diff --git a/Makefile b/Makefile index ad53ff8..6f732ea 100644 --- a/Makefile +++ b/Makefile @@ -35,6 +35,13 @@ DESCRIPTION = An ontology to represent genomics cohort attributes. 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 TITLE = Genomics Cohorts Knowledge Ontology +UNAME := $(shell uname) +ifeq ($(UNAME), Darwin) + RDFTAB_URL := https://github.com/ontodev/rdftab.rs/releases/download/v0.1.1/rdftab-x86_64-apple-darwin +else + RDFTAB_URL := https://github.com/ontodev/rdftab.rs/releases/download/v0.1.1/rdftab-x86_64-unknown-linux-musl +endif + .PHONY: all all: gecko.owl views/ihcc-gecko.owl build/gecko.html build/ihcc-gecko.html build/report.html @@ -43,11 +50,17 @@ clean: rm -rf build .PHONY: update -update: clean build/templates.xlsx all +update: + rm -rf build/templates.xlsx + make build/templates.xlsx + make all build: mkdir -p $@ +build/imports: | build + mkdir -p $@ + build/robot.jar: | build curl -L -o $@ https://build.obolibrary.io/job/ontodev/job/robot/job/html-report/lastSuccessfulBuild/artifact/bin/robot.jar #curl -L -o $@ https://github.com/ontodev/robot/releases/download/v1.6.0/robot.jar @@ -55,31 +68,33 @@ build/robot.jar: | build build/robot-tree.jar: | build curl -L -o $@ https://build.obolibrary.io/job/ontodev/job/robot/job/tree-view/lastSuccessfulBuild/artifact/bin/robot.jar +build/rdftab: | build + curl -L -o $@ $(RDFTAB_URL) + chmod +x $@ + + ### GECKO build/templates.xlsx: | build curl -L -o $@ "https://docs.google.com/spreadsheets/d/1bYnbxvPPFO7D7zg9Tr2e32jb8l13kMZ81vP_iaSZCXg/export?format=xlsx" -src/ontology/templates/gecko.tsv src/ontology/templates/properties.tsv src/ontology/templates/external.tsv: build/templates.xlsx | build/robot.jar - xlsx2csv -d tab -n $(basename $(notdir $@)) $< $@ +src/ontology/templates/index.tsv src/ontology/templates/gecko.tsv src/ontology/templates/properties.tsv src/ontology/templates/external.tsv: build/templates.xlsx | build/robot.jar + xlsx2csv -d tab -n $(basename $(notdir $@)) --ignoreempty $< $@ build/properties.ttl: src/ontology/templates/properties.tsv | build/robot.jar $(ROBOT) template \ --template $< \ --output $@ -build/external.ttl: build/properties.ttl src/ontology/templates/external.tsv | build/robot.jar - $(ROBOT) template \ - --input $< \ - --template $(word 2,$^) \ - --merge-before \ - --output $@ - -gecko.owl: build/external.ttl src/ontology/templates/gecko.tsv | build/robot.jar +gecko.owl: build/properties.ttl src/ontology/templates/index.tsv src/ontology/templates/gecko.tsv src/ontology/templates/external.tsv src/ontology/annotations.owl | build/robot.jar $(ROBOT) template \ --input $< \ --template $(word 2,$^) \ + --template $(word 3,$^) \ + --template $(word 4,$^) \ --merge-before \ + merge \ + --input $(word 5,$^) \ annotate \ --link-annotation dcterms:license $(LICENSE) \ --annotation dc11:description "$(DESCRIPTION)" \ @@ -89,19 +104,65 @@ gecko.owl: build/external.ttl src/ontology/templates/gecko.tsv | build/robot.jar --version-iri $(OBO)/gecko/$(DATE)/gecko.owl \ --output $@ + +### Imports + +IMPORTS := bfo eupath go iao mf mondo obi omrse pato pco pdro stato uberon # cmo ogms +IMPORT_MODS := $(foreach I,$(IMPORTS),build/imports/$(I).ttl) + +UC = $(shell echo '$1' | tr '[:lower:]' '[:upper:]') + +build/imports/%.owl: | build/imports + curl -Lk -o $@ http://purl.obolibrary.org/obo/$(notdir $@) + +build/imports/%.db: src/scripts/prefixes.sql build/imports/%.owl | build/rdftab + rm -rf $@ + sqlite3 $@ < $< + ./build/rdftab $@ < $(word 2,$^) + +build/imports/%.txt: src/ontology/templates/index.tsv | build/imports + awk -F '\t' '{print $$1}' $< | tail -n +3 | sed -n '/$(call UC,$(notdir $(basename $@))):/p' > $@ + +build/imports/%.ttl: build/imports/%.db build/imports/%.txt + python3 -m gizmos.extract -d $< -T $(word 2,$^) -n > $@ + +build/annotation-properties.owl: src/ontology/templates/annotation-properties.tsv | build/robot.jar + $(ROBOT) template \ + --template $< \ + --output $@ + +src/ontology/annotations.owl: $(IMPORT_MODS) src/queries/fix_annotations.rq build/annotation-properties.owl | build/robot.jar + $(ROBOT) merge \ + $(foreach I,$(IMPORT_MODS), --input $(I)) \ + remove \ + --term rdfs:label \ + query \ + --update src/queries/fix_annotations.rq \ + merge \ + --input build/annotation-properties.owl \ + annotate \ + --ontology-iri "http://purl.obolibrary.org/obo/cob/$(notdir $@)" \ + --output $@ + + ### IHCC Browser View -build/query_result.csv: gecko.owl src/get_ihcc_view.rq | build/robot.jar +build/query_result.csv: gecko.owl src/queries/get_ihcc_view.rq | build/robot.jar $(ROBOT) query \ --input $< \ --query $(word 2,$^) $@ -build/ihcc_view_template.csv: src/ihcc_view.py build/query_result.csv +build/ihcc_view_template.csv: src/scripts/ihcc_view.py build/query_result.csv python3 $^ $@ -views/ihcc-gecko.owl: build/ihcc_view_template.csv | build/robot.jar +build/ihcc_annotations.ttl: gecko.owl src/queries/build_ihcc_annotations.rq | build/robot.jar + $(ROBOT) query --input $< --query $(word 2,$^) $@ + +views/ihcc-gecko.owl: build/ihcc_view_template.csv build/ihcc_annotations.ttl | build/robot.jar $(ROBOT) template \ --template $< \ + merge \ + --input $(word 2,$^) \ annotate \ --ontology-iri $(OBO)/ihcc-gecko.owl \ --version-iri $(OBO)/gecko/$(DATE)/ihcc-gecko.owl \ diff --git a/gecko.owl b/gecko.owl index a76a210..9ede1eb 100644 --- a/gecko.owl +++ b/gecko.owl @@ -8,9 +8,10 @@ xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:terms="http://purl.org/dc/terms/"> + xmlns:terms="http://purl.org/dc/terms/" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + An ontology to represent genomics cohort attributes. Genomics Cohorts Knowledge Ontology @@ -30,6 +31,18 @@ + + + + + + + + + + + + @@ -46,6 +59,22 @@ + + + + editor preferred term + + + + + + + + example of usage + + + + @@ -54,6 +83,30 @@ + + + + editor note + + + + + + + + term editor + + + + + + + + alternative term + + + + @@ -62,6 +115,202 @@ + + + + curator note + + + + + + + + term tracker item + + + + + + + + ontology term requester + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + external_definition + + + + + + + + axiom_lost_from_external_ontology + + + + + + + + homology_notes + + + + + + + + has_relational_adjective + + + + + + + + taxon_notes + + + + + + + + external_ontology_notes + + + + + + + + + + + + + + + + + + + + + + + + + + has_alternative_id + + + + + + + + has_broad_synonym + + + + + + + + + + + + + + has_exact_synonym + + + + + + + + has_narrow_synonym + + + + + + + + has_obo_namespace + + + + + + + + has_related_synonym + + + + + + + + id + + + + + + + + in_subset + + + + @@ -70,6 +319,22 @@ + + + + label + + + + + + + + see also + + + + + + + process + Process + a process of cell-division, \ a beating of the heart + a process of meiosis + a process of sleeping + the course of a disease + the flight of a bird + the life of an organism + your process of aging. + 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]) + BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + process + + + + + + + + + disposition + Disposition + an atom of element X has the disposition to decay to an atom of element Y + certain people have a predisposition to colon cancer + children are innately disposed to categorize objects in certain ways. + the cell wall is disposed to filter chemicals in endocytosis and exocytosis + BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) + (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] + (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] + disposition + + + + + + + + realizable + RealizableEntity + the disposition of this piece of metal to conduct electricity. + the disposition of your blood to coagulate + the function of your reproductive organs + the role of being a doctor + the role of this boundary to delineate where Utah and Colorado meet + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + realizable entity + + + + + + + + quality + Quality + the ambient temperature of this portion of air + the color of a tomato + the length of the circumference of your waist + the mass of this piece of gold. + the shape of your nose + the shape of your nostril + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) + If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) + (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] + (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] + quality + + + + + + + + + site + Site + Manhattan Canyon) + a hole in the interior of a portion of cheese + a rabbit hole + an air traffic control region defined in the airspace above an airport + the Grand Canyon + the Piazza San Marco + the cockpit of an aircraft + the hold of a ship + the interior of a kangaroo pouch + the interior of the trunk of your car + the interior of your bedroom + the interior of your office + the interior of your refrigerator + the lumen of your gut + your left nostril (a fiat part – the opening – of your left nasal cavity) + b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) + (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] + site + + + + + + + + material + MaterialEntity + a flame + a forest fire + a human being + a hurricane + a photon + a puff of smoke + a sea wave + a tornado + an aggregate of human beings. + an energy wave + an epidemic + the undetached arm of a human being + BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 + BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. + BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + material entity + + + + + + + + immaterial entity + + + + questionnaire/survey data physiological measurements - A quantitative or qualitative value which is the result of an act of assessing a morphological or physiological state or property in a single individual or sample or a group of individuals or samples, based on direct observation or experimental manipulation. - Replaces GECKO 'physiological measurements' clinical measurement data item @@ -135,8 +544,6 @@ physiological measurements circulation and respiration - Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart and/or blood vessels. - Replaces GECKO 'circulation and respiration' cardiovascular measurement data item @@ -148,8 +555,6 @@ circulation and respiration blood pressure - Measurement of the pressure, or force per area, exerted by circulating blood against the walls of the blood vessels. The pressure is dependent on the energy of the heart action, elasticity of the vessel walls and volume and viscosity of the blood. - Replaces GECKO 'blood pressure' blood pressure measurement data item @@ -161,8 +566,6 @@ anthropometry weight - The heaviness or degree to which an entire organism's body is drawn to the earth by gravity. - Replaces GECKO 'weight' body weight data item @@ -174,8 +577,6 @@ physiological measurements anthropometry - Measurement of the structure or forms of the entire body or parts of the body of an organism. - Replaces GECKO 'anthropometry' body morphological measurement data item @@ -187,8 +588,6 @@ anthropometry height - The vertical measurement of a body. - Replaces GECKO 'height' body height data item @@ -200,159 +599,90 @@ circulation and respiration heart rate (HR) - The count of the rhythmic contractions and expansions of an artery due to the surge of blood from the beat of the heart. - Replaces GECKO 'heart rate (HR)' pulse data item - - - - quality - - - - - - - - material entity - - - - - - - - immaterial entity - - - - - - - - - geographical location - - - - - - - - realizable - - - - - - - - process - - - - - - - - - planned process - - - - - - - - - biological process - - - - - - - - - collection of organisms - - - - - + - - information + + + other questionnaire/survey data + cause of death + An information content entity indicating the cause of death for a participant in the study. + Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey + Penn Group + PRISM + cause of participant death - + - - - directive information entity + + + healthcare information + hospitalizations + an information content entity that is about a part of a health care encounter that occurs in a hospital facility + Person: John Judkins + EuPathDB + ICEMR protein array + hospitalization information - + - - - basic cohort attributes - aims and objectives - Replaces GECKO 'aims and objectives' - objective specification - - - - - - - - - plan specification - - - - - - - - - document + + + 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. + occupation - + - - - data item + + + 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 + Person: John Judkins + EuPathDB, BFO's 'relational quality' examples + marital status - + - - - assay + + + questionnaire/survey data + healthcare information + An information content entity about healthcare that is private or public. + healthcare information - + - - - disposition + + + questionnaire/survey data + physical environment + environmental system associated with the dwelling used by humans. + Person: Cristian Cocos, Jie Zheng, Chris Stoeckert + Penn Group + GEMS + environment associated with human dwelling @@ -360,7 +690,7 @@ - + basic cohort attributes timeline A directive information entity that specifies the sequence in which a series of events occurred or will occur. @@ -377,12 +707,12 @@ - + - + basic cohort attributes population data A data item that is about a population of organisms. @@ -398,7 +728,7 @@ - + population data @@ -416,7 +746,7 @@ - + population data @@ -435,12 +765,12 @@ - + - + basic cohort attributes demographic data A quality which inheres in a population of organisms. @@ -488,7 +818,7 @@ - + basic cohort attributes data collection events A planned process that is a part of an investigation in which raw data is collected. @@ -524,7 +854,7 @@ - + laboratory measures genomics An assay that investigates the genome or genomes of an individual organism or population of organisms. @@ -627,7 +957,7 @@ - + socio-demographic and economic characteristics birthplace A geographical location in which an individual was born. @@ -639,7 +969,7 @@ - + socio-demographic and economic characteristics residence A geographical location in which an individual currently resides. @@ -663,7 +993,7 @@ - + socio-demographic and economic characteristics family and household structure Information that is about the structure of an individual's family and/or household. @@ -736,7 +1066,7 @@ - questionnaire/survey data + 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. physician contact textual entity @@ -750,6 +1080,7 @@ questionnaire/survey data non-pharmacological interventions + A treatment history that is about any non-pharamacological treatments such as surgery or physical therapy. non-pharmacological treatment history @@ -782,7 +1113,7 @@ - + @@ -800,7 +1131,7 @@ - + medication drug response(s) A biological process that results from a drug stimulus. @@ -877,7 +1208,7 @@ - questionnaire/survey data + other questionnaire/survey data reproduction A clinical history that is about pregnancy, maternity, fertility, menses, and any other reproductive aspect. reproductive history @@ -895,10 +1226,316 @@ + + + + + questionnaire/survey data + cognitive and psychological measurements + A measurement datum of some aspect of human psychology. + EFO:0009095 + See also EFO:0009095 + psychological measurement + + + + + + + + + cognitive and psychological measurements + cognitive functioning + A psychological measurement of some aspect of intellectual functions such as memory, problem solving, and comprehension. + Wikipedia:Cognition + cognitive measurement + + + + + + + + + cognitive and psychological measurements + personality + A psychological measurement of a person's individual sets of behaviours, cognitions, and emotional patterns. + Wikipedia:Personality + personality measurement + + + + + + + + + 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 + emotion + + + + + + + + + lifestyle and behaviours + oral health and hygiene + A lifestyle history that is about oral health and hygiene. + oral health history + + + + + + + + + non-pharmacological interventions + psychological interventions + A non-pharmacological treatment history that is about psychological treatments such as counselling. + psychological treatment history + + + + + + + + + non-pharmacological interventions + radiological interventions + A non-pharmacological treatment history that is about use of radiology for treatment of