Genomics Cohorts Knowledge Ontology
type: Ontology
version IRI: gecko.owl
description: An ontology to represent genomics cohort attributes.
license: https://creativecommons.org/licenses/by/4.0/
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

IHCC category
type: AnnotationProperty

IHCC browser label
type: AnnotationProperty

example of usage
type: AnnotationProperty

definition
type: AnnotationProperty

alternative term
type: AnnotationProperty

definition source
type: AnnotationProperty

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

comment
type: AnnotationProperty

label
type: AnnotationProperty

see also
type: AnnotationProperty

part of
type: ObjectProperty

is about
type: ObjectProperty

inheres in
type: ObjectProperty

process
type: Class
example of usage: a process of cell-division, \ a beating of the heart
example of usage: a process of meiosis
example of usage: a process of sleeping
example of usage: the course of a disease
example of usage: the flight of a bird
example of usage: the life of an organism
example of usage: your process of aging.
definition: 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])

disposition
type: Class
subclass of: realizable entity
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis

realizable entity
type: Class
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet

quality
type: Class
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril

site
type: Class
subclass of: immaterial entity
example of usage: Manhattan Canyon)
example of usage: a hole in the interior of a portion of cheese
example of usage: a rabbit hole
example of usage: an air traffic control region defined in the airspace above an airport
example of usage: the Grand Canyon
example of usage: the Piazza San Marco
example of usage: the cockpit of an aircraft
example of usage: the hold of a ship
example of usage: the interior of a kangaroo pouch
example of usage: the interior of the trunk of your car
example of usage: the interior of your bedroom
example of usage: the interior of your office
example of usage: the interior of your refrigerator
example of usage: the lumen of your gut
example of usage: your left nostril (a fiat part – the opening – of your left nasal cavity)

material entity
type: Class
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being

immaterial entity
type: Class

clinical measurement data item
type: Class
subclass of: measurement datum
IHCC category: questionnaire/survey data
IHCC browser label: physiological measurements

cardiovascular measurement data item
type: Class
subclass of: clinical measurement data item
IHCC category: physiological measurements
IHCC browser label: circulation and respiration

blood pressure measurement data item
type: Class
subclass of: cardiovascular measurement data item
IHCC category: circulation and respiration
IHCC browser label: blood pressure

body weight data item
type: Class
subclass of: body morphological measurement data item
IHCC category: anthropometry
IHCC browser label: weight

body morphological measurement data item
type: Class
subclass of: clinical measurement data item
IHCC category: physiological measurements
IHCC browser label: anthropometry

body height data item
type: Class
subclass of: body morphological measurement data item
IHCC category: anthropometry
IHCC browser label: height

pulse data item
type: Class
subclass of: cardiovascular measurement data item
IHCC category: circulation and respiration
IHCC browser label: heart rate (HR)

cause of participant death
type: Class
subclass of: information content entity
IHCC category: other questionnaire/survey data
IHCC browser label: cause of death
definition: An information content entity indicating the cause of death for a participant in the study.
definition source: Penn Group

aggregated clinical visit information
type: Class
subclass of: information content entity
IHCC category: healthcare information
IHCC browser label: routine clincial visits
definition: a data item that is about an investigation and is the specified output of a data transformation that has only clinical visit data as input
definition source: EuPathDB

hospitalization information
type: Class
subclass of: information content entity
IHCC category: healthcare information
IHCC browser label: hospitalizations
definition: an information content entity that is about a part of a health care encounter that occurs in a hospital facility
definition source: EuPathDB

occupation
type: Class
subclass of: information content entity
IHCC category: socio-demographic and economic characteristics
IHCC browser label: occupation
definition: An information content entity that is about an activity that realizes a social role and is often performed for payment.

marital status
type: Class
subclass of: information content entity
IHCC category: socio-demographic and economic characteristics
IHCC browser label: marital status
definition: a categorical value specification that is about a human being and specifies whether that human being is joined to another human being in marriage
definition source: EuPathDB, BFO's 'relational quality' examples

healthcare information
type: Class
subclass of: information content entity
IHCC category: questionnaire/survey data
IHCC browser label: healthcare information
definition: An information content entity about healthcare that is private or public.

environment associated with human dwelling
type: Class
subclass of: material entity
IHCC category: questionnaire/survey data
IHCC browser label: physical environment
definition: environmental system associated with the dwelling used by humans.
definition source: Penn Group

timeline
type: Class
subclass of: directive information entity
IHCC category: basic cohort attributes
IHCC browser label: timeline
definition: A directive information entity that specifies the sequence in which a series of events occurred or will occur.

population data item
type: Class
equivalent class: Restriction
  on property: is about
  some values from: collection of organisms
subclass of: data item
IHCC category: basic cohort attributes
IHCC browser label: population data
definition: A data item that is about a population of organisms.

