@prefix rdf: . @prefix owl: . @prefix rdfs: . @prefix xml: . @prefix xsd: . a owl:Ontology; owl:versionIRI ; "An ontology to represent genomics cohort attributes."; "Genomics Cohorts Knowledge Ontology"; ; rdfs:comment "The GECKO is maintained by the CINECA project, https://www.cineca-project.eu, and standardises attributes commonly used for genomics cohort description as well as individual-level data items. A series of tools is being developed to enable automated generation of harmonised data files based on a JSON schema mapping file. For more information please contact info@cineca-project.eu" . a owl:AnnotationProperty; rdfs:label "IHCC category" . a owl:AnnotationProperty; rdfs:label "IHCC browser label" . a owl:AnnotationProperty; rdfs:label "example of usage" . a owl:AnnotationProperty; rdfs:label "definition" . a owl:AnnotationProperty; rdfs:label "alternative term" . a owl:AnnotationProperty; rdfs:label "definition source" . a owl:AnnotationProperty; rdfs:label "has_alternative_id" . a owl:AnnotationProperty; rdfs:label "has_broad_synonym" . a owl:AnnotationProperty; rdfs:label "has_exact_synonym" . a owl:AnnotationProperty; rdfs:label "has_narrow_synonym" . a owl:AnnotationProperty; rdfs:label "has_related_synonym" . rdfs:comment a owl:AnnotationProperty; rdfs:label "comment" . rdfs:label a owl:AnnotationProperty; rdfs:label "label" . rdfs:seeAlso a owl:AnnotationProperty; rdfs:label "see also" . a owl:ObjectProperty; rdfs:label "part of" . a owl:ObjectProperty; rdfs:label "is about" . a owl:ObjectProperty; rdfs:label "inheres in" . a owl:Class; "a process of cell-division, \\ a beating of the heart"@en, "a process of meiosis"@en, "a process of sleeping"@en, "the course of a disease"@en, "the flight of a bird"@en, "the life of an organism"@en, "your process of aging."@en; "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:label "process" . a owl:Class; rdfs:subClassOf ; "an atom of element X has the disposition to decay to an atom of element Y"@en, "certain people have a predisposition to colon cancer"@en, "children are innately disposed to categorize objects in certain ways."@en, "the cell wall is disposed to filter chemicals in endocytosis and exocytosis"@en; rdfs:label "disposition" . a owl:Class; "the disposition of this piece of metal to conduct electricity."@en, "the disposition of your blood to coagulate"@en, "the function of your reproductive organs"@en, "the role of being a doctor"@en, "the role of this boundary to delineate where Utah and Colorado meet"@en; rdfs:label "realizable entity" . a owl:Class; "the ambient temperature of this portion of air"@en, "the color of a tomato"@en, "the length of the circumference of your waist"@en, "the mass of this piece of gold."@en, "the shape of your nose"@en, "the shape of your nostril"@en; rdfs:label "quality" . a owl:Class; rdfs:subClassOf ; "Manhattan Canyon)"@en, "a hole in the interior of a portion of cheese"@en, "a rabbit hole"@en, "an air traffic control region defined in the airspace above an airport"@en, "the Grand Canyon"@en, "the Piazza San Marco"@en, "the cockpit of an aircraft"@en, "the hold of a ship"@en, "the interior of a kangaroo pouch"@en, "the interior of the trunk of your car"@en, "the interior of your bedroom"@en, "the interior of your office"@en, "the interior of your refrigerator"@en, "the lumen of your gut"@en, "your left nostril (a fiat part – the opening – of your left nasal cavity)"@en; rdfs:label "site" . a owl:Class; "a flame"@en, "a forest fire"@en, "a human being"@en, "a hurricane"@en, "a photon"@en, "a puff of smoke"@en, "a sea wave"@en, "a tornado"@en, "an aggregate of human beings."@en, "an energy wave"@en, "an epidemic"@en, "the undetached arm of a human being"@en; rdfs:label "material entity" . a owl:Class; rdfs:label "immaterial entity" . a owl:Class; rdfs:subClassOf ; "questionnaire/survey data"; "physiological measurements"; rdfs:label "clinical measurement data item" . a owl:Class; rdfs:subClassOf ; "physiological measurements"; "circulation and respiration"; rdfs:label "cardiovascular measurement data item" . a owl:Class; rdfs:subClassOf ; "circulation and respiration"; "blood pressure"; rdfs:label "blood pressure measurement data item" . a owl:Class; rdfs:subClassOf ; "anthropometry"; "weight"; rdfs:label "body weight data item" . a owl:Class; rdfs:subClassOf ; "physiological measurements"; "anthropometry"; rdfs:label "body morphological measurement data item" . a owl:Class; rdfs:subClassOf ; "anthropometry"; "height"; rdfs:label "body height data item" . a owl:Class; rdfs:subClassOf ; "circulation and respiration"; "heart rate (HR)"; rdfs:label "pulse data item" . a owl:Class; rdfs:subClassOf ; "other questionnaire/survey data"; "cause of death"; "An information content entity indicating the cause of death for a participant in the study."; "Penn Group"; rdfs:label "cause of participant death" . a owl:Class; rdfs:subClassOf ; "healthcare information"; "routine clincial visits"; "a data item that is about an investigation and is the specified output of a data transformation that has only clinical visit data as input"@en; "EuPathDB"@en; rdfs:label "aggregated clinical visit information" . a owl:Class; rdfs:subClassOf ; "healthcare information"; "hospitalizations"; "an information content entity that is about a part of a health care encounter that occurs in a hospital facility"@en; "EuPathDB"@en; rdfs:label "hospitalization information" . a owl:Class; rdfs:subClassOf ; "socio-demographic and economic characteristics"; "occupation"; "An information content entity that is about an activity that realizes a social role and is often performed for payment."