disease, disorder, or symptom. + radiological treatment history + + + + + + + + + non-pharmacological interventions + physical therapy interventions + A non-pharmacological treatment history that is about physical therapy treatments such as physical rehabilitation. + physical therapy history + + + + + + + + + perception of health and quality of life + perception of health + A psychological measurement of an individual's subjective perception of health. + perception of health measurement + + + + + + + + + perception of health and quality of life + quality of life + A psychological measurement of an individual's perception of their quality of life. + quality of life measurement + + + + + + + + + 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 + information on functional limitations + + + + + + + + + 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 + information on use of assistive devices + + + + + + + + + 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 + religious affiliation + + + + + + + + + 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 + human social environment + + + + + + + + + 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. + jl + 2012-09-19T15:05:24Z + GO:0000004 + GO:0007582 + GO:0044699 + Wikipedia:Biological_process + biological process + physiological process + biological_process + single organism process + single-organism process + GO:0008150 + 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. + biological_process + + + + + + + + + basic cohort attributes + aims and objectives + objective specification + In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. + 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. + 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." + 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. + Answers the question, why did you do this experiment? + PERSON: Alan Ruttenberg + PERSON: Barry Smith + PERSON: Bjoern Peters + PERSON: Jennifer Fostel + goal specification + OBI Plan and Planned Process/Roles Branch + OBI_0000217 + objective specification + + + + + + + + + data item + Data items include counts of things, analyte concentrations, and statistical summaries. + 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. + 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ + PERSON: Alan Ruttenberg + PERSON: Chris Stoeckert + PERSON: Jonathan Rees + data + data item + + + + + + + + information content entity + Examples of information content entites include journal articles, data, graphical layouts, and graphs. + A generically dependent continuant that is about some thing. + 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). + information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. + PERSON: Chris Stoeckert + OBI_0000142 + information content entity + + + + + + + + + An information content entity whose concretizations indicate to their bearer how to realize them in a process. + 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. + 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. + 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO + Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + directive information entity + + + + + + + + + plan specification + PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. + 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. + 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. + 2014-03-31: A plan specification can have other parts, such as conditional specifications. + Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved + Alan Ruttenberg + OBI Plan and Planned Process branch + OBI_0000344 + 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 + plan specification + + + + - + + measurement datum + 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,}. + A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. + 2/2/2009 is_specified_output of some assay? + person:Chris Stoeckert + OBI_0000305 + group:OBI measurement datum @@ -907,16 +1544,42 @@ - + + textual entity + Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities + 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. + AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. + MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. + PERSON: Lawrence Hunter + text textual entity + + + + + document + A journal article, patent application, laboratory notebook, or a book + A collection of information content entities intended to be understood together as a whole + PERSON: Lawrence Hunter + document + + + + + availability textual entity + 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 + A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained. + PERSON: Bill Baumgartner availability textual entity @@ -928,8 +1591,12 @@ survey administration consent/accessibility - A textual entity that documents the consenting process used to enroll patients in a study. - Replaces GECKO 'consent/accessibility' + consent textual entity + 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. + A textual entity that documents the consenting process used to enroll patients in a study. + PERSON: Bill Baumgartner consent textual entity @@ -938,21 +1605,138 @@ - + + identifier + 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. identifier + + + + + other questionnaire/survey data + personal beliefs and values + belief + + + + - + 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. - Replaces GECKO 'diseases' - disease or disorder + A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. + DOID:4 + EFO:0000408 + ICD10:N18 + ICD9:799.9 + MESH:D004194 + NCIT:C2991 + OGMS:0000031 + Orphanet:377788 + SCTID:64572001 + UMLS:C0012634 + condition + disease + disease or disorder + disease or disorder, non-neoplastic + diseases + diseases and disorders + disorder + disorders + medical condition + other disease + MONDO:0000001 + disease or disorder + + + + + + + + + diseases + skin and subcutaneous tissue + A disease involving the integumental system. + MONDO:0045027 + DOID:16 + SCTID:128598002 + UMLS:C1290011 + 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 + MONDO:0002051 + integumentary system disease + + + + + + + + + diseases + musculoskeletal system + A disease involving the musculoskeletal system. + DOID:17 + ICD9:729.99 + MESH:D009140 + NCIT:C107377 + SCTID:928000 + UMLS:C0026857 + 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 + MONDO:0002081 + musculoskeletal system disease + + + + + + + + + diseases + connective tissue + A disease involving the connective tissue. + COHD:253549 + DOID:65 + MESH:D003240 + NCIT:C26729 + SCTID:105969002 + UMLS:C0009782 + connective tissue disease + connective tissue disease or disorder + connective tissue diseases + connective tissue disorder + connective tissue disorders + disease of connective tissue + disease or disorder of connective tissue + disease, connective tissue + disorder of connective tissue + primary disorder of connective tissue + tissue disease, connective + disorder of connective tissue + MONDO:0003900 + connective tissue disease @@ -963,9 +1747,36 @@ diseases digestive system - A disease or disorder that involves the digestive system. - Replaces GECKO 'digestive system' - digestive system disease + A disease or disorder that involves the digestive system. + COHD:4201745 + DOID:77 + EFO:0000405 + ICD10:K92.9 + ICD9:520-579.99 + ICD9:V47.3 + MESH:D005767 + NCIT:C2990 + SCTID:53619000 + 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 + MONDO:0004335 + digestive system disease @@ -976,9 +1787,40 @@ diseases oncological - 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. - Replaces GECKO 'oncological' - 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. + COHD:443392 + DOID:0050686 + DOID:0050687 + DOID:162 + EFO:0000311 + GARD:0011960 + ICD10:C80 + ICD10:C80.1 + ICD9:195.8 + ICD9:199 + ICD9:199.1 + ICDO:8000/3 + NCIT:C9305 + NIFSTD:birnlex_406 + ONCOTREE:MT + SCTID:363346000 + UMLS:C0006826 + 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 + MONDO:0004992 + cancer @@ -989,9 +1831,40 @@ diseases circulatory system - A disease involving the cardiovascular system. - Replaces GECKO 'circulatory system' - cardiovascular disease + A disease involving the cardiovascular system. + DOID:1287 + EFO:0000319 + ICD10:I00.I99 + ICD9:390-459.99 + ICD9:420-429.99 + ICD9:423 + ICD9:423.8 + ICD9:424 + ICD9:429 + ICD9:429.2 + ICD9:429.7 + ICD9:429.8 + ICD9:429.81 + ICD9:429.89 + ICD9:459.89 + ICD9:459.9 + MESH:D002318 + NCIT:C2931 + SCTID:49601007 + UMLS:C0007222 + 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 + MONDO:0004995 + cardiovascular disease @@ -1002,9 +1875,33 @@ diseases nervous system - A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves. - Replaces GECKO 'nervous system' - nervous system disorder + A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves. + DOID:863 + EFO:0000618 + ICD10:G00-G99 + ICD10:G00.G99 + ICD10:G98 + ICD10:G98.8 + ICD9:349.89 + ICD9:349.9 + MESH:D009422 + NCIT:C26835 + SCTID:118940003 + UMLS:C0027765 + Wikipedia:Nervous_system_disease + 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 + MONDO:0005071 + nervous system disorder @@ -1015,8 +1912,20 @@ diseases mental and behaviour disorders - A disease that has its basis in the disruption of mental process. - Replaces GECKO 'mental and behaviour disorders' + A disease that has its basis in the disruption of mental process. + EFO:0000677 + ICD10:F00.F99 + ICD9:290-299.99 + ICD9:298.8 + ICD9:V11.9 + NIFSTD:birnlex_12669 + SCTID:74732009 + UMLS:CN240636 + disorder of mental process + mental or behavioural disorder + mental process disease + disorder of mental process + MONDO:0005084 mental disorder @@ -1028,9 +1937,45 @@ diseases respiratory system - 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. - Replaces GECKO 'respiratory system' - respiratory system disease + 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. + DOID:1579 + EFO:0000684 + ICD10:J96-J99 + ICD10:J98 + ICD9:460-519.99 + ICD9:500-508.99 + ICD9:503 + ICD9:508 + ICD9:508.1 + ICD9:508.8 + ICD9:508.9 + ICD9:510-519.99 + ICD9:516 + ICD9:516.8 + ICD9:516.9 + ICD9:517 + ICD9:517.8 + ICD9:519 + ICD9:519.1 + ICD9:519.3 + ICD9:519.8 + ICD9:519.9 + ICD9:V12.60 + ICD9:V47.2 + MESH:D012140 + NCIT:C26871 + SCTID:50043002 + 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 + MONDO:0005087 + respiratory system disease @@ -1041,9 +1986,63 @@ diseases endocrine/nutritional/metabolic disorders - A disease involving the endocrine system. - Replaces GECKO 'endocrine/nutritional/metabolic disorders' - endocrine system disease + A disease involving the endocrine system. + DOID:28 + EFO:0001379 + ICD10:E34.9 + ICD9:259.8 + ICD9:259.9 + MESH:D004700 + NCIT:C3009 + SCTID:362969004 + UMLS:C0014130 + 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 + MONDO:0005151 + endocrine system disease + + + + + + + + + diseases + infectious disease + A disorder resulting from the presence and activity of a microbial, viral, or parasitic agent. It can be transmitted by direct or indirect contact. + DOID:0050117 + EFO:0005741 + ICD10:A00.B99 + ICD9:079.0 + ICD9:136.8 + ICD9:136.9 + IDO:0000436 + MESH:D003141 + NCIT:C26726 + SCTID:40733004 + ID + clinical infection + communicable disease + infection + infectious + infectious disease + infectious diseases and manifestations + infectious disorder + transmissible disease + disease by infectious agent + MONDO:0005550 + 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. + infectious disease @@ -1054,9 +2053,187 @@ diseases blood-related disorders - A disease involving the hematopoietic system. - Replaces GECKO 'blood-related disorders' + A disease involving the hematopoietic system. + DOID:74 + EFO:0005803 + GTR:AN1320635 + ICD10:D75.9 + ICD9:280-289.99 + ICD9:289.8 + ICD9:289.9 + MESH:D006402 + NCIT:C26323 + Orphanet:97992 + SCTID:414022008 + UMLS:C0018939 + UMLS:CN206939 + UMLS:CN882913 + 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 + MONDO:0005570 + placeholder for lymphoid disease hematologic disease + https://github.com/monarch-initiative/mondo/issues/254 + + + + + + + + + diseases + injury + Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity. + COHD:440921 + EFO:0000546 + ICD10:S00.T98 + MESH:D014947 + NCIT:C3671 + injury + trauma + traumatic injury + wound + MONDO:0021178 + injury + + + + + + + + + diseases + visual system + A disease that involves the visual system. + SCTID:128127008 + 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 + MONDO:0024458 + disease of visual system + + + + + + + + + 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. + ICD9:478.19 + MESH:D010038 + NCIT:C118420 + SCTID:232208008 + UMLS:C0029896 + UMLS:C0395797 + 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 + MONDO:0024623 + Editor note: consider uberon class + otorhinolaryngologic disease + + + + + + + + + diseases + poisoning + A condition or physical state produced by the ingestion, injection, inhalation of or exposure to a deleterious agent. + EFO:0008546 + MESH:D011041 + SCTID:75478009 + UMLS:C0302332 + Poisonings + intoxication + poisoning syndrome + MONDO:0029000 + poisoning + + + + + + + + + planned process + Injecting mice with a vaccine in order to test its efficacy + A processual entity that realizes a plan which is the concretization of a plan specification. + 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process. + Bjoern Peters + branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent + planned process + + + + + + + + + assay + 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. + 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. + PlanAndPlannedProcess Branch + measuring + scientific observation + OBI branch derived + study assay + any method + assay @@ -1064,8 +2241,17 @@ - - material processing + + material processing + A cell lysis, production of a cloning vector, creating a buffer. + A planned process which results in physical changes in a specified input material + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca Serra + material transformation + OBI branch derived + material processing @@ -1076,9 +2262,14 @@ genomics DNA/Genotyping - 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. - Replaces GECKO 'DNA/Genotyping' - genotyping assay + genotyping assay + 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. + Philippe Rocca-Serra + SNP analysis + genotype profiling + OBI Biomaterial + genotyping assay @@ -1089,9 +2280,12 @@ genomics Sequence variants (CNV, SNP arrays) - 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 - Replaces GECKO 'Sequence variants (CNV, SNP arrays)' - copy number variation profiling assay + copy number variation profiling assay + 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 + Philippe Rocca-Serra + CNV analysis + copy number variation profiling assay @@ -1102,9 +2296,12 @@ 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. - Replaces GECKO 'RNAseq/gene expression' - RNA-seq assay + RNA-seq assay + An transcription profiling assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance. + James Malone + transcription profiling by high throughput sequencing + EFO:0002770 + RNA-seq assay @@ -1112,12 +2309,15 @@ - + laboratory measures microbiology - An assay that identifies the organism species in a specimen. - Replaces GECKO 'microbiology' - organism identification assay + organism identification assay + An assay that identifies the organism species in a specimen. + Chris Stoeckert + Jie Zheng + NIAID GSCID-BRC metadata working group + organism identification assay @@ -1128,9 +2328,12 @@ genomics Epigenetics - An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation. - Replaces GECKO 'Epigenetics' - epigenetic modification assay + epigenetic modification assay + An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation. + Chris Stoeckert + Jie Zheng + Penn group + epigenetic modification assay @@ -1141,9 +2344,15 @@ genomics WGS - A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. - Replaces GECKO 'WGS' - whole genome sequencing assay + whole genome sequencing assay + 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. + Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. + ImmPort + WGS + PMID:23095910 + PMID:25827230 + whole genome sequencing assay @@ -1154,9 +2363,29 @@ genomics WES - A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons). - Replaces GECKO 'WES' - exome sequencing assay + exome sequencing assay + 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). + ImmPort + WES + PMID:25827230 + exome sequencing assay + + + + + + + + + physical environment + exposure to carcinogens + exposure to environmental and workplace carcinogens history + A information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + exposure to environmental and workplace carcinogens history @@ -1167,9 +2396,15 @@ 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. - Replaces GECKO 'Metagenomics' - whole metagenome sequencing assay + whole metagenome sequencing assay + 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. + Whole metagenome sequencing has been used to explore the composition and metabolic capability of communities of microbes found in the environment (e.g. in soil, water, etc.) and in humans and other species (e.g. in the gut, oral cavity, etc.). + Rebecca Jackson + WMS + Bjoern Peters + Michelle Giglio + https://github.com/obi-ontology/obi/issues/1056 + whole metagenome sequencing assay @@ -1177,8 +2412,13 @@ - - storage + + storage + PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10. + 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 + Philippe Rocca-Serra + OBI-Branch + storage @@ -1186,11 +2426,16 @@ - + basic cohort attributes study design - 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. - Replaces GECKO 'study design' + 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. + 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. + Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. + PERSON: Chris Stoeckert + experimental design + rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. study design @@ -1199,11 +2444,16 @@ - + population data criteria for enrollment and recruitment procedures - 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. - Replaces GECKO 'criteria for enrollment and recruitment procedures' + inclusion criterion + 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) . + 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. + Person: Philippe Rocca-Serra + inclusion condition + inclusion rule + Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group inclusion criterion @@ -1212,7 +2462,7 @@ - + clinical history @@ -1221,24 +2471,34 @@ - - questionnaire/survey data + + other questionnaire/survey data signs and symptoms - A quality of a patient that is observed by the patient or a processual entity experienced by the patient, either of which is hypothesized by the patient to be a realization of a disease. - Replaces GECKO 'signs and symptoms' symptom + + + + + socio-demographic and economic characteristics + income and possessions + income data + + + + - + socio-demographic and economic characteristics age/birthdate - A time quality inhering in a bearer by virtue of how long the bearer has existed. - Replaces GECKO 'age/birthdate' + A time quality inhering in a bearer by virtue of how long the bearer has existed. + quality + PATO:0000011 age @@ -1250,7 +2510,9 @@ 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. + 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. + quality + PATO:0000047 biological sex @@ -1259,23 +2521,34 @@ - + questionnaire/survey data socio-demographic and economic characteristics - A quality that inheres in an entire organism or part of an organism. + A quality that inheres in an entire organism or part of an organism. + quality + PATO:0001995 organismal quality + + + + + collection of organisms + + + + - + medication prescription - A health care prescription specifying the initiation, modification or cessation of a drug administration. - Replaces GECKO '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. drug prescription @@ -1284,17 +2557,18 @@ - - - - - - - + medication administration - 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 - Replaces GECKO 'administration' + prescribed drug administration specification + '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 drug administration specification @@ -1304,6 +2578,11 @@ + + a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data. + Orlaith Burke + STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic). + statistic statistic @@ -1313,6 +2592,11 @@ + a count of 4 resulting from counting limbs in humans + a count is a data item denoted by an integer and represented the number of instances or occurences of an entity + Orlaith Burke + STATO + count @@ -1324,8 +2608,11 @@ survey administration date and time-related information - Information about a calendar date or timestamp indicating day, month, year and time of an event. - Replaces GECKO 'date and time-related information' + Information about a calendar date or timestamp indicating day, month, year and time of an event. + Alejandra Gonzalez-Beltran + Orlaith Burke + Philippe Rocca-Serra + STATO date @@ -1334,10 +2621,30 @@ - - questionnaire/survey data + + other questionnaire/survey data life stage/time point - An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. + A spatiotemporal region encompassing some part of the life cycle of an organism. + this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here + the WBls class 'all stages' belongs here as it is the superclass of other WBls stages + we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage + BILS:0000105 + EFO:0000399 + FBdv:00007012 + FMA:24120 + HsapDv:0000000 + MmusDv:0000000 + OlatDv:0000010 + PdumDv:0000090 + WBls:0000002 + XAO:1000000 + ZFS:0000000 + ZFS:0100000 + ncithesaurus:Developmental_Stage + developmental stage + stage + uberon + UBERON:0000105 life cycle stage @@ -1349,8 +2656,39 @@ sample type blood - A fluid that is composed of blood plasma and erythrocytes. - Replaces GECKO 'blood' + A fluid that is composed of blood plasma and erythrocytes. + This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. + A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] + Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] + relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] + Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] + AAO:0000046 + BTO:0000089 + CALOHA:TS-0079 + EFO:0000296 + EHDAA2:0000176 + EHDAA:418 + EMAPA:16332 + ENVO:02000027 + EV:0100047 + FMA:9670 + GAID:965 + MA:0000059 + MESH:D001769 + MIAA:0000315 + NCIT:C12434 + OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA + TAO:0000007 + UMLS:C0005767 + VHOG:0000224 + XAO:0000124 + ZFA:0000007 + galen:Blood + portion of blood + vertebrate blood + uberon + whole blood + UBERON:0000178 blood @@ -1359,12 +2697,37 @@ - + 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. - Replaces GECKO 'sample type' - organism substance + 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. + AAO:0010839 + AEO:0000004 + BILA:0000004 + CALOHA:TS-2101 + CARO:0000004 + EHDAA2:0003004 + EMAPA:35178 + FBbt:00007019 + FMA:9669 + HAO:0000004 + MA:0002450 + NCIT:C13236 + SPD:0000008 + TAO:0001487 + TGMA:0001824 + VHOG:0001726 + XAO:0004001 + ZFA:0001487 + galen:BodySubstance + body fluid or substance + body substance + organism substance + portion of body substance + portion of organism substance + uberon + UBERON:0000463 + organism substance @@ -1375,8 +2738,25 @@ sample type urine - Excretion that is the output of a kidney. - Replaces GECKO 'urine' + Excretion that is the output of a kidney + kidney excreta from some taxa (e.g. in aves) may not be liquid + BTO:0001419 + CALOHA:TS-1092 + EFO:0001939 + EMAPA:36554 + ENVO:00002047 + FMA:12274 + GAID:1189 + MA:0002545 + MAT:0000058 + MESH:D014556 + MIAA:0000058 + NCIT:C13283 + OpenCyc:Mx4rvVjGppwpEbGdrcN5Y29ycA + UMLS:C0042036 + galen:Urine + uberon + UBERON:0001088 urine @@ -1388,8 +2768,28 @@ sample type saliva - A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. - Replaces GECKO 'saliva' + A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. + salivary + We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin + BTO:0001202 + CALOHA:TS-0891 + EMAPA:36536 + ENVO:02000036 + FMA:59862 + GAID:1167 + MA:0002507 + MAT:0000444 + MESH:D012463 + NCIT:C13275 + OpenCyc:Mx4rvVjJ95wpEbGdrcN5Y29ycA + UMLS:C0036087 + galen:Saliva + salivary gland secretion + uberon + sailva normalis + saliva atomaris + saliva molecularis + UBERON:0001836 saliva @@ -1401,8 +2801,56 @@ sample type stool - Portion of semisolid bodily waste discharged through the anus. - Replaces GECKO 'stool' + Portion of semisolid bodily waste discharged through the anus[MW,modified] + Excretion in semisolid state processed by the intestine.[FMA] + fecal + excreta + BTO:0000440 + CALOHA:TS-2345 + ENVO:00002003 + FMA:64183 + GAID:1199 + MA:0002509 + MAT:0000053 + MESH:D005243 + MIAA:0000053 + NCIT:C13234 + OpenCyc:Mx4rvVjJMZwpEbGdrcN5Y29ycA + UMLS:C0015733 + galen:Feces + 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 + uberon + droppings + excrement + ordure + spoor + UBERON:0001988 feces diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..6719541 --- /dev/null +++ b/requirements.txt @@ -0,0 +1 @@ +ontodev-gizmos==0.1.1 \ No newline at end of file diff --git a/src/ontology/annotations.owl b/src/ontology/annotations.owl new file mode 100644 index 0000000..1eb4b1f --- /dev/null +++ b/src/ontology/annotations.owl @@ -0,0 +1,1722 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + editor preferred term + + + + + + + + example of usage + + + + + + + + definition + + + + + + + + editor note + + + + + + + + term editor + + + + + + + + alternative term + + + + + + + + + + + + + + curator note + + + + + + + + term tracker item + + + + + + + + ontology term requester + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + external_definition + + + + + + + + axiom_lost_from_external_ontology + + + + + + + + homology_notes + + + + + + + + has_relational_adjective + + + + + + + + taxon_notes + + + + + + + + external_ontology_notes + + + + + + + + + + + + + + + + + + + + + + + + + + has_alternative_id + + + + + + + + has_broad_synonym + + + + + + + + + + + + + + has_exact_synonym + + + + + + + + has_narrow_synonym + + + + + + + + has_obo_namespace + + + + + + + + has_related_synonym + + + + + + + + id + + + + + + + + in_subset + + + + + + + + label + + + + + + + + see also + + + + + + + + + + + + + process + Process + a process of cell-division, \ a beating of the heart + a process of meiosis + a process of sleeping + the course of a disease + the flight of a bird + the life of an organism + your process of aging. + 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]) + BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + + + + + + + disposition + Disposition + an atom of element X has the disposition to decay to an atom of element Y + certain people have a predisposition to colon cancer + children are innately disposed to categorize objects in certain ways. + the cell wall is disposed to filter chemicals in endocytosis and exocytosis + BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) + (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] + (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] + + + + + + + + realizable + RealizableEntity + the disposition of this piece of metal to conduct electricity. + the disposition of your blood to coagulate + the function of your reproductive organs + the role of being a doctor + the role of this boundary to delineate where Utah and Colorado meet + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + + + + + + + quality + Quality + the ambient temperature of this portion of air + the color of a tomato + the length of the circumference of your waist + the mass of this piece of gold. + the shape of your nose + the shape of your nostril + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) + If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) + (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] + (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] + + + + + + + + site + Site + Manhattan Canyon) + a hole in the interior of a portion of cheese + a rabbit hole + an air traffic control region defined in the airspace above an airport + the Grand Canyon + the Piazza San Marco + the cockpit of an aircraft + the hold of a ship + the interior of a kangaroo pouch + the interior of the trunk of your car + the interior of your bedroom + the interior of your office + the interior of your refrigerator + the lumen of your gut + your left nostril (a fiat part – the opening – of your left nasal cavity) + b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) + (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] + + + + + + + + material + MaterialEntity + a flame + a forest fire + a human being + a hurricane + a photon + a puff of smoke + a sea wave + a tornado + an aggregate of human beings. + an energy wave + an epidemic + the undetached arm of a human being + BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 + BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. + BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + + + + + + + An information content entity indicating the cause of death for a participant in the study. + Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey + Penn Group + PRISM + + + + + + + + an information content entity that is about a part of a health care encounter that occurs in a hospital facility + Person: John Judkins + EuPathDB + ICEMR protein array + + + + + + + + An information content entity that is about an activity that realizes a social role and is often performed for payment. + + + + + + + + a categorical value specification that is about a human being and specifies whether that human being is joined to another human being in marriage + Person: John Judkins + EuPathDB, BFO's 'relational quality' examples + + + + + + + + An information content entity about healthcare that is private or public. + + + + + + + + environmental system associated with the dwelling used by humans. + Person: Cristian Cocos, Jie Zheng, Chris Stoeckert + Penn Group + GEMS + + + + + + + + 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. + jl + 2012-09-19T15:05:24Z + GO:0000004 + GO:0007582 + GO:0044699 + Wikipedia:Biological_process + biological process + physiological process + biological_process + single organism process + single-organism process + GO:0008150 + 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. + + + + + + + + objective specification + In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. + 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. + 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." + 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. + Answers the question, why did you do this experiment? + PERSON: Alan Ruttenberg + PERSON: Barry Smith + PERSON: Bjoern Peters + PERSON: Jennifer Fostel + goal specification + OBI Plan and Planned Process/Roles Branch + OBI_0000217 + + + + + + + + data item + Data items include counts of things, analyte concentrations, and statistical summaries. + 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. + 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ + PERSON: Alan Ruttenberg + PERSON: Chris Stoeckert + PERSON: Jonathan Rees + data + + + + + + + + information content entity + Examples of information content entites include journal articles, data, graphical layouts, and graphs. + A generically dependent continuant that is about some thing. + 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). + information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. + PERSON: Chris Stoeckert + OBI_0000142 + + + + + + + + An information content entity whose concretizations indicate to their bearer how to realize them in a process. + 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. + 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. + 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO + Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + + + + + + + + plan specification + PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. + 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. + 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. + 2014-03-31: A plan specification can have other parts, such as conditional specifications. + Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved + Alan Ruttenberg + OBI Plan and Planned Process branch + OBI_0000344 + 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 + + + + + + + + measurement datum + 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,}. + A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. + 