population location
type: Class
subclass of: population data item
subclass of: Restriction
  on property: is about
  some values from: site
IHCC category: population data
IHCC browser label: location
definition: A population data item that is about the geographical location of a population of organisms.

population size
type: Class
subclass of: sample size
subclass of: Restriction
  on property: is about
  some values from: collection of organisms
IHCC category: population data
IHCC browser label: num. participants
definition: A sample size that is about the count of individual organisms in a population.

population quality
type: Class
equivalent class: Restriction
  on property: inheres in
  some values from: collection of organisms
subclass of: quality
IHCC category: basic cohort attributes
IHCC browser label: demographic data
definition: A quality which inheres in a population of organisms.

population sex or sexes
type: Class
subclass of: population quality
IHCC category: demographic data
IHCC browser label: sex(es) studied in cohort
definition: A population quality concerning the sex or sexes of the population.

population gender or genders
type: Class
subclass of: population quality
IHCC category: demographic data
IHCC browser label: gender(s) studied in cohort
definition: A population quality concerning the gender or genders of the population.

population age range
type: Class
subclass of: population quality
IHCC category: demographic data
IHCC browser label: age range
definition: A population quality concerning the age range of a population.

data collection
type: Class
subclass of: planned process
IHCC category: basic cohort attributes
IHCC browser label: data collection events
definition: A planned process that is a part of an investigation in which raw data is collected.

blood collected from fasting subject
type: Class
subclass of: blood
IHCC category: blood
IHCC browser label: fasting or non-fasting
definition: Blood that is collected from an organism which has been fasting for a given amount of time.

biosample storage
type: Class
subclass of: storage
IHCC category: biosample
IHCC browser label: storage method
definition: A storage process for a biosample collected from an organism.

genomic assay
type: Class
subclass of: assay
IHCC category: laboratory measures
IHCC browser label: genomics
definition: An assay that investigates the genome or genomes of an individual organism or population of organisms.
comment: Merged GECKO 'data type' into 'genomics'.

microbiome sequencing assay
type: Class
subclass of: genomic assay
IHCC category: genomics
IHCC browser label: Microbiome markers (rRNA, etc)
definition: A genomic assay that profiles the microorganisms present in a sample.
comment: Potential new OBI request

eQTL analysis
type: Class
subclass of: genomic assay
IHCC category: genomics
IHCC browser label: eQTL (Cis eQTLs and/or Trans eQTLs)
definition: A genomic assay that identifies genetic loci and candidate genes correlated with phenotypes.
definition source: PMID:27964730
comment: Potential new OBI request

biosample size
type: Class
subclass of: count
IHCC category: biosample
IHCC browser label: sample size
definition: A count of the number of biosamples collected for an investigation.

biosample processing
type: Class
subclass of: material processing
IHCC category: biosample
IHCC browser label: processing method
definition: A material processing which prepares a biosample for investigation.

unique identifier
type: Class
subclass of: identifier
IHCC category: survey administration
IHCC browser label: unique identifiers
definition: An identifier that is guaranteed to be unique among all identifiers in a particular domain.
definition source: Wikipedia:Unique_identifier

gender
type: Class
subclass of: organismal quality
IHCC category: socio-demographic and economic characteristics
IHCC browser label: gender
definition: 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.
definition source: Wikipedia:Gender|PATO:0000047

ethnicity
type: Class
subclass of: organismal quality
IHCC category: socio-demographic and economic characteristics
IHCC browser label: ethnicity/race
definition: 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.
definition source: Wikipedia:Ethnic_group

birthplace location
type: Class
subclass of: site
IHCC category: socio-demographic and economic characteristics
IHCC browser label: birthplace
definition: A geographical location in which an individual was born.

residence location
type: Class
subclass of: site
IHCC category: socio-demographic and economic characteristics
IHCC browser label: residence
definition: A geographical location in which an individual currently resides.

education level
type: Class
subclass of: organismal quality
IHCC category: socio-demographic and economic characteristics
IHCC browser label: education
definition: An organismal quality inhering in a bearer by virute of the bearer's highest level of formal education completed.

family and household structure
type: Class
subclass of: information content entity
IHCC category: socio-demographic and economic characteristics
IHCC browser label: family and household structure
definition: Information that is about the structure of an individual's family and/or household.

lifestyle history
type: Class
subclass of: clinical history
IHCC category: questionnaire/survey data
IHCC browser label: lifestyle and behaviours
definition: A clinical history that is about the lifestyle and behaviors of an individual which may impact health outcomes.

tobacco use history
type: Class
subclass of: lifestyle history
IHCC category: lifestyle and behaviours
IHCC browser label: tobacco use history
definition: A lifestyle history that is about the tobacco use or exposure of an individual.