@en; rdfs:label "occupation" . a owl:Class; rdfs:subClassOf ; "socio-demographic and economic characteristics"; "marital status"; "a categorical value specification that is about a human being and specifies whether that human being is joined to another human being in marriage"@en; "EuPathDB, BFO's 'relational quality' examples"@en; rdfs:label "marital status" . a owl:Class; rdfs:subClassOf ; "questionnaire/survey data"; "healthcare information"; "An information content entity about healthcare that is private or public."; rdfs:label "healthcare information" . a owl:Class; rdfs:subClassOf ; "questionnaire/survey data"; "physical environment"; "environmental system associated with the dwelling used by humans."; "Penn Group"; rdfs:label "environment associated with human dwelling" . a owl:Class; rdfs:subClassOf ; "basic cohort attributes"; "timeline"; "A directive information entity that specifies the sequence in which a series of events occurred or will occur."; rdfs:label "timeline" . a owl:Class; owl:equivalentClass _:5; rdfs:subClassOf ; "basic cohort attributes"; "population data"; "A data item that is about a population of organisms."; rdfs:label "population data item" . _:5 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:subClassOf , _:15; "population data"; "location"; "A population data item that is about the geographical location of a population of organisms."; rdfs:label "population location" . _:15 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:subClassOf , _:25; "population data"; "num. participants"; "A sample size that is about the count of individual organisms in a population."; rdfs:label "population size" . _:25 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; owl:equivalentClass _:35; rdfs:subClassOf ; "basic cohort attributes"; "demographic data"; "A quality which inheres in a population of organisms."; rdfs:label "population quality" . _:35 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:subClassOf ; "demographic data"; "sex(es) studied in cohort"; "A population quality concerning the sex or sexes of the population."; rdfs:label "population sex or sexes" . a owl:Class; rdfs:subClassOf ; "demographic data"; "gender(s) studied in cohort"; "A population quality concerning the gender or genders of the population."; rdfs:label "population gender or genders" . a owl:Class; rdfs:subClassOf ; "demographic data"; "age range"; "A population quality concerning the age range of a population."; rdfs:label "population age range" . a owl:Class; rdfs:subClassOf ; "basic cohort attributes"; "data collection events"; "A planned process that is a part of an investigation in which raw data is collected."; rdfs:label "data collection" . a owl:Class; rdfs:subClassOf ; "blood"; "fasting or non-fasting"; "Blood that is collected from an organism which has been fasting for a given amount of time."; rdfs:label "blood collected from fasting subject" . a owl:Class; rdfs:subClassOf ; "biosample"; "storage method"; "A storage process for a biosample collected from an organism."; rdfs:label "biosample storage" . a owl:Class; rdfs:subClassOf ; "laboratory measures"; "genomics"; "An assay that investigates the genome or genomes of an individual organism or population of organisms."; rdfs:comment "Merged GECKO 'data type' into 'genomics'."; rdfs:label "genomic assay" . a owl:Class; rdfs:subClassOf ; "genomics"; "Microbiome markers (rRNA, etc)"; "A genomic assay that profiles the microorganisms present in a sample."; rdfs:comment "Potential new OBI request"; rdfs:label "microbiome sequencing assay" . a owl:Class; rdfs:subClassOf ; "genomics"; "eQTL (Cis eQTLs and/or Trans eQTLs)"; "A genomic assay that identifies genetic loci and candidate genes correlated with phenotypes."; "PMID:27964730"; rdfs:comment "Potential new OBI request"; rdfs:label "eQTL analysis" . a owl:Class; rdfs:subClassOf ; "biosample"; "sample size"; "A count of the number of biosamples collected for an investigation."; rdfs:label "biosample size" . a owl:Class; rdfs:subClassOf ; "biosample"; "processing method"; "A material processing which prepares a biosample for investigation."; rdfs:label "biosample processing" . a owl:Class; rdfs:subClassOf ; "survey administration"; "unique identifiers"; "An identifier that is guaranteed to be unique among all identifiers in a particular domain."; "Wikipedia:Unique_identifier"; rdfs:label "unique identifier" . a owl:Class; rdfs:subClassOf ; "socio-demographic and economic characteristics"; "gender"; "An organismal quality inhering in a bearer by virtue of the bearer's preference towards a range of characteristics pertaining to, and differentiating between, masculinity and femininity."; "Wikipedia:Gender|PATO:0000047"; rdfs:label "gender" . a owl:Class; rdfs:subClassOf ; "socio-demographic and economic characteristics"; "ethnicity/race"; "An organismal quality inhering in a bearer by virtue of the bearer's identification with a group of other individuals on the basis of presumed similarities such as language or common ancestry."; "Wikipedia:Ethnic_group"; rdfs:label "ethnicity" . a owl:Class; rdfs:subClassOf ; "socio-demographic and economic characteristics"; "birthplace"; "A geographical location in which an individual was born."; rdfs:label "birthplace location" . a owl:Class; rdfs:subClassOf ; "socio-demographic and economic characteristics"; "residence"; "A geographical location in which an individual currently resides."; rdfs:label "residence location" . a owl:Class; rdfs:subClassOf ; "socio-demographic and economic characteristics"; "education"; "An organismal quality inhering in a bearer by virute of the bearer's highest level of formal education completed."; rdfs:label "education level" . a