2/2/2009 is_specified_output of some assay? + person:Chris Stoeckert + OBI_0000305 + group:OBI + + + + + + + + textual entity + Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities + 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. + AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. + MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. + PERSON: Lawrence Hunter + text + + + + + + + + document + A journal article, patent application, laboratory notebook, or a book + A collection of information content entities intended to be understood together as a whole + PERSON: Lawrence Hunter + + + + + + + + availability textual entity + 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 + A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained. + PERSON: Bill Baumgartner + + + + + + + + consent textual entity + 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. + A textual entity that documents the consenting process used to enroll patients in a study. + PERSON: Bill Baumgartner + + + + + + + + identifier + 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. + + + + + + + + A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. + DOID:4 + EFO:0000408 + ICD10:N18 + ICD9:799.9 + MESH:D004194 + NCIT:C2991 + OGMS:0000031 + Orphanet:377788 + SCTID:64572001 + UMLS:C0012634 + condition + disease + disease or disorder + disease or disorder, non-neoplastic + diseases + diseases and disorders + disorder + disorders + medical condition + other disease + MONDO:0000001 + + + + + + + + A disease involving the integumental system. + MONDO:0045027 + DOID:16 + SCTID:128598002 + UMLS:C1290011 + 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 + MONDO:0002051 + + + + + + + + A disease involving the musculoskeletal system. + DOID:17 + ICD9:729.99 + MESH:D009140 + NCIT:C107377 + SCTID:928000 + UMLS:C0026857 + 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 + MONDO:0002081 + + + + + + + + A disease involving the connective tissue. + COHD:253549 + DOID:65 + MESH:D003240 + NCIT:C26729 + SCTID:105969002 + UMLS:C0009782 + connective tissue disease + connective tissue disease or disorder + connective tissue diseases + connective tissue disorder + connective tissue disorders + disease of connective tissue + disease or disorder of connective tissue + disease, connective tissue + disorder of connective tissue + primary disorder of connective tissue + tissue disease, connective + disorder of connective tissue + MONDO:0003900 + + + + + + + + A disease or disorder that involves the digestive system. + COHD:4201745 + DOID:77 + EFO:0000405 + ICD10:K92.9 + ICD9:520-579.99 + ICD9:V47.3 + MESH:D005767 + NCIT:C2990 + SCTID:53619000 + 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 + MONDO:0004335 + + + + + + + + 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. + COHD:443392 + DOID:0050686 + DOID:0050687 + DOID:162 + EFO:0000311 + GARD:0011960 + ICD10:C80 + ICD10:C80.1 + ICD9:195.8 + ICD9:199 + ICD9:199.1 + ICDO:8000/3 + NCIT:C9305 + NIFSTD:birnlex_406 + ONCOTREE:MT + SCTID:363346000 + UMLS:C0006826 + 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 + MONDO:0004992 + + + + + + + + A disease involving the cardiovascular system. + DOID:1287 + EFO:0000319 + ICD10:I00.I99 + ICD9:390-459.99 + ICD9:420-429.99 + ICD9:423 + ICD9:423.8 + ICD9:424 + ICD9:429 + ICD9:429.2 + ICD9:429.7 + ICD9:429.8 + ICD9:429.81 + ICD9:429.89 + ICD9:459.89 + ICD9:459.9 + MESH:D002318 + NCIT:C2931 + SCTID:49601007 + UMLS:C0007222 + 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 + MONDO:0004995 + + + + + + + + A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves. + DOID:863 + EFO:0000618 + ICD10:G00-G99 + ICD10:G00.G99 + ICD10:G98 + ICD10:G98.8 + ICD9:349.89 + ICD9:349.9 + MESH:D009422 + NCIT:C26835 + SCTID:118940003 + UMLS:C0027765 + Wikipedia:Nervous_system_disease + 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 + MONDO:0005071 + + + + + + + + A disease that has its basis in the disruption of mental process. + EFO:0000677 + ICD10:F00.F99 + ICD9:290-299.99 + ICD9:298.8 + ICD9:V11.9 + NIFSTD:birnlex_12669 + SCTID:74732009 + UMLS:CN240636 + disorder of mental process + mental or behavioural disorder + mental process disease + disorder of mental process + MONDO:0005084 + + + + + + + + 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. + DOID:1579 + EFO:0000684 + ICD10:J96-J99 + ICD10:J98 + ICD9:460-519.99 + ICD9:500-508.99 + ICD9:503 + ICD9:508 + ICD9:508.1 + ICD9:508.8 + ICD9:508.9 + ICD9:510-519.99 + ICD9:516 + ICD9:516.8 + ICD9:516.9 + ICD9:517 + ICD9:517.8 + ICD9:519 + ICD9:519.1 + ICD9:519.3 + ICD9:519.8 + ICD9:519.9 + ICD9:V12.60 + ICD9:V47.2 + MESH:D012140 + NCIT:C26871 + SCTID:50043002 + 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 + MONDO:0005087 + + + + + + + + A disease involving the endocrine system. + DOID:28 + EFO:0001379 + ICD10:E34.9 + ICD9:259.8 + ICD9:259.9 + MESH:D004700 + NCIT:C3009 + SCTID:362969004 + UMLS:C0014130 + 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 + MONDO:0005151 + + + + + + + + A disorder resulting from the presence and activity of a microbial, viral, or parasitic agent. It can be transmitted by direct or indirect contact. + DOID:0050117 + EFO:0005741 + ICD10:A00.B99 + ICD9:079.0 + ICD9:136.8 + ICD9:136.9 + IDO:0000436 + MESH:D003141 + NCIT:C26726 + SCTID:40733004 + ID + clinical infection + communicable disease + infection + infectious + infectious disease + infectious diseases and manifestations + infectious disorder + transmissible disease + disease by infectious agent + MONDO:0005550 + 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. + + + + + + + + A disease involving the hematopoietic system. + DOID:74 + EFO:0005803 + GTR:AN1320635 + ICD10:D75.9 + ICD9:280-289.99 + ICD9:289.8 + ICD9:289.9 + MESH:D006402 + NCIT:C26323 + Orphanet:97992 + SCTID:414022008 + UMLS:C0018939 + UMLS:CN206939 + UMLS:CN882913 + 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 + MONDO:0005570 + placeholder for lymphoid disease + https://github.com/monarch-initiative/mondo/issues/254 + + + + + + + + Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity. + COHD:440921 + EFO:0000546 + ICD10:S00.T98 + MESH:D014947 + NCIT:C3671 + injury + trauma + traumatic injury + wound + MONDO:0021178 + + + + + + + + A disease that involves the visual system. + SCTID:128127008 + 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 + MONDO:0024458 + + + + + + + + Pathological processes of the ear, the nose, and the throat, also known as the ENT diseases. + ICD9:478.19 + MESH:D010038 + NCIT:C118420 + SCTID:232208008 + UMLS:C0029896 + UMLS:C0395797 + 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 + MONDO:0024623 + Editor note: consider uberon class + + + + + + + + A condition or physical state produced by the ingestion, injection, inhalation of or exposure to a deleterious agent. + EFO:0008546 + MESH:D011041 + SCTID:75478009 + UMLS:C0302332 + Poisonings + intoxication + poisoning syndrome + MONDO:0029000 + + + + + + + + planned process + 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. + 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process. + Bjoern Peters + branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent + + + + + + + + assay + 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. + 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. + PlanAndPlannedProcess Branch + measuring + scientific observation + OBI branch derived + study assay + any method + + + + + + + + material processing + A cell lysis, production of a cloning vector, creating a buffer. + A planned process which results in physical changes in a specified input material + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca Serra + material transformation + OBI branch derived + + + + + + + + genotyping assay + 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. + Philippe Rocca-Serra + SNP analysis + genotype profiling + OBI Biomaterial + + + + + + + + copy number variation profiling assay + 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 + Philippe Rocca-Serra + CNV analysis + + + + + + + + RNA-seq assay + An transcription profiling assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance. + James Malone + transcription profiling by high throughput sequencing + EFO:0002770 + + + + + + + + organism identification assay + An assay that identifies the organism species in a specimen. + Chris Stoeckert + Jie Zheng + NIAID GSCID-BRC metadata working group + + + + + + + + epigenetic modification assay + An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation. + Chris Stoeckert + Jie Zheng + Penn group + + + + + + + + whole genome sequencing assay + 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. + Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. + ImmPort + WGS + PMID:23095910 + PMID:25827230 + + + + + + + + exome sequencing assay + 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). + ImmPort + WES + PMID:25827230 + + + + + + + + exposure to environmental and workplace carcinogens history + A information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + + + + + + + + whole metagenome sequencing assay + 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. + Whole metagenome sequencing has been used to explore the composition and metabolic capability of communities of microbes found in the environment (e.g. in soil, water, etc.) and in humans and other species (e.g. in the gut, oral cavity, etc.). + Rebecca Jackson + WMS + Bjoern Peters + Michelle Giglio + https://github.com/obi-ontology/obi/issues/1056 + + + + + + + + storage + PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10. + 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 + Philippe Rocca-Serra + OBI-Branch + + + + + + + + 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. + 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. + Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. + PERSON: Chris Stoeckert + experimental design + rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. + + + + + + + + inclusion criterion + 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) . + 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. + Person: Philippe Rocca-Serra + inclusion condition + inclusion rule + Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group + + + + + + + + A time quality inhering in a bearer by virtue of how long the bearer has existed. + quality + PATO:0000011 + + + + + + + + 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. + quality + PATO:0000047 + + + + + + + + A quality that inheres in an entire organism or part of an organism. + quality + PATO:0001995 + + + + + + + + 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. + group of organism + organism collection + May be of the same or different species. + + + + + + + + "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. + + + + + + + + prescribed drug administration specification + '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 + + + + + + + + + a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data. + Orlaith Burke + STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic). + statistic + + + + + + + + a count of 4 resulting from counting limbs in humans + a count is a data item denoted by an integer and represented the number of instances or occurences of an entity + Orlaith Burke + STATO + + + + + + + + + Information about a calendar date or timestamp indicating day, month, year and time of an event. + Alejandra Gonzalez-Beltran + Orlaith Burke + Philippe Rocca-Serra + STATO + + + + + + + + A spatiotemporal region encompassing some part of the life cycle of an organism. + this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here + the WBls class 'all stages' belongs here as it is the superclass of other WBls stages + we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage + BILS:0000105 + EFO:0000399 + FBdv:00007012 + FMA:24120 + HsapDv:0000000 + MmusDv:0000000 + OlatDv:0000010 + PdumDv:0000090 + WBls:0000002 + XAO:1000000 + ZFS:0000000 + ZFS:0100000 + ncithesaurus:Developmental_Stage + developmental stage + stage + uberon + UBERON:0000105 + + + + + + + + A fluid that is composed of blood plasma and erythrocytes. + This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. + A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] + Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] + relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] + Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] + AAO:0000046 + BTO:0000089 + CALOHA:TS-0079 + EFO:0000296 + EHDAA2:0000176 + EHDAA:418 + EMAPA:16332 + ENVO:02000027 + EV:0100047 + FMA:9670 + GAID:965 + MA:0000059 + MESH:D001769 + MIAA:0000315 + NCIT:C12434 + OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA + TAO:0000007 + UMLS:C0005767 + VHOG:0000224 + XAO:0000124 + ZFA:0000007 + galen:Blood + portion of blood + vertebrate blood + uberon + whole blood + UBERON:0000178 + + + + + + + + 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. + AAO:0010839 + AEO:0000004 + BILA:0000004 + CALOHA:TS-2101 + CARO:0000004 + EHDAA2:0003004 + EMAPA:35178 + FBbt:00007019 + FMA:9669 + HAO:0000004 + MA:0002450 + NCIT:C13236 + SPD:0000008 + TAO:0001487 + TGMA:0001824 + VHOG:0001726 + XAO:0004001 + ZFA:0001487 + galen:BodySubstance + body fluid or substance + body substance + organism substance + portion of body substance + portion of organism substance + uberon + UBERON:0000463 + + + + + + + + Excretion that is the output of a kidney + kidney excreta from some taxa (e.g. in aves) may not be liquid + BTO:0001419 + CALOHA:TS-1092 + EFO:0001939 + EMAPA:36554 + ENVO:00002047 + FMA:12274 + GAID:1189 + MA:0002545 + MAT:0000058 + MESH:D014556 + MIAA:0000058 + NCIT:C13283 + OpenCyc:Mx4rvVjGppwpEbGdrcN5Y29ycA + UMLS:C0042036 + galen:Urine + uberon + UBERON:0001088 + + + + + + + + A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. + salivary + We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin + BTO:0001202 + CALOHA:TS-0891 + EMAPA:36536 + ENVO:02000036 + FMA:59862 + GAID:1167 + MA:0002507 + MAT:0000444 + MESH:D012463 + NCIT:C13275 + OpenCyc:Mx4rvVjJ95wpEbGdrcN5Y29ycA + UMLS:C0036087 + galen:Saliva + salivary gland secretion + uberon + sailva normalis + saliva atomaris + saliva molecularis + UBERON:0001836 + + + + + + + + Portion of semisolid bodily waste discharged through the anus[MW,modified] + Excretion in semisolid state processed by the intestine.