000081 .
obo:BFO_0000003 a rdfs:Class ;
rdfs:label "occurrent"@en ;
rdfs:subClassOf obo:BFO_0000001 .
obo:OBI_0002462 a rdfs:Class ;
rdfs:label "ERCC RNA spike-in" ;
rdfs:comment "A processed material developed by the External RNA Controls Consortium (ERCC) that consists of 92 transcripts, derived and traceable from NIST-certified DNA plasmids."@en ;
rdfs:subClassOf obo:OBI_0000047 .
obo:OBI_0001967 a rdfs:Class ;
rdfs:label "multiplexing sequence identifier"@en ;
rdfs:comment "A multiplexing sequence identifier is a nucleic acid sequence which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library"@en ;
rdfs:subClassOf obo:CHEBI_16991 .
obo:OBI_0002473 a rdfs:Class ;
rdfs:label "material amplification role"@en ;
rdfs:comment "A worker role played by the person who runs the enzymatic amplifying process."@en ;
rdfs:subClassOf obo:OBI_0000116 .
obo:ORNASEQ_0000004 a rdfs:Class ;
rdfs:label "experiment name"@en ;
rdfs:subClassOf obo:IAO_0000028 .
obo:OBI_0100051 a rdfs:Class ;
rdfs:label "specimen"@en ;
rdfs:comment "A material entity that has the specimen role."@en ;
rdfs:subClassOf obo:BFO_0000040 .
obo:OBI_0002485 a rdfs:Class ;
rdfs:label "transcript analysis by single-end sequencing"@en ;
rdfs:comment "A sequencing assay that incorporates single-end reads and sequencing technology to determine transcripts, gene structures, and gene expressions."@en ;
rdfs:subClassOf obo:OBI_0600047 .
obo:GENEPIO_0001170 a rdfs:Class ;
rdfs:label "organism datum"@en ;
rdfs:subClassOf obo:IAO_0000109 .
obo:OBI_0000025 a rdfs:Class ;
rdfs:label "reference substance role"@en ;
rdfs:comment "a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference."@en ;
rdfs:subClassOf obo:BFO_0000023 .
obo:OBI_0001494 a rdfs:Class ;
rdfs:label "linear amplification"@en ;
rdfs:comment "An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template." ;
rdfs:subClassOf obo:OBI_0600058 .
obo:OMIABIS_0000100 a rdfs:Class ;
rdfs:label "study principle investigator or responsible"@en ;
rdfs:comment "The principle investigtor or responsible person for a study or a sample collection."@en ;
rdfs:subClassOf obo:NCBITaxon_9606 .
obo:IAO_0000594 a rdfs:Class ;
rdfs:label "software application"@en ;
rdfs:comment "A software application is software that can be directly executed by some processing unit."@en ;
rdfs:subClassOf obo:IAO_0000010 .
obo:BFO_0000031 a rdfs:Class ;
rdfs:label "generically dependent continuant"@en ;
rdfs:comment "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en ;
rdfs:subClassOf obo:BFO_0000002 .
obo:GO_0044297 a rdfs:Class ;
rdfs:label "cell body" ;
rdfs:comment "The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections." ;
rdfs:subClassOf obo:GO_0044464 .
a rdfs:Class ;
rdfs:comment "An unconstrained type or object" .
obo:OBI_0001140 a rdfs:Class ;
rdfs:label "spike-in quality control role"@en ;
rdfs:comment "a reference substance role that is borne by a material entity with a known amount which is mixed into the evaluant of assays for quality control or data normalization purposes"@en ;
rdfs:subClassOf obo:OBI_0000025 .
obo:OBI_0001169 a rdfs:Class ;
rdfs:label "age since birth measurement datum"@en ;
rdfs:comment "An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother." ;
rdfs:subClassOf obo:OBI_0001167 .