owl:Class; rdfs:subClassOf ; "socio-demographic and economic characteristics"; "family and household structure"; "Information that is about the structure of an individual's family and/or household."; rdfs:label "family and household structure" . a owl:Class; rdfs:subClassOf ; "questionnaire/survey data"; "lifestyle and behaviours"; "A clinical history that is about the lifestyle and behaviors of an individual which may impact health outcomes."; rdfs:label "lifestyle history" . a owl:Class; rdfs:subClassOf ; "lifestyle and behaviours"; "tobacco use history"; "A lifestyle history that is about the tobacco use or exposure of an individual."; rdfs:label "tobacco use history" . a owl:Class; rdfs:subClassOf ; "lifestyle and behaviours"; "alcohol use history"; "A lifestyle history that is about the alcohol consumption of an individual."; rdfs:label "alcohol use history" . a owl:Class; rdfs:subClassOf ; "lifestyle and behaviours"; "sleep history"; "A lifestyle history that is about the sleep quality and duration of an individual."; rdfs:label "sleep history" . a owl:Class; rdfs:subClassOf ; "lifestyle and behaviours"; "dietary history"; "A lifestyle history that is about the diet and nutrition of an individual."; rdfs:label "nutritional history" . a owl:Class; rdfs:subClassOf ; "healthcare information"; "physician/practitioner info"; "A textual entity that contains contact details for an individual's physician, which may include: name, phone number, address, etc."; rdfs:label "physician contact textual entity" . a owl:Class; rdfs:subClassOf ; "questionnaire/survey data"; "non-pharmacological interventions"; "A treatment history that is about any non-pharamacological treatments such as surgery or physical therapy."; rdfs:label "non-pharmacological treatment history" . a owl:Class; rdfs:subClassOf ; "non-pharmacological interventions"; "surgical interventions"; "A clinical history that is about surgical operations performed on an individual."; rdfs:label "surgical history" . a owl:Class; rdfs:subClassOf ; "questionnaire/survey data"; "medication"; "A clinical history that is about the prescription drugs taken by an individual."; rdfs:label "prescription drug history" . a owl:Class; rdfs:subClassOf , _:45; "medication"; "associated disease(s)"; "Information that is about the disease treated by a drug prescribed to an individual."; rdfs:label "disease treated by prescription drug" . _:45 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:subClassOf ; "medication"; "drug response(s)"; "A biological process that results from a drug stimulus."; rdfs:label "response to medication" . a owl:Class; rdfs:subClassOf ; "statistics"; "summary statistics for additional data from federated sources"; "A statistic that summarizes a set of federated data."; rdfs:label "summary statistic for federated data" . a owl:Class; rdfs:subClassOf ; "lifestyle and behaviours"; "recreational drug history"; "A lifestyle history that is about the use of unprescribed and/or non-prescription drugs."; rdfs:label "recreational drug history" . a owl:Class; rdfs:subClassOf ; "lifestyle and behaviours"; "physical activity history"; "A lifestyle history that is about the typical physical activity of an individual."; rdfs:label "physical activity history" . a owl:Class; rdfs:subClassOf ; "A count which represents the subset of a collection chosen for an investigation, survey, or assay."; rdfs:label "sample size" . a owl:Class; rdfs:subClassOf , _:55; "biosample"; "availability"; "An availability textual entity that is about a substance from an organism (a biosample)."; rdfs:label "biosample availability textual entity" . _:55 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:subClassOf ; "other questionnaire/survey data"; "reproduction"; "A clinical history that is about pregnancy, maternity, fertility, menses, and any other reproductive aspect."; rdfs:label "reproductive history" . a owl:Class; rdfs:subClassOf ; "A clinical history that is about any treatment (surgical, prescription, etc.) for disease, disorder, or symptom."; rdfs:label "treatment history" . a owl:Class; rdfs:subClassOf ; "questionnaire/survey data"; "cognitive and psychological measurements"; "A measurement datum of some aspect of human psychology."; "EFO:0009095"; rdfs:comment "See also EFO:0009095"; rdfs:label "psychological measurement" . a owl:Class; rdfs:subClassOf ; "cognitive and psychological measurements"; "cognitive functioning"; "A psychological measurement of some aspect of intellectual functions such as memory, problem solving, and comprehension."; "Wikipedia:Cognition"; rdfs:label "cognitive measurement" . a owl:Class; rdfs:subClassOf ; "cognitive and psychological measurements"; "personality"; "A psychological measurement of a person's individual sets of behaviours, cognitions, and emotional patterns."; "Wikipedia:Personality"; rdfs:label "personality measurement" . a owl:Class; rdfs:subClassOf ; "cognitive and psychological measurements"; "psychological distress and emotions"; "A biological process that results from neurophysiological changes in response to internal and external events."; "Wikipedia:Emotion"; rdfs:label "emotion" . a owl:Class; rdfs:subClassOf ; "lifestyle and behaviours"; "oral health history"; "A lifestyle history that is about oral health and hygiene."; rdfs:label "oral health history" . a owl:Class; rdfs:subClassOf ; "non-pharmacological interventions"; "psychological interventions"; "A non-pharmacological treatment history that is about psychological treatments such as counselling."; rdfs:label "psychological treatment history" . a owl:Class; rdfs:subClassOf ; "non-pharmacological interventions"; "radiological interventions"; "A