alcohol use history
type: Class
subclass of: lifestyle history
IHCC category: lifestyle and behaviours
IHCC browser label: alcohol use history
definition: A lifestyle history that is about the alcohol consumption of an individual.

sleep history
type: Class
subclass of: lifestyle history
IHCC category: lifestyle and behaviours
IHCC browser label: sleep history
definition: A lifestyle history that is about the sleep quality and duration of an individual.

nutritional history
type: Class
subclass of: lifestyle history
IHCC category: lifestyle and behaviours
IHCC browser label: dietary history
definition: A lifestyle history that is about the diet and nutrition of an individual.

physician contact textual entity
type: Class
subclass of: textual entity
IHCC category: healthcare information
IHCC browser label: physician/practitioner info
definition: A textual entity that contains contact details for an individual's physician, which may include: name, phone number, address, etc.

non-pharmacological treatment history
type: Class
subclass of: treatment history
IHCC category: questionnaire/survey data
IHCC browser label: non-pharmacological interventions
definition: A treatment history that is about any non-pharamacological treatments such as surgery or physical therapy.

surgical history
type: Class
subclass of: non-pharmacological treatment history
IHCC category: non-pharmacological interventions
IHCC browser label: surgical interventions
definition: A clinical history that is about surgical operations performed on an individual.

prescription drug history
type: Class
subclass of: treatment history
IHCC category: questionnaire/survey data
IHCC browser label: medication
definition: A clinical history that is about the prescription drugs taken by an individual.

disease treated by prescription drug
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: part of
  some values from: prescription drug history
IHCC category: medication
IHCC browser label: associated disease(s)
definition: Information that is about the disease treated by a drug prescribed to an individual.

response to medication
type: Class
subclass of: biological_process
IHCC category: medication
IHCC browser label: drug response(s)
definition: A biological process that results from a drug stimulus.

summary statistic for federated data
type: Class
subclass of: statistic
IHCC category: statistics
IHCC browser label: summary statistics for additional data from federated sources
definition: A statistic that summarizes a set of federated data.

recreational drug history
type: Class
subclass of: lifestyle history
IHCC category: lifestyle and behaviours
IHCC browser label: recreational drug history
definition: A lifestyle history that is about the use of unprescribed and/or non-prescription drugs.

physical activity history
type: Class
subclass of: lifestyle history
IHCC category: lifestyle and behaviours
IHCC browser label: physical activity history
definition: A lifestyle history that is about the typical physical activity of an individual.

sample size
type: Class
subclass of: count
definition: A count which represents the subset of a collection chosen for an investigation, survey, or assay.

biosample availability textual entity
type: Class
subclass of: availability textual entity
subclass of: Restriction
  on property: is about
  some values from: organism substance
IHCC category: biosample
IHCC browser label: availability
definition: An availability textual entity that is about a substance from an organism (a biosample).

reproductive history
type: Class
subclass of: clinical history
IHCC category: other questionnaire/survey data
IHCC browser label: reproduction
definition: A clinical history that is about pregnancy, maternity, fertility, menses, and any other reproductive aspect.

treatment history
type: Class
subclass of: clinical history
definition: A clinical history that is about any treatment (surgical, prescription, etc.) for disease, disorder, or symptom.

psychological measurement
type: Class
subclass of: measurement datum
IHCC category: questionnaire/survey data
IHCC browser label: cognitive and psychological measurements
definition: A measurement datum of some aspect of human psychology.
definition source: EFO:0009095
comment: See also EFO:0009095

cognitive measurement
type: Class
subclass of: psychological measurement
IHCC category: cognitive and psychological measurements
IHCC browser label: cognitive functioning
definition: A psychological measurement of some aspect of intellectual functions such as memory, problem solving, and comprehension.
definition source: Wikipedia:Cognition

personality measurement
type: Class
subclass of: psychological measurement
IHCC category: cognitive and psychological measurements
IHCC browser label: personality
definition: A psychological measurement of a person's individual sets of behaviours, cognitions, and emotional patterns.
definition source: Wikipedia:Personality

emotion
type: Class
subclass of: biological_process
IHCC category: cognitive and psychological measurements
IHCC browser label: psychological distress and emotions
definition: A biological process that results from neurophysiological changes in response to internal and external events.
definition source: Wikipedia:Emotion

oral health history
type: Class
subclass of: lifestyle history
IHCC category: lifestyle and behaviours
IHCC browser label: oral health history
definition: A lifestyle history that is about oral health and hygiene.

psychological treatment history
type: Class
subclass of: non-pharmacological treatment history
IHCC category: non-pharmacological interventions
IHCC browser label: psychological interventions
definition: A non-pharmacological treatment history that is about psychological treatments such as counselling.

radiological treatment history
type: Class
subclass of: non-pharmacological treatment history
IHCC category: non-pharmacological interventions
IHCC browser label: radiological interventions
definition: A non-pharmacological treatment history that is about use of radiology for treatment of disease, disorder, or symptom.