obo:OBI_0000659 a rdfs:Class ;
rdfs:label "specimen collection process" ;
rdfs:comment "A planned process with the objective of collecting a specimen." ;
rdfs:subClassOf obo:OBI_0000011 .
obo:GO_0005575 a rdfs:Class ;
rdfs:label "cellular_component" ;
rdfs:comment "A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome)." ;
rdfs:subClassOf obo:BFO_0000040 .
obo:CL_0000746 a rdfs:Class ;
rdfs:label "cardiac muscle cell" ;
rdfs:comment "Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei." ;
rdfs:subClassOf obo:CL_0000000 .
obo:IAO_0000027 a rdfs:Class ;
rdfs:label "data item"@en ;
rdfs:comment "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en ;
rdfs:subClassOf obo:IAO_0000030 .
obo:OBI_0002480 a rdfs:Class ;
rdfs:label "sequencing library input quantity measurement datum"@en ;
rdfs:comment "A scalar measurement datum that indicates the amount of sequencing library used as input for a sequencer."@en ;
rdfs:subClassOf obo:IAO_0000032 .
obo:OBI_0001959 a rdfs:Class ;
rdfs:label "sequencing library multiplexing"@en ;
rdfs:comment "a planned process which consists in running a set of samples as a pool in one single instrument run of data acquisition process while retaining the ability to associate individual results to each of the individual input samples thanks to the use of a multiplex identifier, introduced during the ligation step of the individual library preparation and specific to a given sample."@en ;
rdfs:subClassOf obo:OBI_0000094 .
obo:OBI_0001616 a rdfs:Class ;
rdfs:label "specimen identifier"@en ;
rdfs:comment "A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation."@en ;
rdfs:subClassOf obo:IAO_0000028 .
obo:OGMS_0000090 a rdfs:Class ;
rdfs:label "treatment" ;
rdfs:comment "A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder"@en ;
rdfs:subClassOf obo:OBI_0000011 .
obo:OBI_0000097 a rdfs:Class ;
rdfs:label "participant under investigation role"@en ;
rdfs:comment "A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected." ;
rdfs:subClassOf obo:BFO_0000023 .
obo:BFO_0000050 a rdf:Property ;
rdfs:label "part of"@en ;
rdfs:comment "a core relation that holds between a part and its whole"@en ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002131 .
obo:IAO_0000115 a rdf:Property ;
rdfs:label "textual definition" ;
rdfs:comment "English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software." ;
rdfs:range xsd:string .
obo:IAO_0000116 a rdf:Property ;
rdfs:label "editor note" ;
rdfs:comment "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en ;
rdfs:range xsd:string .
obo:IAO_0000117 a rdf:Property ;
rdfs:label "term editor" ;
rdfs:comment "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en ;
rdfs:range xsd:string .
obo:IAO_0000118 a rdf:Property ;
rdfs:label "alternative term"@en ;
rdfs:comment "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)"@en ;
rdfs:range xsd:string .
obo:IAO_0000119 a rdf:Property ;
rdfs:label "definition source" ;
rdfs:comment "formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en ;
rdfs:range xsd:string .
obo:IAO_0000412 a rdf:Property ;
rdfs:label "imported from"@en ;
rdfs:range xsd:string .
obo:RO_0000053 a rdf:Property ;
rdfs:label "bearer of"@en ;
rdfs:comment "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence"@en ;
rdfs:range .
obo:RO_0000056 a rdf:Property ;
rdfs:label "participates in"@en ;
rdfs:comment "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en ;
rdfs:range .
obo:RO_0002131 a rdf:Property ;
rdfs:label "overlaps"@en ;
rdfs:comment "x overlaps y if and only if there exists some z such that x has part z and z part of y" ;
rdfs:range xsd:string ;
rdfs:subPropertyOf obo:RO_0002323 .
obo:RO_0002323 a rdf:Property ;
rdfs:label "mereotopologically related to"@en ;
rdfs:comment "A mereological relationship or a topological relationship" ;
rdfs:range .