non-pharmacological treatment history that is about use of radiology for treatment of disease, disorder, or symptom."; rdfs:label "radiological treatment history" . a owl:Class; rdfs:subClassOf ; "non-pharmacological interventions"; "physical therapy interventions"; "A non-pharmacological treatment history that is about physical therapy treatments such as physical rehabilitation."; rdfs:label "physical therapy history" . a owl:Class; rdfs:subClassOf ; "perception of health and quality of life"; "perception of health"; "A psychological measurement of an individual's subjective perception of health."; rdfs:label "perception of health measurement" . a owl:Class; rdfs:subClassOf ; "perception of health and quality of life"; "quality of life"; "A psychological measurement of an individual's perception of their quality of life."; rdfs:label "quality of life measurement" . a owl:Class; rdfs:subClassOf ; "perception of health and quality of life"; "functional limitations"; "Information that is about an individual's limitations in activities that involve caring for an moving the body."; "Maelstrom:Act_daily_living"; rdfs:label "information on functional limitations" . a owl:Class; rdfs:subClassOf ; "perception of health and quality of life"; "use of assistive devices"; "Information about an individual's use of assistive devices in performing daily activities."; "Maelstrom:Use_devices"; rdfs:label "information on use of assistive devices" . a owl:Class; rdfs:subClassOf ; "socio-demographic and economic characteristics"; "religion"; "Information about an individual's association with a religion, denomiation, or sub- or non-denominational religious group."; "url:http://archive.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/religious-affiliation/definition.aspx"; rdfs:label "religious affiliation" . a owl:Class; rdfs:subClassOf ; "other questionnaire/survey data"; "social environment"; "An immaterial entity that encompasses the domain made up of interactions between the individual's physical environment, social processes, and relationships with other individuals and groups."; "PMID:10352860"; rdfs:label "human social environment" . a owl:Class; rdfs:subClassOf ; "other questionnaire/survey data"; "family history of disease"; "A clinical history that is about any family history of disease."; rdfs:label "family history of disease" . a owl:Class; rdfs:subClassOf ; "non-pharmacological interventions"; "diagnostic interventions"; "A non-pharmacological treatment history that is about diagnostic procedures to determine a condition or disease."; rdfs:comment "Includes procedures such as colonoscopies, ultrasounds, etc., but excludes laboratory tests."; rdfs:label "diagnostic procedure history" . a owl:Class; rdfs:subClassOf ; "cognitive functioning"; "ADAS"; "A cognitive measurement that is an output (score) from the Alzheimer's Disease Assessment Scale."; rdfs:label "Alzheimer's Disease Assessment Scale score" . a owl:Class; rdfs:subClassOf ; "cognitive functioning"; "MMSE"; "A cognitive measurement that is an output (score) from the Mini-Mental State Exam."; rdfs:label "Mini-Mental State Exam score" . a owl:Class; rdfs:subClassOf ; "socio-demographic and economic characteristics"; "native language"; "Information about the language an individual has been exposed to from birth and is their first language."; "url:https://en.wikipedia.org/wiki/First_language"; rdfs:label "native language of individual" . a owl:Class; rdfs:subClassOf ; "cognitive functioning"; "MoCA"; "A cognitive measurement that is the output (score) from the Montreal Cognitive Assessment Test (MoCA) for Dementia"; rdfs:label "Montreal Cognitive Assessment Test score" . a owl:Class; rdfs:subClassOf ; "cognitive functioning"; "CERAD Battery"; "A cognitive measurement that is the output (score) from the CERAD Neurophyschological Battery."; rdfs:label "CERAD Neuropsychological Battery score" . a owl:Class; rdfs:subClassOf ; "cognitive functioning"; "Penn CNB"; "A cognitive measurement that is the output (score) from the Penn Computerized Neurocognitive Battery."; rdfs:label "Penn Computerized Neurocognitive Battery score" . a owl:Class; rdfs:subClassOf ; "diseases"; "congenital and genetic disorders"; "A disorder that is present at birth due to genetics or environmental factors during development."; rdfs:label "congenital disorder" . a owl:Class; rdfs:subClassOf ; "cognitive functioning"; "SIB"; "A cognitive measurement that is the output (score) from the Severe Impairment Battery."; rdfs:label "Severe Impairment Battery score" . a owl:Class; rdfs:subClassOf ; "cognitive functioning"; "NPI"; "A cognitive measurement that is the output (score) from the Neuropsychiatric Inventory."; rdfs:label "Neuropsychiatric Inventory score" . a owl:Class; rdfs:subClassOf ; "cognitive functioning"; "CDR"; "A cognitive measurement that is the output (score) from the Clinical Dementia Rating Scale."; rdfs:label "Clinical Dementia Rating Scale score" . a owl:Class; rdfs:subClassOf ; "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence."; "GO:0000004", "GO:0007582", "GO:0044699"; "biological process", "physiological process"; "single organism process", "single-organism process"; rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this."; rdfs:label "biological_process" . a owl:Class; rdfs:subClassOf ; "basic cohort attributes"; "aims and objectives"; "In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction."@en; "A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved."@en; "goal specification"@en; "OBI Plan and Planned Process/Roles Branch"@en, "OBI_0000217"@en; rdfs:label "objective specification" . a owl:Class; rdfs:subClassOf ; "Data items include counts of things, analyte concentrations, and statistical summaries."