[FMA] + fecal + excreta + BTO:0000440 + CALOHA:TS-2345 + ENVO:00002003 + FMA:64183 + GAID:1199 + MA:0002509 + MAT:0000053 + MESH:D005243 + MIAA:0000053 + NCIT:C13234 + OpenCyc:Mx4rvVjJMZwpEbGdrcN5Y29ycA + UMLS:C0015733 + galen:Feces + 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 + uberon + droppings + excrement + ordure + spoor + UBERON:0001988 + + + + + + + diff --git a/src/ontology/templates/annotation-properties.tsv b/src/ontology/templates/annotation-properties.tsv new file mode 100644 index 0000000..3e8ddf3 --- /dev/null +++ b/src/ontology/templates/annotation-properties.tsv @@ -0,0 +1,27 @@ +ID Label Type +ID LABEL TYPE +IAO:0000111 editor preferred term owl:AnnotationProperty +IAO:0000112 example of usage owl:AnnotationProperty +IAO:0000115 definition owl:AnnotationProperty +IAO:0000116 editor note owl:AnnotationProperty +IAO:0000117 term editor owl:AnnotationProperty +IAO:0000118 alternative term owl:AnnotationProperty +IAO:0000232 curator note owl:AnnotationProperty +IAO:0000233 term tracker item owl:AnnotationProperty +IAO:0000234 ontology term requester owl:AnnotationProperty +obo:UBPROP_0000001 external_definition owl:AnnotationProperty +obo:UBPROP_0000002 axiom_lost_from_external_ontology owl:AnnotationProperty +obo:UBPROP_0000003 homology_notes owl:AnnotationProperty +obo:UBPROP_0000007 has_relational_adjective owl:AnnotationProperty +obo:UBPROP_0000008 taxon_notes owl:AnnotationProperty +obo:UBPROP_0000012 external_ontology_notes owl:AnnotationProperty +oboInOwl:hasAlternativeId has_alternative_id owl:AnnotationProperty +oboInOwl:hasBroadSynonym has_broad_synonym owl:AnnotationProperty +oboInOwl:hasExactSynonym has_exact_synonym owl:AnnotationProperty +oboInOwl:hasNarrowSynonym has_narrow_synonym owl:AnnotationProperty +oboInOwl:hasOBONamespace has_obo_namespace owl:AnnotationProperty +oboInOwl:hasRelatedSynonym has_related_synonym owl:AnnotationProperty +oboInOwl:id id owl:AnnotationProperty +oboInOwl:inSubset in_subset owl:AnnotationProperty +rdfs:label label owl:AnnotationProperty +rdfs:seeAlso see also owl:AnnotationProperty diff --git a/src/ontology/templates/external.tsv b/src/ontology/templates/external.tsv index 3b49f6d..492c7eb 100644 --- a/src/ontology/templates/external.tsv +++ b/src/ontology/templates/external.tsv @@ -1,27 +1,85 @@ -ID Label Parent Defintion -ID LABEL SC % A definition -COB:0000001 quality -COB:0000006 material entity -COB:0000031 immaterial entity -COB:0000032 geographical location immaterial entity -COB:0000033 realizable -COB:0000034 process -COB:0000035 planned process process -COB:0000037 biological process process -COB:0000055 collection of organisms material entity -COB:0000061 information -COB:0000069 directive information entity information -COB:0000079 plan specification directive information entity -COB:0000101 document information -COB:0000102 data item information -COB:0000107 assay planned process -COB:0000111 disposition realizable -IAO:0000109 measurement datum data item -IAO:0000300 textual entity information -IAO:0000612 availability textual entity textual entity -IAO:0020000 identifier information -OBI:0000094 material processing planned process -OBI:0302893 storage planned process -OGMS:0000015 clinical history information -STATO:0000039 statistic measurement datum -STATO:0000047 count measurement datum +Label IHCC Browser Label Parent Category Comment +LABEL A 'IHCC browser label' SC % A 'IHCC category' +age age/birthdate quality socio-demographic and economic characteristics Replaces GECKO 'age/birthdate' +assay planned process +availability textual entity textual entity +belief personal beliefs and values disposition other questionnaire/survey data +biological_process process +biological sex biological sex organismal quality socio-demographic and economic characteristics +blood blood organism substance sample type Replaces GECKO 'blood' +blood pressure measurement data item blood pressure cardiovascular measurement data item circulation and respiration Replaces GECKO 'blood pressure' +body height data item height body morphological measurement data item anthropometry Replaces GECKO 'height' +body morphological measurement data item anthropometry clinical measurement data item physiological measurements Replaces GECKO 'anthropometry' +body weight data item weight body morphological measurement data item anthropometry Replaces GECKO 'weight' +cancer oncological disease or disorder diseases Replaces GECKO 'oncological' +cardiovascular disease circulatory system disease or disorder diseases Replaces GECKO 'circulatory system' +cardiovascular measurement data item circulation and respiration clinical measurement data item physiological measurements Replaces GECKO 'circulation and respiration' +cause of participant death cause of death information content entity other questionnaire/survey data +clinical history information content entity +clinical measurement data item physiological measurements measurement datum questionnaire/survey data Replaces GECKO 'physiological measurements' +collection of organisms material entity +connective tissue disease connective tissue disease or disorder diseases +consent textual entity consent/accessibility textual entity survey administration Replaces GECKO 'consent/accessibility' +copy number variation profiling assay Sequence variants (CNV, SNP arrays) genomic assay genomics Replaces GECKO 'Sequence variants (CNV, SNP arrays)' +count measurement datum +data item information content entity +date date and time-related information measurement datum survey administration Replaces GECKO 'date and time-related information' +digestive system disease digestive system disease or disorder diseases Replaces GECKO 'digestive system' +directive information entity information content entity +disease of visual system visual system disease or disorder diseases +disease or disorder diseases disposition questionnaire/survey data Replaces GECKO 'diseases' +disposition realizable entity +document information content entity +drug administration specification administration directive information entity medication Replaces GECKO 'administration' +drug prescription prescription document medication Replaces GECKO 'prescription' +endocrine system disease endocrine/nutritional/metabolic disorders disease or disorder diseases Replaces GECKO 'endocrine/nutritional/metabolic disorders' +environment associated with human dwelling physical environment material entity questionnaire/survey data +epigenetic modification assay Epigenetics genomic assay genomics Replaces GECKO 'Epigenetics' +exome sequencing assay WES genomic assay genomics Replaces GECKO 'WES' +exposure to environmental and workplace carcinogens history exposure to carcinogens information content entity physical environment +feces stool organism substance sample type Replaces GECKO 'stool' +genotyping assay DNA/Genotyping genomic assay genomics Replaces GECKO 'DNA/Genotyping' +healthcare information healthcare information information content entity questionnaire/survey data +hematologic disease blood-related disorders disease or disorder diseases Replaces GECKO 'blood-related disorders' +hospitalization information hospitalizations information content entity healthcare information +identifier information content entity +immaterial entity +inclusion criterion criteria for enrollment and recruitment procedures directive information entity population data Replaces GECKO 'criteria for enrollment and recruitment procedures' +income data income and possessions data item socio-demographic and economic characteristics +infectious disease infectious disease disease or disorder diseases +information content entity +injury injury disease or disorder diseases +integumentary system disease skin and subcutaneous tissue disease or disorder diseases +life cycle stage life stage/time point process other questionnaire/survey data +marital status marital status information content entity socio-demographic and economic characteristics +material entity +material processing planned process +measurement datum data item +mental disorder mental and behaviour disorders disease or disorder diseases Replaces GECKO 'mental and behaviour disorders' +musculoskeletal system disease musculoskeletal system disease or disorder diseases +nervous system disorder nervous system disease or disorder diseases Replaces GECKO 'nervous system' +objective specification aims and objectives directive information entity basic cohort attributes Replaces GECKO 'aims and objectives' +occupation occupation information content entity socio-demographic and economic characteristics +organism identification assay microbiology assay laboratory measures Replaces GECKO 'microbiology' +organism substance sample type material entity biosample Replaces GECKO 'sample type' +organismal quality socio-demographic and economic characteristics quality questionnaire/survey data +otorhinolaryngologic disease diseases of the ear, nose, and/or throat disease or disorder diseases +plan specification directive information entity +planned process process +poisoning poisoning disease or disorder diseases +process +pulse data item heart rate (HR) cardiovascular measurement data item circulation and respiration Replaces GECKO 'heart rate (HR)' +quality +realizable entity +respiratory system disease respiratory system disease or disorder diseases Replaces GECKO 'respiratory system' +RNA-seq assay RNAseq/gene expression genomic assay genomics Replaces GECKO 'RNAseq/gene expression' +saliva saliva organism substance sample type Replaces GECKO 'saliva' +site immaterial entity +statistic measurement datum +storage planned process +study design study design plan specification basic cohort attributes Replaces GECKO 'study design' +symptom signs and symptoms quality other questionnaire/survey data Replaces GECKO 'signs and symptoms' +textual entity information content entity +urine urine organism substance sample type Replaces GECKO 'urine' +whole genome sequencing assay WGS genomic assay genomics Replaces GECKO 'WGS' +whole metagenome sequencing assay Metagenomics genomic assay genomics Replaces GECKO 'Metagenomics' diff --git a/src/ontology/templates/gecko.tsv b/src/ontology/templates/gecko.tsv index 2cf375a..e6afa18 100644 --- a/src/ontology/templates/gecko.tsv +++ b/src/ontology/templates/gecko.tsv @@ -1,84 +1,57 @@ -ID Label IHCC Browser Label Parent Definition Definition Source Category Class Type About Inheres In Part Of Comment -ID LABEL A 'IHCC browser label' SC % SPLIT=| A definition A definition source A 'IHCC category' CLASS_TYPE C 'is about' some % C 'inheres in' some % C 'part of' some % A comment -CMO:0000000 clinical measurement data item physiological measurements measurement datum A quantitative or qualitative value which is the result of an act of assessing a morphological or physiological state or property in a single individual or sample or a group of individuals or samples, based on direct observation or experimental manipulation. questionnaire/survey data Replaces GECKO 'physiological measurements' -CMO:0000001 cardiovascular measurement data item circulation and respiration clinical measurement data item Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart and/or blood vessels. physiological measurements Replaces GECKO 'circulation and respiration' -CMO:0000003 blood pressure measurement data item blood pressure cardiovascular measurement data item Measurement of the pressure, or force per area, exerted by circulating blood against the walls of the blood vessels. The pressure is dependent on the energy of the heart action, elasticity of the vessel walls and volume and viscosity of the blood. circulation and respiration Replaces GECKO 'blood pressure' -CMO:0000012 body weight data item weight body morphological measurement data item The heaviness or degree to which an entire organism's body is drawn to the earth by gravity. anthropometry Replaces GECKO 'weight' -CMO:0000021 body morphological measurement data item anthropometry clinical measurement data item Measurement of the structure or forms of the entire body or parts of the body of an organism. physiological measurements Replaces GECKO 'anthropometry' -CMO:0000106 body height data item height body morphological measurement data item The vertical measurement of a body. anthropometry Replaces GECKO 'height' -CMO:0000294 pulse data item heart rate (HR) cardiovascular measurement data item The count of the rhythmic contractions and expansions of an artery due to the surge of blood from the beat of the heart. circulation and respiration Replaces GECKO 'heart rate (HR)' -COB:0000076 objective specification aims and objectives directive information entity basic cohort attributes Replaces GECKO 'aims and objectives' -GECKO:0000003 timeline timeline directive information entity A directive information entity that specifies the sequence in which a series of events occurred or will occur. basic cohort attributes -GECKO:0000005 population data item population data data item A data item that is about a population of organisms. basic cohort attributes equivalent collection of organisms -GECKO:0000006 population location location population data item A population data item that is about the geographical location of a population of organisms. population data geographical location -GECKO:0000008 population size num. participants sample size A sample size that is about the count of individual organisms in a population. population data collection of organisms -GECKO:0000009 population quality demographic data quality A quality which inheres in a population of organisms. basic cohort attributes equivalent collection of organisms -GECKO:0000010 population sex or sexes sex(es) studied in cohort population quality A population quality concerning the sex or sexes of the population. demographic data -GECKO:0000011 population gender or genders gender(s) studied in cohort population quality A population quality concerning the gender or genders of the population. demographic data -GECKO:0000012 population age range age range population quality A population quality concerning the age range of a population. demographic data -GECKO:0000013 data collection data collection events planned process A planned process that is a part of an investigation in which raw data is collected. basic cohort attributes -GECKO:0000019 blood collected from fasting subject fasting or non-fasting blood Blood that is collected from an organism which has been fasting for a given amount of time. blood -GECKO:0000026 biosample storage storage method storage A storage process for a biosample collected from an organism. biosample -GECKO:0000032 genomic assay genomics assay An assay that investigates the genome or genomes of an individual organism or population of organisms. laboratory measures Merged GECKO 'data type' into 'genomics'. -GECKO:0000040 microbiome sequencing assay Microbiome markers (rRNA, etc) genomic assay A genomic assay that profiles the microorganisms present in a sample. genomics Potential new OBI request -GECKO:0000042 eQTL analysis eQTL (Cis eQTLs and/or Trans eQTLs) genomic assay A genomic assay that identifies genetic loci and candidate genes correlated with phenotypes. PMID:27964730 genomics Potential new OBI request -GECKO:0000044 biosample size sample size count A count of the number of biosamples collected for an investigation. biosample -GECKO:0000047 biosample processing processing method material processing A material processing which prepares a biosample for investigation. biosample -GECKO:0000055 unique identifier unique identifiers identifier An identifier that is guaranteed to be unique among all identifiers in a particular domain. Wikipedia:Unique_identifier survey administration -GECKO:0000060 gender gender organismal quality 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 socio-demographic and economic characteristics -GECKO:0000061 ethnicity ethnicity/race organismal quality 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 socio-demographic and economic characteristics -GECKO:0000063 birthplace location birthplace geographical location A geographical location in which an individual was born. socio-demographic and economic characteristics -GECKO:0000064 residence location residence geographical location A geographical location in which an individual currently resides. socio-demographic and economic characteristics -GECKO:0000065 education level education organismal quality An organismal quality inhering in a bearer by virute of the bearer's highest level of formal education completed. socio-demographic and economic characteristics -GECKO:0000066 family and household structure family and household structure information Information that is about the structure of an individual's family and/or household. socio-demographic and economic characteristics -GECKO:0000067 lifestyle history lifestyle and behaviours clinical history A clinical history that is about the lifestyle and behaviors of an individual which may impact health outcomes. questionnaire/survey data -GECKO:0000068 tobacco use history tobacco lifestyle history A lifestyle history that is about the tobacco use or exposure of an individual. lifestyle and behaviours -GECKO:0000069 alcohol use history alcohol lifestyle history A lifestyle history that is about the alcohol consumption of an individual. lifestyle and behaviours -GECKO:0000071 sleep history sleep lifestyle history A lifestyle history that is about the sleep quality and duration of an individual. lifestyle and behaviours -GECKO:0000072 nutritional history nutrition lifestyle history A lifestyle history that is about the diet and nutrition of an individual. lifestyle and behaviours -GECKO:0000073 physician contact textual entity physician/practitioner info textual entity A textual entity that contains contact details for an individual's physician, which may include: name, phone number, address, etc. questionnaire/survey data -GECKO:0000091 non-pharmacological treatment history non-pharmacological interventions treatment history questionnaire/survey data -GECKO:0000092 surgical history surgical interventions non-pharmacological treatment history A clinical history that is about surgical operations performed on an individual. non-pharmacological