physical therapy history
type: Class
subclass of: non-pharmacological treatment history
IHCC category: non-pharmacological interventions
IHCC browser label: physical therapy interventions
definition: A non-pharmacological treatment history that is about physical therapy treatments such as physical rehabilitation.

perception of health measurement
type: Class
subclass of: psychological measurement
IHCC category: perception of health and quality of life
IHCC browser label: perception of health
definition: A psychological measurement of an individual's subjective perception of health.

quality of life measurement
type: Class
subclass of: psychological measurement
IHCC category: perception of health and quality of life
IHCC browser label: quality of life
definition: A psychological measurement of an individual's perception of their quality of life.

information on functional limitations
type: Class
subclass of: information content entity
IHCC category: perception of health and quality of life
IHCC browser label: functional limitations
definition: Information that is about an individual's limitations in activities that involve caring for an moving the body.
definition source: Maelstrom:Act_daily_living

information on use of assistive devices
type: Class
subclass of: information content entity
IHCC category: perception of health and quality of life
IHCC browser label: use of assistive devices
definition: Information about an individual's use of assistive devices in performing daily activities.
definition source: Maelstrom:Use_devices

religious affiliation
type: Class
subclass of: information content entity
IHCC category: socio-demographic and economic characteristics
IHCC browser label: religion
definition: Information about an individual's association with a religion, denomiation, or sub- or non-denominational religious group.
definition source: url:http://archive.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/religious-affiliation/definition.aspx

human social environment
type: Class
subclass of: immaterial entity
IHCC category: other questionnaire/survey data
IHCC browser label: social environment
definition: 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.
definition source: PMID:10352860

family history of disease
type: Class
subclass of: clinical history
IHCC category: other questionnaire/survey data
IHCC browser label: family history of disease
definition: A clinical history that is about any family history of disease.

diagnostic procedure history
type: Class
subclass of: non-pharmacological treatment history
IHCC category: non-pharmacological interventions
IHCC browser label: diagnostic interventions
definition: A non-pharmacological treatment history that is about diagnostic procedures to determine a condition or disease.
comment: Includes procedures such as colonoscopies, ultrasounds, etc., but excludes laboratory tests.

Alzheimer's Disease Assessment Scale score
type: Class
subclass of: cognitive measurement
IHCC category: cognitive functioning
IHCC browser label: ADAS
definition: A cognitive measurement that is an output (score) from the Alzheimer's Disease Assessment Scale.

Mini-Mental State Exam score
type: Class
subclass of: cognitive measurement
IHCC category: cognitive functioning
IHCC browser label: MMSE
definition: A cognitive measurement that is an output (score) from the Mini-Mental State Exam.

native language of individual
type: Class
subclass of: information content entity
IHCC category: socio-demographic and economic characteristics
IHCC browser label: native language
definition: Information about the language an individual has been exposed to from birth and is their first language.
definition source: url:https://en.wikipedia.org/wiki/First_language

Montreal Cognitive Assessment Test score
type: Class
subclass of: cognitive measurement
IHCC category: cognitive functioning
IHCC browser label: MoCA
definition: A cognitive measurement that is the output (score) from the Montreal Cognitive Assessment Test (MoCA) for Dementia

CERAD Neuropsychological Battery score
type: Class
subclass of: cognitive measurement
IHCC category: cognitive functioning
IHCC browser label: CERAD Battery
definition: A cognitive measurement that is the output (score) from the CERAD Neurophyschological Battery.

Penn Computerized Neurocognitive Battery score
type: Class
subclass of: cognitive measurement
IHCC category: cognitive functioning
IHCC browser label: Penn CNB
definition: A cognitive measurement that is the output (score) from the Penn Computerized Neurocognitive Battery.

congenital disorder
type: Class
subclass of: disease or disorder
IHCC category: diseases
IHCC browser label: congenital and genetic disorders
definition: A disorder that is present at birth due to genetics or environmental factors during development.

Severe Impairment Battery score
type: Class
subclass of: cognitive measurement
IHCC category: cognitive functioning
IHCC browser label: SIB
definition: A cognitive measurement that is the output (score) from the Severe Impairment Battery.

Neuropsychiatric Inventory score
type: Class
subclass of: cognitive measurement
IHCC category: cognitive functioning
IHCC browser label: NPI
definition: A cognitive measurement that is the output (score) from the Neuropsychiatric Inventory.