@en; "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; "data"@en; rdfs:label "data item" . a owl:Class; "Examples of information content entites include journal articles, data, graphical layouts, and graphs."@en; "A generically dependent continuant that is about some thing."@en; "OBI_0000142"@en; rdfs:label "information content entity" . a owl:Class; rdfs:subClassOf ; "An information content entity whose concretizations indicate to their bearer how to realize them in a process."@en; rdfs:label "directive information entity" . a owl:Class; rdfs:subClassOf ; "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice."@en; "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; "OBI Plan and Planned Process branch"@en, "OBI_0000344"@en; rdfs:comment """2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them"""@en; rdfs:label "plan specification" . a owl:Class; rdfs:subClassOf ; "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}."@en; "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; "OBI_0000305"@en, "group:OBI"@en; rdfs:label "measurement datum" . a owl:Class; rdfs:subClassOf ; "Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities"@en; "A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc."@en; "text"@en; rdfs:label "textual entity" . a owl:Class; rdfs:subClassOf ; "A journal article, patent application, laboratory notebook, or a book"@en; "A collection of information content entities intended to be understood together as a whole"@en; rdfs:label "document" . a owl:Class; rdfs:subClassOf ; """From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): Project home page:http://krux.googlecode.com"""@en; "A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained."@en; rdfs:label "availability textual entity" . a owl:Class; rdfs:subClassOf ; "survey administration"; "consent/accessibility"; """From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal."""@en; "A textual entity that documents the consenting process used to enroll patients in a study."@en; rdfs:label "consent textual entity" . a owl:Class; rdfs:subClassOf ; "An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity."@en; rdfs:label "identifier" . a owl:Class; rdfs:subClassOf ; "other questionnaire/survey data"; "personal beliefs and values"; rdfs:label "belief" . a owl:Class; rdfs:subClassOf ; "questionnaire/survey data"; "diseases"; "A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism."; "condition", "disease", "disease or disorder", "disease or disorder, non-neoplastic", "diseases", "diseases and disorders", "disorder", "disorders", "medical condition", "other disease"; rdfs:label "disease or disorder" . a owl:Class; rdfs:subClassOf ; "diseases"; "skin and subcutaneous tissue diseases"; "A disease involving the integumental system."; "MONDO:0045027"; "disease of integumental system", "disease or disorder of integumental system", "disorder of integumental system", "integumental system disease", "integumental system disease or disorder", "integumentary disease"; "disorder of integument", "disorder of integumental system"; rdfs:label "integumentary system disease" . a owl:Class; rdfs:subClassOf ; "diseases"; "musculoskeletal system diseases"; "A disease involving the musculoskeletal system."; "disease of musculoskeletal system", "disease or disorder of musculoskeletal system", "disorder of musculoskeletal system", "musculoskeletal disease", "musculoskeletal system disease", "musculoskeletal system disease or disorder", "musculoskeletal system disorder"; "disorder of musculoskeletal system", "musculoskeletal disorder"; rdfs:label "musculoskeletal system disease" . a owl:Class; rdfs:subClassOf ; "diseases"; "urinary system diseases"; "A disease involving the renal system."; "disease of renal system", "disease or disorder of renal system", "disorder of renal system", "disorder of the urinary system", "disorder of urinary system", "non-neoplastic urinary tract disease", "renal disease", "renal system disease", "renal system disease or disorder", "urinary system disease", "urinary tract disease", "urinary tract disorder", "urologic disorder", "urological disorders"; "disease, urinary tract", "disease, urologic", "disease, urological", "diseases, urinary tract", "diseases, urologic", "diseases, urological", "disorder of renal system", "urinary disease", "urinary system disorder", "urinary tract diseases", "urologic disease", "urological disease", "urological diseases", "urological disorder"; rdfs:label "urinary system disease" . a owl:Class; rdfs:subClassOf ; "diseases"; "digestive system diseases"; "A disease or disorder that involves the digestive system."; "alimentary system disease", "digestive disease", "digestive system disease", "digestive system disease or disorder", "digestive system disorder", "disease of digestive system", "disease or disorder of digestive system", "disorder of digestive system", "gastroenterological system disease", "gastroenterological system disorder", "gastroenteropathy", "gastrointestinal disease", "gastrointestinal disorder", "gastrointestinal system disease", "gastrointestinal system disorder", "git disease", "stomach or intestinal disorder"; "disorder of digestive system"; rdfs:label "digestive system disease" . a owl:Class; rdfs:subClassOf ; "diseases"; "cancer"; "A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas."; "CA", "cancer", "cell type cancer", "malignancy", "malignant Growth", "malignant neoplasm", "malignant neoplasm (disease)", "malignant neoplastic disease", "malignant tumor", "neoplasm (disease), malignant", "neoplasm, malignant", "organ system