interventions -GECKO:0000093 prescription drug history medication treatment history A clinical history that is about the prescription drugs taken by an individual. questionnaire/survey data -GECKO:0000094 disease treated by prescription drug associated disease(s) information Information that is about the disease treated by a drug prescribed to an individual. medication prescription drug history -GECKO:0000096 response to medication drug response(s) biological process A biological process that results from a drug stimulus. medication -GECKO:0000102 summary statistic for federated data summary statistics for additional data from federated sources statistic A statistic that summarizes a set of federated data. statistics -GECKO:0000103 recreational drug history drugs lifestyle history A lifestyle history that is about the use of unprescribed and/or non-prescription drugs. lifestyle and behaviours -GECKO:0000104 physical activity history physical activity lifestyle history A lifestyle history that is about the typical physical activity of an individual. lifestyle and behaviours -GECKO:0000106 sample size count A count which represents the subset of a collection chosen for an investigation, survey, or assay. -GECKO:0000113 biosample availability textual entity availability availability textual entity An availability textual entity that is about a substance from an organism (a biosample). biosample organism substance -GECKO:0000114 reproductive history reproduction clinical history A clinical history that is about pregnancy, maternity, fertility, menses, and any other reproductive aspect. questionnaire/survey data -GECKO:0000115 treatment history clinical history A clinical history that is about any treatment (surgical, prescription, etc.) for disease, disorder, or symptom. -IAO:0000619 consent textual entity consent/accessibility textual entity A textual entity that documents the consenting process used to enroll patients in a study. survey administration Replaces GECKO 'consent/accessibility' -MONDO:0000001 disease or disorder diseases disposition A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. questionnaire/survey data Replaces GECKO 'diseases' -MONDO:0004335 digestive system disease digestive system disease or disorder A disease or disorder that involves the digestive system. diseases Replaces GECKO 'digestive system' -MONDO:0004992 cancer oncological disease or disorder 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. diseases Replaces GECKO 'oncological' -MONDO:0004995 cardiovascular disease circulatory system disease or disorder A disease involving the cardiovascular system. diseases Replaces GECKO 'circulatory system' -MONDO:0005071 nervous system disorder nervous system disease or disorder A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves. diseases Replaces GECKO 'nervous system' -MONDO:0005084 mental disorder mental and behaviour disorders disease or disorder A disease that has its basis in the disruption of mental process. diseases Replaces GECKO 'mental and behaviour disorders' -MONDO:0005087 respiratory system disease respiratory system disease or disorder 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. diseases Replaces GECKO 'respiratory system' -MONDO:0005151 endocrine system disease endocrine/nutritional/metabolic disorders disease or disorder A disease involving the endocrine system. diseases Replaces GECKO 'endocrine/nutritional/metabolic disorders' -MONDO:0005570 hematologic disease blood-related disorders disease or disorder A disease involving the hematopoietic system. diseases Replaces GECKO 'blood-related disorders' -OBI:0000435 genotyping assay DNA/Genotyping genomic assay 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. genomics Replaces GECKO 'DNA/Genotyping' -OBI:0000537 copy number variation profiling assay Sequence variants (CNV, SNP arrays) genomic assay 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 genomics Replaces GECKO 'Sequence variants (CNV, SNP arrays)' -OBI:0001271 RNA-seq assay RNAseq/gene expression genomic assay An transcription profiling assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance. genomics Replaces GECKO 'RNAseq/gene expression' -OBI:0001624 organism identification assay microbiology assay An assay that identifies the organism species in a specimen. laboratory measures Replaces GECKO 'microbiology' -OBI:0002020 epigenetic modification assay Epigenetics genomic assay An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation. genomics Replaces GECKO 'Epigenetics' -OBI:0002117 whole genome sequencing assay WGS genomic assay A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. genomics Replaces GECKO 'WGS' -OBI:0002118 exome sequencing assay WES genomic assay A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons). genomics Replaces GECKO 'WES' -OBI:0002623 whole metagenome sequencing assay Metagenomics genomic assay 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. genomics Replaces GECKO 'Metagenomics' -OBI:0500000 study design study design plan specification 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. basic cohort attributes Replaces GECKO 'study design' -OBI:0500027 inclusion criterion criteria for enrollment and recruitment procedures directive information entity 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. population data Replaces GECKO 'criteria for enrollment and recruitment procedures' -OGMS:0000020 symptom signs and symptoms quality A quality of a patient that is observed by the patient or a processual entity experienced by the patient, either of which is hypothesized by the patient to be a realization of a disease. questionnaire/survey data Replaces GECKO 'signs and symptoms' -PATO:0000011 age age/birthdate quality A time quality inhering in a bearer by virtue of how long the bearer has existed. socio-demographic and economic characteristics Replaces GECKO 'age/birthdate' -PATO:0000047 biological sex biological sex organismal quality 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. socio-demographic and economic characteristics -PATO:0001995 organismal quality socio-demographic and economic characteristics quality A quality that inheres in an entire organism or part of an organism. questionnaire/survey data -PDRO:0000024 drug prescription prescription document A health care prescription specifying the initiation, modification or cessation of a drug administration. medication Replaces GECKO 'prescription' -PDRO:0010022 drug administration specification administration directive information entity 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 medication drug prescription Replaces GECKO 'administration' -STATO:0000093 date date and time-related information measurement datum Information about a calendar date or timestamp indicating day, month, year and time of an event. survey administration Replaces GECKO 'date and time-related information' -UBERON:0000178 blood blood organism substance A fluid that is composed of blood plasma and erythrocytes. sample type Replaces GECKO 'blood' -UBERON:0000463 organism substance sample type material entity 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. biosample Replaces GECKO 'sample type' -UBERON:0001088 urine urine organism substance Excretion that is the output of a kidney. sample type Replaces GECKO 'urine' -UBERON:0001836 saliva saliva organism substance A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. sample type Replaces GECKO 'saliva' -UBERON:0001988 feces stool organism substance Portion of semisolid bodily waste discharged through the anus. sample type Replaces GECKO 'stool' -UBERON:0000105 life cycle stage life stage/time point process An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. questionnaire/survey data +Label IHCC Browser Label Parent Definition Definition Source Category Class Type About Inheres In Part Of Comment +LABEL A 'IHCC browser label' SC % SPLIT=| A definition A definition source A 'IHCC category' CLASS_TYPE C 'is about' some % C 'inheres in' some % C 'part of' some % A comment +timeline timeline directive information entity A directive information entity that specifies the sequence in which a series of events occurred or will occur. basic cohort attributes +population data item population data data item A data item that is about a population of organisms. basic cohort attributes equivalent collection of organisms +population location location population data item A population data item that is about the geographical location of a population of organisms. population data site +population size num. participants sample size A sample size that is about the count of individual organisms in a population. population data collection of organisms +population quality demographic data quality A quality which inheres in a population of organisms. basic cohort attributes equivalent collection of organisms +population sex or sexes sex(es) studied in cohort population quality A population quality concerning the sex or sexes of the population. demographic data +population gender or genders gender(s) studied in cohort population quality A population quality concerning the gender or genders of the population. demographic data +population age range age range population quality A population quality concerning the age range of a population. demographic data +data collection data collection events planned process A planned process that is a part of an investigation in which raw data is collected. basic cohort attributes +blood collected from fasting subject fasting or non-fasting blood Blood that is collected from an organism which has been fasting for a given amount of time. blood +biosample storage storage method storage A storage process for a biosample collected from an organism. biosample +genomic assay genomics assay An assay that investigates the genome or genomes of an individual organism or population of organisms. laboratory measures Merged GECKO 'data type' into 'genomics'. +microbiome sequencing assay Microbiome markers (rRNA, etc) genomic assay A genomic assay that profiles the microorganisms present in a sample. genomics Potential new OBI request +eQTL analysis eQTL (Cis eQTLs and/or Trans eQTLs) genomic assay A genomic assay that identifies genetic loci and candidate genes correlated with phenotypes. PMID:27964730 genomics Potential new OBI request +biosample size sample size count A count of the number of biosamples collected for an investigation. biosample +biosample processing processing method material processing A material processing which prepares a biosample for investigation. biosample +unique identifier unique identifiers identifier An identifier that is guaranteed to be unique among all identifiers in a particular domain. Wikipedia:Unique_identifier survey administration +gender gender organismal quality 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 socio-demographic and economic characteristics +ethnicity ethnicity/race organismal quality 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 socio-demographic and economic characteristics +birthplace location birthplace site A geographical location in which an individual was born. socio-demographic and economic characteristics +residence location residence site A geographical location in which an individual currently resides. socio-demographic and economic characteristics +education level education organismal quality An organismal quality inhering in a bearer by virute of the bearer's highest level of formal education completed. socio-demographic and economic characteristics +family and household structure family and household structure information content entity Information that is about the structure of an individual's family and/or household. socio-demographic and economic characteristics +lifestyle history lifestyle and behaviours clinical history A clinical history that is about the lifestyle and behaviors of an individual which may impact health outcomes. questionnaire/survey data +tobacco use history tobacco lifestyle history A lifestyle history that is about the tobacco use or exposure of an individual. lifestyle and behaviours +alcohol use history alcohol lifestyle history A lifestyle history that is about the alcohol consumption of an individual. lifestyle and behaviours +sleep history sleep lifestyle history A lifestyle history that is about the sleep quality and duration of an individual. lifestyle and behaviours +nutritional history nutrition lifestyle history A lifestyle history that is about the diet and nutrition of an individual. lifestyle and behaviours +physician contact textual entity physician/practitioner info textual entity A textual entity that contains contact details for an individual's physician, which may include: name, phone number, address, etc. healthcare information +non-pharmacological treatment history non-pharmacological interventions treatment history A treatment history that is about any non-pharamacological treatments such as surgery or physical therapy. questionnaire/survey data +surgical history surgical interventions non-pharmacological treatment history A clinical history that is about surgical operations performed on an individual. non-pharmacological interventions +prescription drug history medication treatment history A clinical history that is about the prescription drugs taken by an individual. questionnaire/survey data +disease treated by prescription drug associated disease(s) information content entity Information that is about the disease treated by a drug prescribed to an individual. medication prescription drug history +response to medication drug response(s) biological_process A biological process that results from a drug stimulus. medication +summary statistic for federated data summary statistics for additional data from federated sources statistic A statistic that summarizes a set of federated data. statistics +recreational drug history drugs lifestyle history A lifestyle history that is about the use of unprescribed and/or non-prescription drugs. lifestyle and behaviours +physical activity history physical activity lifestyle history A lifestyle history that is about the typical physical activity of an individual. lifestyle and behaviours +sample size count A count which represents the subset of a collection chosen for an investigation, survey, or assay. +biosample availability textual entity availability availability textual entity An availability textual entity that is about a substance from an organism (a biosample). biosample organism substance +reproductive history reproduction clinical history A clinical history that is about pregnancy, maternity, fertility, menses, and any other reproductive aspect. other questionnaire/survey data +treatment history clinical history A clinical history that is about any treatment (surgical, prescription, etc.) for disease, disorder, or symptom. +psychological measurement cognitive and psychological measurements measurement datum A measurement datum of some aspect of human psychology. EFO:0009095 questionnaire/survey data See also EFO:0009095 +cognitive measurement cognitive functioning psychological measurement A psychological measurement of some aspect of intellectual functions such as memory, problem solving, and comprehension. Wikipedia:Cognition cognitive and psychological measurements +personality measurement personality psychological measurement A psychological measurement of a person's individual sets of behaviours, cognitions, and emotional patterns. Wikipedia:Personality cognitive and psychological measurements +emotion psychological distress and emotions biological_process A biological process that results from neurophysiological changes in response to internal and external events. Wikipedia:Emotion cognitive and psychological measurements +oral health history oral health and hygiene lifestyle history A lifestyle history that is about oral health and hygiene. lifestyle and behaviours +psychological treatment history psychological interventions non-pharmacological treatment history A non-pharmacological treatment history that is about psychological treatments such as counselling. non-pharmacological interventions +radiological treatment history radiological interventions non-pharmacological treatment history A non-pharmacological treatment history that is about use of radiology