Clinical Dementia Rating Scale score
type: Class
subclass of: cognitive measurement
IHCC category: cognitive functioning
IHCC browser label: CDR
definition: A cognitive measurement that is the output (score) from the Clinical Dementia Rating Scale.

biological_process
type: Class
subclass of: process
definition: 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.
has_alternative_id: GO:0000004
has_alternative_id: GO:0007582
has_alternative_id: GO:0044699
has_exact_synonym: biological process
has_exact_synonym: physiological process
has_related_synonym: single organism process
has_related_synonym: single-organism process
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.

objective specification
type: Class
subclass of: directive information entity
IHCC category: basic cohort attributes
IHCC browser label: aims and objectives
example of usage: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
definition: 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.
alternative term: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217

data item
type: Class
subclass of: information content entity
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
definition: 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.
alternative term: data

information content entity
type: Class
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
definition: A generically dependent continuant that is about some thing.
definition source: OBI_0000142

directive information entity
type: Class
subclass of: information content entity
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.

plan specification
type: Class
subclass of: directive information entity
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
definition: 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.
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
comment: 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them

measurement datum
type: Class
subclass of: data item
example of usage: 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,}.
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
definition source: OBI_0000305
definition source: group:OBI

textual entity
type: Class
subclass of: information content entity
example of usage: Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
definition: 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.
alternative term: text

document
type: Class
subclass of: information content entity
example of usage: A journal article, patent application, laboratory notebook, or a book
definition: A collection of information content entities intended to be understood together as a whole

availability textual entity
type: Class
subclass of: textual entity
example of usage: 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
definition: A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained.

consent textual entity
type: Class
subclass of: textual entity
IHCC category: survey administration
IHCC browser label: consent/accessibility
example of usage: 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.
definition: A textual entity that documents the consenting process used to enroll patients in a study.

identifier
type: Class
subclass of: information content entity
definition: 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.

belief
type: Class
subclass of: disposition
IHCC category: other questionnaire/survey data
IHCC browser label: personal beliefs and values

disease or disorder
type: Class
subclass of: disposition
IHCC category: questionnaire/survey data
IHCC browser label: diseases
definition: A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
has_exact_synonym: condition
has_exact_synonym: disease
has_exact_synonym: disease or disorder
has_exact_synonym: disease or disorder, non-neoplastic
has_exact_synonym: diseases
has_exact_synonym: diseases and disorders
has_exact_synonym: disorder
has_exact_synonym: disorders
has_exact_synonym: medical condition
has_exact_synonym: other disease

integumentary system disease
type: Class
subclass of: disease or disorder
IHCC category: diseases
IHCC browser label: skin and subcutaneous tissue diseases
definition: A disease involving the integumental system.
has_alternative_id: MONDO:0045027
has_exact_synonym: disease of integumental system
has_exact_synonym: disease or disorder of integumental system
has_exact_synonym: disorder of integumental system
has_exact_synonym: integumental system disease
has_exact_synonym: integumental system disease or disorder
has_exact_synonym: integumentary disease
has_related_synonym: disorder of integument
has_related_synonym: disorder of integumental system

musculoskeletal system disease
type: Class
subclass of: disease or disorder
IHCC category: diseases
IHCC browser label: musculoskeletal system diseases
definition: A disease involving the musculoskeletal system.
has_exact_synonym: disease of musculoskeletal system
has_exact_synonym: disease or disorder of musculoskeletal system
has_exact_synonym: disorder of musculoskeletal system
has_exact_synonym: musculoskeletal disease
has_exact_synonym: musculoskeletal system disease
has_exact_synonym: musculoskeletal system disease or disorder
has_exact_synonym: musculoskeletal system disorder
has_related_synonym: disorder of musculoskeletal system
has_related_synonym: musculoskeletal disorder

urinary system disease
type: Class
subclass of: disease or disorder
IHCC category: diseases
IHCC browser label: urinary system diseases
definition: A disease involving the renal system.
has_exact_synonym: disease of renal system
has_exact_synonym: disease or disorder of renal system
has_exact_synonym: disorder of renal system
has_exact_synonym: disorder of the urinary system
has_exact_synonym: disorder of urinary system
has_exact_synonym: non-neoplastic urinary tract disease
has_exact_synonym: renal disease
has_exact_synonym: renal system disease
has_exact_synonym: renal system disease or disorder
has_exact_synonym: urinary system disease
has_exact_synonym: urinary tract disease
has_exact_synonym: urinary tract disorder
has_exact_synonym: urologic disorder
has_exact_synonym: urological disorders
has_related_synonym: disease, urinary tract
has_related_synonym: disease, urologic
has_related_synonym: disease, urological
has_related_synonym: diseases, urinary tract
has_related_synonym: diseases, urologic
has_related_synonym: diseases, urological
has_related_synonym: disorder of renal system
has_related_synonym: urinary disease
has_related_synonym: urinary system disorder
has_related_synonym: urinary tract diseases
has_related_synonym: urologic disease
has_related_synonym: urological disease
has_related_synonym: urological diseases
has_related_synonym: urological disorder