cancer", "primary cancer"; "MT"; rdfs:label "cancer" . a owl:Class; rdfs:subClassOf ; "diseases"; "cardiovascular diseases"; "A disease involving the cardiovascular system."; "cardiovascular disease", "cardiovascular disease (CVD)", "cardiovascular disorder", "cardiovascular system disease", "cardiovascular system disease or disorder", "disease of cardiovascular system", "disease of subdivision of hemolymphoid system", "disease or disorder of cardiovascular system", "disorder of cardiovascular system"; "circulatory system disease", "disorder of cardiovascular system"; rdfs:label "cardiovascular disease" . a owl:Class; rdfs:subClassOf ; "diseases"; "reproductive system diseases"; "A disease involving the reproductive system."; "disease of reproductive system", "disease or disorder of reproductive system", "disorder of reproductive system", "genital disorders", "genital system disease", "reproductive disease", "reproductive system disease", "reproductive system disease or disorder", "reproductive system disorder"; "disorder of reproductive system"; rdfs:label "reproductive system disease" . a owl:Class; rdfs:subClassOf ; "diseases"; "immune system diseases"; "A disorder resulting from an abnormality in the immune system."; "disease of immune system", "disease or disorder of immune system", "disorder of immune system", "immune disease", "immune disorder", "immune dysfunction", "immune system disease or disorder", "immune system disorder"; "disorder of immune system", "immune disorder, NOS"; rdfs:label "immune system disease" . a owl:Class; rdfs:subClassOf ; "diseases"; "nervous system disorders"; "A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves."; "disease of nervous system", "disease or disorder of nervous system", "disorder of nervous system", "nervous system disease", "nervous system disease or disorder", "nervous system disorder", "neurologic disease", "neurologic disorder", "neurological disease", "neurological disorder"; "disorder of nervous system"; rdfs:label "nervous system disorder" . a owl:Class; rdfs:subClassOf ; "diseases"; "mental and behaviour disorders"; "A disease that has its basis in the disruption of mental process."; "disorder of mental process", "mental or behavioural disorder", "mental process disease"; "disorder of mental process"; rdfs:label "mental disorder" . a owl:Class; rdfs:subClassOf ; "diseases"; "respiratory system diseases"; "A non-neoplastic or neoplastic disorder that affects the respiratory system. Representative examples include pneumonia, chronic obstructive pulmonary disease, pulmonary failure, lung adenoma, lung carcinoma, and tracheal carcinoma."; "disease of respiratory system", "disease or disorder of respiratory system", "disorder of respiratory system", "respiratory disease", "respiratory disorder", "respiratory system disease", "respiratory system disease or disorder", "respiratory system disorder"; "disorder of respiratory system"; rdfs:label "respiratory system disease" . a owl:Class; rdfs:subClassOf ; "diseases"; "endocrine system diseases"; "A disease involving the endocrine system."; "disease of endocrine system", "disease or disorder of endocrine system", "disorder of endocrine system", "endocrine disease", "endocrine disorder", "endocrine system disease", "endocrine system disease or disorder", "endocrine system disorder", "endocrinopathy", "thyroid or other glandular disorders"; "disorder of endocrine system"; rdfs:label "endocrine system disease" . a owl:Class; rdfs:subClassOf ; "diseases"; "infectious diseases"; "A disorder resulting from the presence and activity of a microbial, viral, or parasitic agent. It can be transmitted by direct or indirect contact."; "ID", "clinical infection", "communicable disease", "infection", "infectious", "infectious disease", "infectious diseases and manifestations", "infectious disorder", "transmissible disease"; "disease by infectious agent"; rdfs:comment "Replaces 'infection' in disease hierarchy. OBI imported term infection is moved to pathologic process. This class is a container class for infectious diseases, not the process of infection itself."; rdfs:label "infectious disease" . a owl:Class; rdfs:subClassOf ; "diseases"; "blood-related disorders"; "A disease involving the hematopoietic system."; "blood disease", "blood disorder", "blood dyscrasia", "disease of hematopoietic system", "disease of the blood and blood-forming organs", "disease or disorder of hematopoietic system", "disorder of hematopoietic system", "hematologic and lymphocytic disorder", "hematologic disorder", "hematological disease", "hematological disorder", "hematological system disease", "hematopoietic disease", "hematopoietic system disease", "hematopoietic system disease or disorder", "rare hematologic disease"; "blood dyscrasia NOS", "disorder of hematopoietic system", "hematological disorders and malignancies"; rdfs:comment "placeholder for lymphoid disease"; rdfs:label "hematologic disease"; rdfs:seeAlso "https://github.com/monarch-initiative/mondo/issues/254"^^xsd:anyURI . a owl:Class; rdfs:subClassOf ; "diseases"; "injuries"; "Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity."; "injury", "trauma", "traumatic injury", "wound"; rdfs:label "injury" . a owl:Class; rdfs:subClassOf ; "diseases"; "visual system diseases"; "A disease that involves the visual system."; "disease of visual system", "disease or disorder of visual system", "disorder of visual system", "visual system disease", "visual system disease or disorder", "visual system disorder"; "disorder of visual system"; rdfs:label "disease of visual system" . a owl:Class; rdfs:subClassOf ; "diseases"; "diseases of the ear, nose, and/or throat"; "Pathological