for treatment of disease, disorder, or symptom. non-pharmacological interventions +physical therapy history physical therapy interventions non-pharmacological treatment history A non-pharmacological treatment history that is about physical therapy treatments such as physical rehabilitation. non-pharmacological interventions +perception of health measurement perception of health psychological measurement A psychological measurement of an individual's subjective perception of health. perception of health and quality of life +quality of life measurement quality of life psychological measurement A psychological measurement of an individual's perception of their quality of life. perception of health and quality of life +information on functional limitations functional limitations information content entity Information that is about an individual's limitations in activities that involve caring for an moving the body. Maelstrom:Act_daily_living perception of health and quality of life +information on use of assistive devices use of assistive devices information content entity Information about an individual's use of assistive devices in performing daily activities. Maelstrom:Use_devices perception of health and quality of life +religious affiliation religion information content entity 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 socio-demographic and economic characteristics +human social environment social environment immaterial entity 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 other questionnaire/survey data diff --git a/src/ontology/templates/index.tsv b/src/ontology/templates/index.tsv new file mode 100644 index 0000000..56bf74b --- /dev/null +++ b/src/ontology/templates/index.tsv @@ -0,0 +1,140 @@ +ID Label +ID LABEL +BFO:0000015 process +BFO:0000016 disposition +BFO:0000017 realizable entity +BFO:0000019 quality +BFO:0000029 site +BFO:0000040 material entity +BFO:0000041 immaterial entity +CMO:0000000 clinical measurement data item +CMO:0000001 cardiovascular measurement data item +CMO:0000003 blood pressure measurement data item +CMO:0000012 body weight data item +CMO:0000021 body morphological measurement data item +CMO:0000106 body height data item +CMO:0000294 pulse data item +EUPATH:0000147 cause of participant death +EUPATH:0000308 hospitalization information +EUPATH:0000359 occupation +EUPATH:0000374 marital status +EUPATH:0000451 healthcare information +EUPATH:0010032 environment associated with human dwelling +GECKO:0000003 timeline +GECKO:0000005 population data item +GECKO:0000006 population location +GECKO:0000008 population size +GECKO:0000009 population quality +GECKO:0000010 population sex or sexes +GECKO:0000011 population gender or genders +GECKO:0000012 population age range +GECKO:0000013 data collection +GECKO:0000019 blood collected from fasting subject +GECKO:0000026 biosample storage +GECKO:0000032 genomic assay +GECKO:0000040 microbiome sequencing assay +GECKO:0000042 eQTL analysis +GECKO:0000044 biosample size +GECKO:0000047 biosample processing +GECKO:0000055 unique identifier +GECKO:0000060 gender +GECKO:0000061 ethnicity +GECKO:0000063 birthplace location +GECKO:0000064 residence location +GECKO:0000065 education level +GECKO:0000066 family and household structure +GECKO:0000067 lifestyle history +GECKO:0000068 tobacco use history +GECKO:0000069 alcohol use history +GECKO:0000071 sleep history +GECKO:0000072 nutritional history +GECKO:0000073 physician contact textual entity +GECKO:0000091 non-pharmacological treatment history +GECKO:0000092 surgical history +GECKO:0000093 prescription drug history +GECKO:0000094 disease treated by prescription drug +GECKO:0000096 response to medication +GECKO:0000102 summary statistic for federated data +GECKO:0000103 recreational drug history +GECKO:0000104 physical activity history +GECKO:0000106 sample size +GECKO:0000113 biosample availability textual entity +GECKO:0000114 reproductive history +GECKO:0000115 treatment history +GECKO:0000118 psychological measurement +GECKO:0000119 cognitive measurement +GECKO:0000120 personality measurement +GECKO:0000121 emotion +GECKO:0000122 oral health history +GECKO:0000123 psychological treatment history +GECKO:0000124 radiological treatment history +GECKO:0000125 physical therapy history +GECKO:0000126 perception of health measurement +GECKO:0000127 quality of life measurement +GECKO:0000128 information on functional limitations +GECKO:0000129 information on use of assistive devices +GECKO:0000130 religious affiliation +GECKO:0000131 human social environment +GO:0008150 biological_process +IAO:0000005 objective specification +IAO:0000027 data item +IAO:0000030 information content entity +IAO:0000033 directive information entity +IAO:0000104 plan specification +IAO:0000109 measurement datum +IAO:0000300 textual entity +IAO:0000310 document +IAO:0000612 availability textual entity +IAO:0000619 consent textual entity +IAO:0020000 identifier +MF:0000041 belief +MONDO:0000001 disease or disorder +MONDO:0002051 integumentary system disease +MONDO:0002081 musculoskeletal system disease +MONDO:0003900 connective tissue disease +MONDO:0004335 digestive system disease +MONDO:0004992 cancer +MONDO:0004995 cardiovascular disease +MONDO:0005071 nervous system disorder +MONDO:0005084 mental disorder +MONDO:0005087 respiratory system disease +MONDO:0005151 endocrine system disease +MONDO:0005550 infectious disease +MONDO:0005570 hematologic disease +MONDO:0021178 injury +MONDO:0024458 disease of visual system +MONDO:0024623 otorhinolaryngologic disease +MONDO:0029000 poisoning +OBI:0000011 planned process +OBI:0000070 assay +OBI:0000094 material processing +OBI:0000435 genotyping assay +OBI:0000537 copy number variation profiling assay +OBI:0001271 RNA-seq assay +OBI:0001624 organism identification assay +OBI:0002020 epigenetic modification assay +OBI:0002117 whole genome sequencing assay +OBI:0002118 exome sequencing assay +OBI:0002415 exposure to environmental and workplace carcinogens history +OBI:0002623 whole metagenome sequencing assay +OBI:0302893 storage +OBI:0500000 study design +OBI:0500027 inclusion criterion +OGMS:0000015 clinical history +OGMS:0000020 symptom +OMRSE:00000501 income data +PATO:0000011 age +PATO:0000047 biological sex +PATO:0001995 organismal quality +PCO:0000000 collection of organisms +PDRO:0000024 drug prescription +PDRO:0010022 drug administration specification +STATO:0000039 statistic +STATO:0000047 count +STATO:0000093 date +UBERON:0000105 life cycle stage +UBERON:0000178 blood +UBERON:0000463 organism substance +UBERON:0001088 urine +UBERON:0001836 saliva +UBERON:0001988 feces diff --git a/src/prefixes.json b/src/prefixes.json index d538eb6..4a5ad54 100644 --- a/src/prefixes.json +++ b/src/prefixes.json @@ -7,15 +7,12 @@ "CMO": "http://purl.obolibrary.org/obo/CMO_", "dcterms": "http://purl.org/dc/terms/", "dc11": "http://purl.org/dc/elements/1.1/", - "GCS": "http://example.com/GCS_", - "GE": "http://example.com/GE_", + "EUPATH": "http://purl.obolibrary.org/obo/EUPATH_", "GECKO": "http://purl.obolibrary.org/obo/GECKO_", "GO": "http://purl.obolibrary.org/obo/GO_", "HP": "http://purl.obolibrary.org/obo/HP_", "IAO": "http://purl.obolibrary.org/obo/IAO_", - "IHCC": "http://example.com/", - "KoGES": "http://example.com/KoGES_", - "MAELSTROM": "http://example.com/MAELSTROM_", + "MF": "http://purl.obolibrary.org/obo/MF_", "MMO": "http://purl.obolibrary.org/obo/MMO_", "MONDO": "http://purl.obolibrary.org/obo/MONDO_", "NCBITaxon": "http://purl.obolibrary.org/obo/NCBITaxon_", @@ -24,15 +21,15 @@ "OGMS": "http://purl.obolibrary.org/obo/OGMS_", "obo": "http://purl.obolibrary.org/obo/", "oboInOwl": "http://www.geneontology.org/formats/oboInOwl#", + "OMRSE": "http://purl.obolibrary.org/obo/OMRSE_", "owl": "http://www.w3.org/2002/07/owl#", "PATO": "http://purl.obolibrary.org/obo/PATO_", + "PCO": "http://purl.obolibrary.org/obo/PCO_", "PDRO": "http://purl.obolibrary.org/obo/PDRO_", "PR": "http://purl.obolibrary.org/obo/PR_", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", "RO": "http://purl.obolibrary.org/obo/RO_", - "SAPRIN": "http://example.com/SAPRIN_", "STATO": "http://purl.obolibrary.org/obo/STATO_", - "UBERON": "http://purl.obolibrary.org/obo/UBERON_", - "VZ": "http://example.com/VZ_" + "UBERON": "http://purl.obolibrary.org/obo/UBERON_" } } diff --git a/src/queries/build_ihcc_annotations.rq b/src/queries/build_ihcc_annotations.rq new file mode 100644 index 0000000..b985cf2 --- /dev/null +++ b/src/queries/build_ihcc_annotations.rq @@ -0,0 +1,19 @@ +PREFIX obo: +PREFIX oboInOwl: +PREFIX owl: +PREFIX rdfs: + +CONSTRUCT { ?s ?p ?o ; + oboInOwl:hasExactSynonym ?label . + ?p a owl:AnnotationProperty ; + rdfs:label ?apLabel . } +WHERE { ?s a owl:Class ; + obo:GECKO_9000001 ?browserLabel ; + rdfs:label ?label ; + ?p ?o . + ?p a owl:AnnotationProperty . + FILTER (?p != rdfs:label) + FILTER (?p != obo:GECKO_9000001) + FILTER (?p != obo:GECKO_9000000) + FILTER (?p != oboInOwl:hasDbXref) + OPTIONAL { ?p rdfs:label ?apLabel . } } diff --git a/src/queries/fix_annotations.rq b/src/queries/fix_annotations.rq new file mode 100644 index 0000000..6f02472 --- /dev/null +++ b/src/queries/fix_annotations.rq @@ -0,0 +1,16 @@ +PREFIX owl: + +DELETE { ?s ?p ?o } +WHERE { ?s ?p ?o . + ?p a owl:AnnotationProperty . + FILTER (LANG(?o) != "") + FILTER (LANG(?o) != "en") + } ; + +DELETE { ?s ?p ?o } +WHERE { ?s ?p ?o . + ?s ?p ?o2 . + ?p a owl:AnnotationProperty . + FILTER (LANG(?o) != "") + FILTER (LANG(?o2) != "en") + } ; diff --git a/src/get_ihcc_view.rq b/src/queries/get_ihcc_view.rq similarity index 100% rename from src/get_ihcc_view.rq rename to src/queries/get_ihcc_view.rq diff --git a/src/ihcc_view.py b/src/scripts/ihcc_view.py similarity index 79% rename from src/ihcc_view.py rename to src/scripts/ihcc_view.py index ecbc211..c8345e4 100644 --- a/src/ihcc_view.py +++ b/src/scripts/ihcc_view.py @@ -11,7 +11,17 @@ {"ID": "GECKO:0000056", "Label": "questionnaire/survey data"}, {"ID": "GECKO:0000101", "Label": "statistics"}, {"ID": "GECKO:0000105", "Label": "other", "Parent": "genomics"}, - {"ID": "GECKO:0000112", "Label": "other biosample type", "Parent": "sample type"} + {"ID": "GECKO:0000112", "Label": "other biosample type", "Parent": "sample type"}, + { + "ID": "GECKO:0000116", + "Label": "other questionnaire/survey data", + "Parent": "questionnaire/survey data", + }, + { + "ID": "GECKO:0000117", + "Label": "perception of health and quality of life", + "Parent": "questionnaire/survey data", + }, ] diff --git a/src/scripts/prefixes.sql b/src/scripts/prefixes.sql new file mode 100644 index 0000000..a4b0256 --- /dev/null +++ b/src/scripts/prefixes.sql @@ -0,0 +1,37 @@ +CREATE TABLE IF NOT EXISTS prefix ( + prefix TEXT PRIMARY KEY, + base TEXT NOT NULL +); + +INSERT OR IGNORE INTO prefix VALUES +("BFO", "http://purl.obolibrary.org/obo/BFO_"), +("COB", "http://purl.obolibrary.org/obo/COB_"), +("CHEBI", "http://purl.obolibrary.org/obo/CHEBI_"), +("CL", "http://purl.obolibrary.org/obo/CL_"), +("CMO", "http://purl.obolibrary.org/obo/CMO_"), +("dcterms", "http://purl.org/dc/terms/"), +("dc11", "http://purl.org/dc/elements/1.1/"), +("EUPATH", "http://purl.obolibrary.org/obo/EUPATH_"), +("GECKO", "http://purl.obolibrary.org/obo/GECKO_"), +("GO", "http://purl.obolibrary.org/obo/GO_"), +("HP", "http://purl.obolibrary.org/obo/HP_"), +("IAO", "http://purl.obolibrary.org/obo/IAO_"), +("MF", "http://purl.obolibrary.org/obo/MF_"), +("MMO", "http://purl.obolibrary.org/obo/MMO_"), +("MONDO", "http://purl.obolibrary.org/obo/MONDO_"), +("NCBITaxon", "http://purl.obolibrary.org/obo/NCBITaxon_"), +("NCIT", "http://purl.obolibrary.org/obo/NCIT_"), +("OBI", "http://purl.obolibrary.org/obo/OBI_"), +("OGMS", "http://purl.obolibrary.org/obo/OGMS_"), +("obo", "http://purl.obolibrary.org/obo/"), +("oboInOwl", "http://www.geneontology.org/formats/oboInOwl#"), +("OMRSE", "http://purl.obolibrary.org/obo/OMRSE_"), +("owl", "http://www.w3.org/2002/07/owl#"), +("PATO", "http://purl.obolibrary.org/obo/PATO_"), +("PCO", "http://purl.obolibrary.org/obo/PCO_"), +("PDRO", "http://purl.obolibrary.org/obo/PDRO_"), +("PR", "http://purl.obolibrary.org/obo/PR_"), +("rdfs", "http://www.w3.org/2000/01/rdf-schema#"), +("RO", "http://purl.obolibrary.org/obo/RO_"), +("STATO", "http://purl.obolibrary.org/obo/STATO_"), +("UBERON", "http://purl.obolibrary.org/obo/UBERON_"); diff --git a/views/ihcc-gecko.owl b/views/ihcc-gecko.owl index 29aaeb5..1603839 100644 --- a/views/ihcc-gecko.owl +++ b/views/ihcc-gecko.owl @@ -1,17 +1,245 @@ + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + + + + + + + + + + editor preferred term + + + + + + + + example of usage + + + + + + + + definition + + + + + + + + editor note + + + + + + + + term editor + + + + + + + + alternative term + + + + + + + + definition source + + + + + + + + curator note + + + + + + + + term tracker item + + + + + + + + ontology term requester + + + + + + + + external_definition + + + + + + + + axiom_lost_from_external_ontology + + + + + + + + homology_notes + + + + + + + + has_relational_adjective + + + + + + + + taxon_notes + + + + + + + + external_ontology_notes + + + + + + + + + + + + + + has_alternative_id + + + + + + + + has_broad_synonym + + + + + + + + has_exact_synonym + + + + + + + + has_narrow_synonym + + + + + + + + has_obo_namespace + + + + + + + + has_related_synonym + + + + + + + + id + + + + + + + + in_subset + + + + + + + + comment + + + + + + + + see also + + + + + - - - aims and objectives + + + An information content entity indicating the cause of death for a participant in the study. + Person: Jie Zheng, Chris Stoeckert, David Roos, Grant Dorsey + Penn Group + PRISM + cause of participant death + cause of death + + + + + + + + + an information content entity that is about a part of a health care encounter that occurs in a hospital facility + Person: John Judkins + EuPathDB + hospitalization information + ICEMR protein array + hospitalizations + + + + + + + + + An information content entity that is about an activity that realizes a social role and is often performed for payment. + occupation + occupation + + + + + + + + + a categorical value specification that is about a human being and specifies whether that human being is joined to another human being in marriage + Person: John Judkins + EuPathDB, BFO's 'relational quality' examples + marital status + marital status + + + + + + + + + An information content entity about healthcare that is private or public. + healthcare information + healthcare information + + + + + + + + + environmental system associated with the dwelling used by humans. + Person: Cristian Cocos, Jie Zheng, Chris Stoeckert + Penn Group + GEMS + environment associated with human dwelling + physical environment @@ -107,7 +403,9 @@ - timeline + A directive information entity that specifies the sequence in which a series of events occurred or will occur. + timeline + timeline @@ -116,6 +414,8 @@ + A data item that is about a population of organisms. + population data item population data @@ -125,6 +425,8 @@ + A population data item that is about the geographical location of a population of organisms. + population location location @@ -134,6 +436,8 @@ + A sample size that is about the count of individual organisms in a population. + population size num. participants @@ -143,6 +447,8 @@ + A quality which inheres in a population of organisms. + population quality demographic data @@ -152,6 +458,8 @@ + A population quality concerning the sex or sexes of the population. + population sex or sexes sex(es) studied in cohort @@ -161,6 +469,8 @@ + A population quality concerning the gender or genders of the population. + population gender or genders gender(s) studied in cohort @@ -170,6 +480,8 @@ + A population quality concerning the age range of a population. + population age range age range @@ -179,6 +491,8 @@ + A planned process that is a part of an investigation in which raw data is collected. + data collection data collection events @@ -196,6 +510,8 @@ + Blood that is collected from an organism which has been fasting for a given amount of time. + blood collected from fasting subject fasting or non-fasting @@ -205,6 +521,8 @@ + A storage process for a biosample collected from an organism. + biosample storage storage method @@ -222,6 +540,9 @@ + An assay that investigates the genome or genomes of an individual organism or