digestive system disease
type: Class
subclass of: disease or disorder
IHCC category: diseases
IHCC browser label: digestive system diseases
definition: A disease or disorder that involves the digestive system.
has_exact_synonym: alimentary system disease
has_exact_synonym: digestive disease
has_exact_synonym: digestive system disease
has_exact_synonym: digestive system disease or disorder
has_exact_synonym: digestive system disorder
has_exact_synonym: disease of digestive system
has_exact_synonym: disease or disorder of digestive system
has_exact_synonym: disorder of digestive system
has_exact_synonym: gastroenterological system disease
has_exact_synonym: gastroenterological system disorder
has_exact_synonym: gastroenteropathy
has_exact_synonym: gastrointestinal disease
has_exact_synonym: gastrointestinal disorder
has_exact_synonym: gastrointestinal system disease
has_exact_synonym: gastrointestinal system disorder
has_exact_synonym: git disease
has_exact_synonym: stomach or intestinal disorder
has_related_synonym: disorder of digestive system

cancer
type: Class
subclass of: disease or disorder
IHCC category: diseases
IHCC browser label: cancer
definition: 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.
has_exact_synonym: CA
has_exact_synonym: cancer
has_exact_synonym: cell type cancer
has_exact_synonym: malignancy
has_exact_synonym: malignant Growth
has_exact_synonym: malignant neoplasm
has_exact_synonym: malignant neoplasm (disease)
has_exact_synonym: malignant neoplastic disease
has_exact_synonym: malignant tumor
has_exact_synonym: neoplasm (disease), malignant
has_exact_synonym: neoplasm, malignant
has_exact_synonym: organ system cancer
has_exact_synonym: primary cancer
has_related_synonym: MT

cardiovascular disease
type: Class
subclass of: disease or disorder
IHCC category: diseases
IHCC browser label: cardiovascular diseases
definition: A disease involving the cardiovascular system.
has_exact_synonym: cardiovascular disease
has_exact_synonym: cardiovascular disease (CVD)
has_exact_synonym: cardiovascular disorder
has_exact_synonym: cardiovascular system disease
has_exact_synonym: cardiovascular system disease or disorder
has_exact_synonym: disease of cardiovascular system
has_exact_synonym: disease of subdivision of hemolymphoid system
has_exact_synonym: disease or disorder of cardiovascular system
has_exact_synonym: disorder of cardiovascular system
has_related_synonym: circulatory system disease
has_related_synonym: disorder of cardiovascular system

reproductive system disease
type: Class
subclass of: disease or disorder
IHCC category: diseases
IHCC browser label: reproductive system diseases
definition: A disease involving the reproductive system.
has_exact_synonym: disease of reproductive system
has_exact_synonym: disease or disorder of reproductive system
has_exact_synonym: disorder of reproductive system
has_exact_synonym: genital disorders
has_exact_synonym: genital system disease
has_exact_synonym: reproductive disease
has_exact_synonym: reproductive system disease
has_exact_synonym: reproductive system disease or disorder
has_exact_synonym: reproductive system disorder
has_related_synonym: disorder of reproductive system

immune system disease
type: Class
subclass of: disease or disorder
IHCC category: diseases
IHCC browser label: immune system diseases
definition: A disorder resulting from an abnormality in the immune system.
has_exact_synonym: disease of immune system
has_exact_synonym: disease or disorder of immune system
has_exact_synonym: disorder of immune system
has_exact_synonym: immune disease
has_exact_synonym: immune disorder
has_exact_synonym: immune dysfunction
has_exact_synonym: immune system disease or disorder
has_exact_synonym: immune system disorder
has_related_synonym: disorder of immune system
has_related_synonym: immune disorder, NOS

nervous system disorder
type: Class
subclass of: disease or disorder
IHCC category: diseases
IHCC browser label: nervous system disorders
definition: A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves.
has_exact_synonym: disease of nervous system
has_exact_synonym: disease or disorder of nervous system
has_exact_synonym: disorder of nervous system
has_exact_synonym: nervous system disease
has_exact_synonym: nervous system disease or disorder
has_exact_synonym: nervous system disorder
has_exact_synonym: neurologic disease
has_exact_synonym: neurologic disorder
has_exact_synonym: neurological disease
has_exact_synonym: neurological disorder
has_related_synonym: disorder of nervous system

mental disorder
type: Class
subclass of: disease or disorder
IHCC category: diseases
IHCC browser label: mental and behaviour disorders
definition: A disease that has its basis in the disruption of mental process.
has_exact_synonym: disorder of mental process
has_exact_synonym: mental or behavioural disorder
has_exact_synonym: mental process disease
has_related_synonym: disorder of mental process