processes of the ear, the nose, and the throat, also known as the ENT diseases."; "ear, nose and throat disorder", "ear, nose or throat disorder", "ear/nose/throat disease", "otolaryngologic disorder", "otorhinolaryngologic disease"; "ENT disease", "ENT diseases", "disease, ENT", "disease, otolaryngologic", "disease, otolaryngological", "disease, otorhinolaryngologic", "disease, otorhinolaryngological", "diseases, ENT", "diseases, otolaryngologic", "diseases, otolaryngological", "diseases, otorhinolaryngologic", "diseases, otorhinolaryngological", "otolaryngologic disease", "otolaryngologic diseases", "otolaryngological disease", "otolaryngological diseases", "otorhinolaryngological disease", "otorhinolaryngological diseases"; rdfs:comment "Editor note: consider uberon class"; rdfs:label "otorhinolaryngologic disease" . a owl:Class; rdfs:subClassOf ; "diseases"; "poisoning"; "A condition or physical state produced by the ingestion, injection, inhalation of or exposure to a deleterious agent."; "Poisonings", "intoxication", "poisoning syndrome"; rdfs:label "poisoning" . a owl:Class; rdfs:subClassOf ; "Injecting mice with a vaccine in order to test its efficacy"; "A process that realizes a plan which is the concretization of a plan specification."@en; "branch derived"; rdfs:label "planned process" . a owl:Class; rdfs:subClassOf ; "Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house."; "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; "measuring"@en, "scientific observation"@en; "OBI branch derived"@en; rdfs:label "assay" . a owl:Class; rdfs:subClassOf ; "A cell lysis, production of a cloning vector, creating a buffer."; "A planned process which results in physical changes in a specified input material"@en; "material transformation"@en; "OBI branch derived"@en; rdfs:label "material processing" . a owl:Class; rdfs:subClassOf ; "laboratory measures"; "imaging"; "An assay that produces a picture of an entity."; "OBI branch derived"; rdfs:label "imaging assay" . a owl:Class; rdfs:subClassOf ; "genomics"; "DNA/Genotyping"; "High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923"; "An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions."; "SNP analysis", "genotype profiling"; "OBI Biomaterial"; rdfs:label "genotyping assay" . a owl:Class; rdfs:subClassOf ; "genomics"; "Sequence variants (CNV, SNP arrays)"; "Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. PMID:18058796"; "An assay that determines lost or amplified genomic regions of DNA by comparing genomic DNA originating from tissues from the same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping"; "CNV analysis"; rdfs:label "copy number variation profiling assay" . a owl:Class; rdfs:subClassOf ; "genomics"; "RNAseq/gene expression"; "An transcription profiling assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance."; "transcription profiling by high throughput sequencing"; "EFO:0002770"; rdfs:label "RNA-seq assay" . a owl:Class; rdfs:subClassOf ; "laboratory measures"; "microbiology"; "An assay that identifies the organism species in a specimen."; "NIAID GSCID-BRC metadata working group"; rdfs:label "organism identification assay" . a owl:Class; rdfs:subClassOf ; "genomics"; "Epigenetics"; "An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation."; "Penn group"; rdfs:label "epigenetic modification assay" . a owl:Class; rdfs:subClassOf ; "genomics"; "WGS"; "WGS permits comprehensive sequencing of introns and exons, whereas whole exome sequencing (WES) allows deeper sequencing of exonic regions at a lower cost. Due to the large number of genetic variants found in each genome, it is necessary to use filtering approaches to distinguish deleterious from benign variants. WES has been used successfully to identify novel genetic causes of primary immunodeficiency. Complex structural variations and non-Mendelian disorders remain challenges for WGS."; "A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism."; "WGS"; "PMID:23095910", "PMID:25827230"; rdfs:label "whole genome sequencing assay" . a owl:Class; rdfs:subClassOf ; "genomics"; "WES"; "DNA was extracted from the Ficoll pellet of blood taken from congenital asplenia patients. Unamplified, high-molecular weight, RNase-treated genomic DNA (4_6 _g) was used for whole exome sequencing (WES) with the use of Agilent 71 Mb (V4 + UTR) singlesample capture and an Illumina HiSeq 2000. Sequencing was carried out so as to obtain 30_ coverage from 2 _ 100-bp paired-end reads. We used the Annovar tool (25) to annotate the resulting highquality (HQ) variants. In the regions targeted by WES capture (81.5% of the consensus coding genome), the mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected per sample were 84,192 and13,325, respectively. After filtering, a mean of 74,398 (95.3%) high-quality (HQ) SNVs and 9,033 (70.6%) HQ indels were called. A mean of 105 coding HQ SNVs and 32 indels was identified."; "A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons)."; "WES"; "PMID:25827230"; rdfs:label "exome sequencing assay" . a owl:Class; rdfs:subClassOf ; "physical environment"; "exposure to carcinogens"; "A information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment."; "OBIB"; rdfs:label "exposure to environmental and workplace carcinogens history" . a owl:Class; rdfs:subClassOf ; "genomics"; "Metagenomics"; "A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample."; "WMS"; "Bjoern Peters", "Michelle Giglio"; rdfs:label "whole metagenome sequencing assay" . a owl:Class; rdfs:subClassOf ; "PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10."