population of organisms. + genomic assay + Merged GECKO 'data type' into 'genomics'. genomics @@ -231,6 +552,9 @@ + A genomic assay that profiles the microorganisms present in a sample. + microbiome sequencing assay + Potential new OBI request Microbiome markers (rRNA, etc) @@ -240,6 +564,10 @@ + A genomic assay that identifies genetic loci and candidate genes correlated with phenotypes. + PMID:27964730 + eQTL analysis + Potential new OBI request eQTL (Cis eQTLs and/or Trans eQTLs) @@ -249,6 +577,8 @@ + A count of the number of biosamples collected for an investigation. + biosample size sample size @@ -258,6 +588,8 @@ + A material processing which prepares a biosample for investigation. + biosample processing processing method @@ -275,6 +607,9 @@ + An identifier that is guaranteed to be unique among all identifiers in a particular domain. + Wikipedia:Unique_identifier + unique identifier unique identifiers @@ -292,7 +627,10 @@ - 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 + gender + gender @@ -301,6 +639,9 @@ + 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 + ethnicity ethnicity/race @@ -310,6 +651,8 @@ + A geographical location in which an individual was born. + birthplace location birthplace @@ -319,6 +662,8 @@ + A geographical location in which an individual currently resides. + residence location residence @@ -328,6 +673,8 @@ + An organismal quality inhering in a bearer by virute of the bearer's highest level of formal education completed. + education level education @@ -337,7 +684,9 @@ - family and household structure + Information that is about the structure of an individual's family and/or household. + family and household structure + family and household structure @@ -346,6 +695,8 @@ + A clinical history that is about the lifestyle and behaviors of an individual which may impact health outcomes. + lifestyle history lifestyle and behaviours @@ -355,6 +706,8 @@ + A lifestyle history that is about the tobacco use or exposure of an individual. + tobacco use history tobacco @@ -364,6 +717,8 @@ + A lifestyle history that is about the alcohol consumption of an individual. + alcohol use history alcohol @@ -373,6 +728,8 @@ + A lifestyle history that is about the sleep quality and duration of an individual. + sleep history sleep @@ -382,6 +739,8 @@ + A lifestyle history that is about the diet and nutrition of an individual. + nutritional history nutrition @@ -390,7 +749,9 @@ - + + A textual entity that contains contact details for an individual's physician, which may include: name, phone number, address, etc. + physician contact textual entity physician/practitioner info @@ -400,6 +761,8 @@ + A treatment history that is about any non-pharamacological treatments such as surgery or physical therapy. + non-pharmacological treatment history non-pharmacological interventions @@ -409,6 +772,8 @@ + A clinical history that is about surgical operations performed on an individual. + surgical history surgical interventions @@ -418,6 +783,8 @@ + A clinical history that is about the prescription drugs taken by an individual. + prescription drug history medication @@ -427,6 +794,8 @@ + Information that is about the disease treated by a drug prescribed to an individual. + disease treated by prescription drug associated disease(s) @@ -436,6 +805,8 @@ + A biological process that results from a drug stimulus. + response to medication drug response(s) @@ -453,6 +824,8 @@ + A statistic that summarizes a set of federated data. + summary statistic for federated data summary statistics for additional data from federated sources @@ -462,6 +835,8 @@ + A lifestyle history that is about the use of unprescribed and/or non-prescription drugs. + recreational drug history drugs @@ -471,6 +846,8 @@ + A lifestyle history that is about the typical physical activity of an individual. + physical activity history physical activity @@ -498,6 +875,8 @@ + An availability textual entity that is about a substance from an organism (a biosample). + biosample availability textual entity availability @@ -506,26 +885,324 @@ - + + A clinical history that is about pregnancy, maternity, fertility, menses, and any other reproductive aspect. + reproductive history reproduction + + + + + other questionnaire/survey data + + + + + + + + + perception of health and quality of life + + + + + + + + + A measurement datum of some aspect of human psychology. + EFO:0009095 + psychological measurement + See also EFO:0009095 + cognitive and psychological measurements + + + + + + + + + A psychological measurement of some aspect of intellectual functions such as memory, problem solving, and comprehension. + Wikipedia:Cognition + cognitive measurement + cognitive functioning + + + + + + + + + A psychological measurement of a person's individual sets of behaviours, cognitions, and emotional patterns. + Wikipedia:Personality + personality measurement + personality + + + + + + + + + A biological process that results from neurophysiological changes in response to internal and external events. + Wikipedia:Emotion + emotion + psychological distress and emotions + + + + + + + + + A lifestyle history that is about oral health and hygiene. + oral health history + oral health and hygiene + + + + + + + + + A non-pharmacological treatment history that is about psychological treatments such as counselling. + psychological treatment history + psychological interventions + + + + + + + + + A non-pharmacological treatment history that is about use of radiology for treatment of disease, disorder, or symptom. + radiological treatment history + radiological interventions + + + + + + + + + A non-pharmacological treatment history that is about physical therapy treatments such as physical rehabilitation. + physical therapy history + physical therapy interventions + + + + + + + + + A psychological measurement of an individual's subjective perception of health. + perception of health measurement + perception of health + + + + + + + + + A psychological measurement of an individual's perception of their quality of life. + quality of life measurement + quality of life + + + + + + + + + Information that is about an individual's limitations in activities that involve caring for an moving the body. + Maelstrom:Act_daily_living + information on functional limitations + functional limitations + + + + + + + + + Information about an individual's use of assistive devices in performing daily activities. + Maelstrom:Use_devices + information on use of assistive devices + use of assistive devices + + + + + + + + + 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 + religious affiliation + religion + + + + + + + + + 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 + human social environment + social environment + + + + + + + + + objective specification + In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. + 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. + 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." + 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. + Answers the question, why did you do this experiment? + PERSON: Alan Ruttenberg + PERSON: Barry Smith + PERSON: Bjoern Peters + PERSON: Jennifer Fostel + goal specification + OBI Plan and Planned Process/Roles Branch + OBI_0000217 + objective specification + aims and objectives + + + + + consent textual entity + 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. + A textual entity that documents the consenting process used to enroll patients in a study. + PERSON: Bill Baumgartner + consent textual entity consent/accessibility + + + + + personal beliefs and values + + + + - 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 + MONDO:0000001 + 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 + integumentary system disease + disorder of integument + disorder of integumental system + MONDO:0002051 + skin and subcutaneous tissue + + + + + + + + + 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 + MONDO:0002081 + musculoskeletal system + + + + + + + + + A disease involving the connective tissue. + connective tissue disease + connective tissue disease or disorder + connective tissue diseases + connective tissue disorder + connective tissue disorders + disease of connective tissue + disease or disorder of connective tissue + disease, connective tissue + disorder of connective tissue + primary disorder of connective tissue + tissue disease, connective + disorder of connective tissue + MONDO:0003900 + connective tissue @@ -534,6 +1211,26 @@ + 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 + MONDO:0004335 digestive system @@ -543,6 +1240,22 @@ + 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 + MONDO:0004992 oncological @@ -552,6 +1265,19 @@ + 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 + MONDO:0004995 circulatory system @@ -561,6 +1287,19 @@ + 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 + MONDO:0005071 nervous system @@ -570,6 +1309,13 @@ + A disease that has its basis in the disruption of mental process. + disorder of mental process + mental disorder + mental or behavioural disorder + mental process disease + disorder of mental process + MONDO:0005084 mental and behaviour disorders @@ -579,6 +1325,17 @@ + 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 + MONDO:0005087 respiratory system @@ -588,16 +1345,158 @@ + 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 + MONDO:0005151 endocrine/nutritional/metabolic disorders + + + + + 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 + MONDO:0005550 + 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. + infectious disease + + + + + 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 disease + 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 + MONDO:0005570 + placeholder for lymphoid disease blood-related disorders + https://github.com/monarch-initiative/mondo/issues/254 + + + + + + + + + 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 + MONDO:0021178 + injury + + + + + + + + + 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 + MONDO:0024458 + visual system + + + + + + + + + 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 + MONDO:0024623 + Editor note: consider uberon class + diseases of the ear, nose, and/or throat + + + + + + + + + A condition or physical state produced by the ingestion, injection, inhalation of or exposure to a deleterious agent. + poisoning + Poisonings + intoxication + poisoning syndrome + MONDO:0029000 + poisoning @@ -606,6 +1505,14 @@ + genotyping assay + 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. + Philippe Rocca-Serra + SNP analysis + genotype profiling + OBI Biomaterial + genotyping assay DNA/Genotyping @@ -615,6 +1522,12 @@ + copy number variation profiling assay + 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 + Philippe Rocca-Serra + CNV analysis + copy number variation profiling assay Sequence variants (CNV, SNP arrays) @@ -624,6 +1537,12 @@ + RNA-seq assay + An transcription profiling assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance. + James Malone + transcription profiling by high throughput sequencing + EFO:0002770 + RNA-seq assay RNAseq/gene expression @@ -633,6 +1552,12 @@ + organism identification assay + An assay that identifies the organism species in a specimen. + Chris Stoeckert + Jie Zheng + NIAID GSCID-BRC metadata working group + organism identification assay microbiology @@ -642,6 +1567,12 @@ + epigenetic modification assay + An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation. + Chris Stoeckert + Jie Zheng + Penn group + epigenetic modification assay Epigenetics @@ -651,7 +1582,16 @@ - WGS + whole genome sequencing assay + 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. + Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. + ImmPort + WGS + PMID:23095910 + PMID:25827230 + whole genome sequencing assay + WGS @@ -660,7 +1600,29 @@ - WES + exome sequencing assay + 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). + ImmPort + WES + PMID:25827230 + exome sequencing assay + WES + + + + + + + + + exposure to environmental and workplace carcinogens history + A information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + exposure to environmental and workplace carcinogens history + exposure to carcinogens @@ -669,6 +1631,15 @@ + whole metagenome sequencing assay + 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. + Whole metagenome sequencing has been used to explore the composition and metabolic capability of communities of microbes found in the environment (e.g. in soil, water, etc.) and in humans and other species (e.g. in the gut, oral cavity, etc.). + Rebecca Jackson + WMS + Bjoern Peters + Michelle Giglio + https://github.com/obi-ontology/obi/issues/1056 + whole metagenome sequencing assay Metagenomics @@ -678,7 +1649,15 @@ - study design + 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. + 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. + Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. + PERSON: Chris Stoeckert + experimental design + rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. + study design + study design @@ -687,6 +1666,14 @@ + inclusion criterion + 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) . + 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. + Person: Philippe Rocca-Serra + inclusion condition + inclusion rule + Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group + inclusion criterion criteria for enrollment and recruitment procedures @@ -695,16 +1682,29 @@ - + signs and symptoms + + + + + income and possessions + + + + + A time quality inhering in a bearer by virtue of how long the bearer has existed. + age + quality + PATO:0000011 age/birthdate @@ -714,7 +1714,11 @@ - 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. + biological sex + quality + PATO:0000047 + biological sex @@ -723,6 +1727,10 @@ + A quality that inheres in an entire organism or part of an organism. + organismal quality + quality + PATO:0001995 socio-demographic and economic characteristics @@ -732,6 +1740,9 @@ + "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. + drug prescription prescription @@ -741,6 +1752,16 @@ + prescribed drug administration specification + '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 + drug administration specification administration @@ -750,6 +1771,12 @@ + Information about a calendar date or timestamp indicating day, month, year and time of an event. + Alejandra Gonzalez-Beltran + Orlaith Burke + Philippe Rocca-Serra + STATO + date date and time-related information @@ -758,7 +1785,16 @@ - + + A spatiotemporal region encompassing some part of the life cycle of an organism. + this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here + the WBls class 'all stages' belongs here as it is the superclass of other WBls stages + we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage + life cycle stage + developmental stage + stage + uberon + UBERON:0000105 life stage/time point @@ -768,7 +1804,19 @@ - blood + A fluid that is composed of blood plasma and erythrocytes. + This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. + A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] + Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] + relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] + Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] + blood + portion of blood + vertebrate blood + uberon + whole blood + UBERON:0000178 + blood @@ -777,6 +1825,14 @@ + 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 + uberon + UBERON:0000463 sample type @@ -786,7 +1842,12 @@ - urine + Excretion that is the output of a kidney + kidney excreta from some taxa (e.g. in aves) may not be liquid + urine + uberon + UBERON:0001088 + urine @@ -795,7 +1856,17 @@ - saliva + A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. + salivary + We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin + saliva + salivary gland secretion + uberon + sailva normalis + saliva atomaris + saliva molecularis + UBERON:0001836 + saliva @@ -804,7 +1875,45 @@ - stool + Portion of semisolid bodily waste discharged through the anus[MW,modified] + Excretion in semisolid state processed by the intestine.[FMA] + fecal + excreta + faeces + fecal material + fecal matter + feces + 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 + uberon + droppings + excrement + ordure + spoor + UBERON:0001988 + stool