respiratory system disease
type: Class
subclass of: disease or disorder
IHCC category: diseases
IHCC browser label: respiratory system diseases
definition: 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.
has_exact_synonym: disease of respiratory system
has_exact_synonym: disease or disorder of respiratory system
has_exact_synonym: disorder of respiratory system
has_exact_synonym: respiratory disease
has_exact_synonym: respiratory disorder
has_exact_synonym: respiratory system disease
has_exact_synonym: respiratory system disease or disorder
has_exact_synonym: respiratory system disorder
has_related_synonym: disorder of respiratory system

endocrine system disease
type: Class
subclass of: disease or disorder
IHCC category: diseases
IHCC browser label: endocrine system diseases
definition: A disease involving the endocrine system.
has_exact_synonym: disease of endocrine system
has_exact_synonym: disease or disorder of endocrine system
has_exact_synonym: disorder of endocrine system
has_exact_synonym: endocrine disease
has_exact_synonym: endocrine disorder
has_exact_synonym: endocrine system disease
has_exact_synonym: endocrine system disease or disorder
has_exact_synonym: endocrine system disorder
has_exact_synonym: endocrinopathy
has_exact_synonym: thyroid or other glandular disorders
has_related_synonym: disorder of endocrine system

infectious disease
type: Class
subclass of: disease or disorder
IHCC category: diseases
IHCC browser label: infectious diseases
definition: A disorder resulting from the presence and activity of a microbial, viral, or parasitic agent. It can be transmitted by direct or indirect contact.
has_exact_synonym: ID
has_exact_synonym: clinical infection
has_exact_synonym: communicable disease
has_exact_synonym: infection
has_exact_synonym: infectious
has_exact_synonym: infectious disease
has_exact_synonym: infectious diseases and manifestations
has_exact_synonym: infectious disorder
has_exact_synonym: transmissible disease
has_related_synonym: disease by infectious agent
comment: Replaces 'infection' in disease hierarchy. OBI imported term infection is moved to pathologic process. This class is a container class for infectious diseases, not the process of infection itself.

hematologic disease
type: Class
subclass of: disease or disorder
IHCC category: diseases
IHCC browser label: blood-related disorders
definition: A disease involving the hematopoietic system.
has_exact_synonym: blood disease
has_exact_synonym: blood disorder
has_exact_synonym: blood dyscrasia
has_exact_synonym: disease of hematopoietic system
has_exact_synonym: disease of the blood and blood-forming organs
has_exact_synonym: disease or disorder of hematopoietic system
has_exact_synonym: disorder of hematopoietic system
has_exact_synonym: hematologic and lymphocytic disorder
has_exact_synonym: hematologic disorder
has_exact_synonym: hematological disease
has_exact_synonym: hematological disorder
has_exact_synonym: hematological system disease
has_exact_synonym: hematopoietic disease
has_exact_synonym: hematopoietic system disease
has_exact_synonym: hematopoietic system disease or disorder
has_exact_synonym: rare hematologic disease
has_related_synonym: blood dyscrasia NOS
has_related_synonym: disorder of hematopoietic system
has_related_synonym: hematological disorders and malignancies
comment: placeholder for lymphoid disease

injury
type: Class
subclass of: disease or disorder
IHCC category: diseases
IHCC browser label: injuries
definition: Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity.
has_exact_synonym: injury
has_exact_synonym: trauma
has_exact_synonym: traumatic injury
has_exact_synonym: wound

disease of visual system
type: Class
subclass of: disease or disorder
IHCC category: diseases
IHCC browser label: visual system diseases
definition: A disease that involves the visual system.
has_exact_synonym: disease of visual system
has_exact_synonym: disease or disorder of visual system
has_exact_synonym: disorder of visual system
has_exact_synonym: visual system disease
has_exact_synonym: visual system disease or disorder
has_exact_synonym: visual system disorder
has_related_synonym: disorder of visual system

otorhinolaryngologic disease
type: Class
subclass of: disease or disorder
IHCC category: diseases
IHCC browser label: diseases of the ear, nose, and/or throat
definition: Pathological processes of the ear, the nose, and the throat, also known as the ENT diseases.
has_exact_synonym: ear, nose and throat disorder
has_exact_synonym: ear, nose or throat disorder
has_exact_synonym: ear/nose/throat disease
has_exact_synonym: otolaryngologic disorder
has_exact_synonym: otorhinolaryngologic disease
has_related_synonym: ENT disease
has_related_synonym: ENT diseases
has_related_synonym: disease, ENT
has_related_synonym: disease, otolaryngologic
has_related_synonym: disease, otolaryngological
has_related_synonym: disease, otorhinolaryngologic
has_related_synonym: disease, otorhinolaryngological
has_related_synonym: diseases, ENT
has_related_synonym: diseases, otolaryngologic
has_related_synonym: diseases, otolaryngological
has_related_synonym: diseases, otorhinolaryngologic
has_related_synonym: diseases, otorhinolaryngological
has_related_synonym: otolaryngologic disease
has_related_synonym: otolaryngologic diseases
has_related_synonym: otolaryngological disease
has_related_synonym: otolaryngological diseases
has_related_synonym: otorhinolaryngological disease
has_related_synonym: otorhinolaryngological diseases
comment: Editor note: consider uberon class