@en; "A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability"@en; "OBI-Branch"; rdfs:label "storage" . a owl:Class; rdfs:subClassOf ; "basic cohort attributes"; "study design"; "a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design."@en; "A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution."; "experimental design"@en; rdfs:label "study design" . a owl:Class; rdfs:subClassOf ; "population data"; "criteria for enrollment and recruitment procedures"; "PMID: 23979341-The major inclusion criterion was patients in whom severe cerebral embolism was diagnosed at age 75 or younger (more than 9 in the NIHSS score on day 7 after the onset of stroke) ."@en; "an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study."@en; "inclusion condition"@en, "inclusion rule"@en; "Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group"@en; rdfs:label "inclusion criterion" . a owl:Class; rdfs:subClassOf ; "A series of statements representing health-relevant qualities of a patient and of a patient's family."@en; "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf"; rdfs:label "clinical history" . a owl:Class; rdfs:subClassOf ; "other questionnaire/survey data"; "signs and symptoms"; "A process experienced by the patient, which can only be experienced by the patient, that is hypothesized to be clinically relevant."@en; "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf"; rdfs:label "symptom" . a owl:Class; rdfs:subClassOf ; "socio-demographic and economic characteristics"; "income and possessions"; rdfs:label "income data" . a owl:Class; rdfs:subClassOf ; "socio-demographic and economic characteristics"; "age/birthdate"; "A time quality inhering in a bearer by virtue of how long the bearer has existed."; rdfs:label "age" . a owl:Class; rdfs:subClassOf ; "socio-demographic and economic characteristics"; "biological sex"; "An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved."; rdfs:label "biological sex" . a owl:Class; rdfs:subClassOf ; "questionnaire/survey data"; "socio-demographic and economic characteristics"; "A quality that inheres in an entire organism or part of an organism."; rdfs:label "organismal quality" . a owl:Class; rdfs:subClassOf ; "Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family."; "A material entity that consists of two or more organisms, viruses, or viroids."@en; "group of organism", "organism collection"; rdfs:comment "May be of the same or different species."; rdfs:label "collection of organisms" . a owl:Class; rdfs:subClassOf ; "medication"; "prescription"; "\"Prescription for John Smith : Ativan 2mg tablets, take 1 tablet twice daily by mouth as needed if anxious, dispense 60 tablets, renew 12 times. Signed by Dr Hazard. Date: 15/10/29\""; "A health care prescription specifying the initiation, modification or cessation of a drug administration."@en; rdfs:label "drug prescription" . a owl:Class; rdfs:subClassOf ; "medication"; "administration"; "'take Aspirin 81 mg oral tablet, 1 tablet once daily by mouth, start today' or the synonymous abbreviated version 'Aspirin 81 mg tablet PO DIE'"; """A drug administration description that specifies a drug administration prescribed or reported by an healthcare provider. It specifies: - The drug product - The posology It may also specify a starting drug administration condition"""@en; rdfs:label "drug administration specification" . a owl:Class; rdfs:subClassOf ; ""@en; "a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data."@en; "STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic)."@en; rdfs:label "statistic" . a owl:Class; rdfs:subClassOf ; "a count of 4 resulting from counting limbs in humans"@en; "a count is a data item denoted by an integer and represented the number of instances or occurences of an entity"@en; "STATO"@en; rdfs:label "count" . a owl:Class; rdfs:subClassOf ; "survey administration"; "date and time-related information"; "Information about a calendar date or timestamp indicating day, month, year and time of an event."@en; "STATO"@en; rdfs:label "date" . a owl:Class; rdfs:subClassOf ; "other questionnaire/survey data"; "life stage/time point"; "A spatiotemporal region encompassing some part of the life cycle of an organism."; "developmental stage", "stage"; rdfs:label "life cycle stage" . a owl:Class; rdfs:subClassOf ; "sample type"; "blood"; "A fluid that is composed of blood plasma and erythrocytes."; "portion of blood", "vertebrate blood"; "whole blood"; rdfs:label "blood" . a owl:Class; rdfs:subClassOf ; "biosample"; "sample type"; "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body."; "body fluid or substance", "body substance", "organism substance", "portion of body substance", "portion of organism substance"; rdfs:label "organism substance" . a owl:Class; rdfs:subClassOf ; "sample type"; "urine"; "Excretion that is the output of a kidney"; rdfs:label "urine" . a owl:Class; rdfs:subClassOf ; "sample type"; "saliva"; "A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions."; "salivary gland secretion"; "sailva normalis", "saliva atomaris", "saliva molecularis"; rdfs:label "saliva" . a owl:Class; rdfs:subClassOf ; "sample type"; "stool"; "Portion of semisolid bodily waste discharged through the anus[MW,modified]"; "excreta"; "faeces", "fecal material", "fecal matter", "matières fécales@fr", "merde@fr", "partie de la merde@fr", "piece of shit", "porción de mierda@es", "portion of excrement", "portion of faeces", "portion of fecal material", "portion of fecal matter", "portion of feces", "portionem cacas", "stool", "teil der fäkalien@de"; "cow dung", "cow pat", "dung", "fewmet", "frass", "guano", "portion of dung", "portion of guano", "portion of scat", "scat", "spraint"; "droppings", "excrement", "ordure", "spoor"; rdfs:label "feces" .