poisoning
type: Class
subclass of: disease or disorder
IHCC category: diseases
IHCC browser label: poisoning
definition: A condition or physical state produced by the ingestion, injection, inhalation of or exposure to a deleterious agent.
has_related_synonym: Poisonings
has_related_synonym: intoxication
has_related_synonym: poisoning syndrome

planned process
type: Class
subclass of: process
example of usage: Injecting mice with a vaccine in order to test its efficacy
definition: A process that realizes a plan which is the concretization of a plan specification.
definition source: branch derived

assay
type: Class
subclass of: planned process
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
definition: A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
alternative term: measuring
alternative term: scientific observation
definition source: OBI branch derived

material processing
type: Class
subclass of: planned process
example of usage: A cell lysis, production of a cloning vector, creating a buffer.
definition: A planned process which results in physical changes in a specified input material
alternative term: material transformation
definition source: OBI branch derived

imaging assay
type: Class
subclass of: assay
IHCC category: laboratory measures
IHCC browser label: imaging
definition: An assay that produces a picture of an entity.
definition source: OBI branch derived

genotyping assay
type: Class
subclass of: genomic assay
IHCC category: genomics
IHCC browser label: DNA/Genotyping
example of usage: 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
definition: 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.
alternative term: SNP analysis
alternative term: genotype profiling
definition source: OBI Biomaterial

copy number variation profiling assay
type: Class
subclass of: genomic assay
IHCC category: genomics
IHCC browser label: Sequence variants (CNV, SNP arrays)
example of usage: 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
definition: 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
alternative term: CNV analysis

RNA-seq assay
type: Class
subclass of: genomic assay
IHCC category: genomics
IHCC browser label: RNAseq/gene expression
definition: An transcription profiling assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance.
alternative term: transcription profiling by high throughput sequencing
definition source: EFO:0002770

organism identification assay
type: Class
subclass of: assay
IHCC category: laboratory measures
IHCC browser label: microbiology
definition: An assay that identifies the organism species in a specimen.
definition source: NIAID GSCID-BRC metadata working group

epigenetic modification assay
type: Class
subclass of: genomic assay
IHCC category: genomics
IHCC browser label: Epigenetics
definition: An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation.
definition source: Penn group

whole genome sequencing assay
type: Class
subclass of: genomic assay
IHCC category: genomics
IHCC browser label: WGS
example of usage: 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.
definition: A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism.
alternative term: WGS
definition source: PMID:23095910
definition source: PMID:25827230

exome sequencing assay
type: Class
subclass of: genomic assay
IHCC category: genomics
IHCC browser label: WES
example of usage: 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.
definition: A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons).
alternative term: WES
definition source: PMID:25827230

exposure to environmental and workplace carcinogens history
type: Class
subclass of: information content entity
IHCC category: physical environment
IHCC browser label: exposure to carcinogens
definition: A information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment.
definition source: OBIB

whole metagenome sequencing assay
type: Class
subclass of: genomic assay
IHCC category: genomics
IHCC browser label: Metagenomics
definition: 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.
alternative term: WMS
definition source: Bjoern Peters
definition source: Michelle Giglio

storage
type: Class
subclass of: planned process
example of usage: PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
definition: 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
definition source: OBI-Branch

study design
type: Class
subclass of: plan specification
IHCC category: basic cohort attributes
IHCC browser label: study design
example of usage: 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.
definition: 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.
alternative term: experimental design

inclusion criterion
type: Class
subclass of: directive information entity
IHCC category: population data
IHCC browser label: criteria for enrollment and recruitment procedures
example of usage: 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) .
definition: 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.
alternative term: inclusion condition
alternative term: inclusion rule
definition source: Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group

clinical history
type: Class
subclass of: information content entity
definition: A series of statements representing health-relevant qualities of a patient and of a patient's family.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

symptom
type: Class
subclass of: quality
IHCC category: other questionnaire/survey data
IHCC browser label: signs and symptoms
definition: A process experienced by the patient, which can only be experienced by the patient, that is hypothesized to be clinically relevant.
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

income data
type: Class
subclass of: data item
IHCC category: socio-demographic and economic characteristics
IHCC browser label: income and possessions

age
type: Class
subclass of: quality
IHCC category: socio-demographic and economic characteristics
IHCC browser label: age/birthdate
definition: A time quality inhering in a bearer by virtue of how long the bearer has existed.

biological sex
type: Class
subclass of: organismal quality
IHCC category: socio-demographic and economic characteristics
IHCC browser label: biological sex
definition: 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.

organismal quality
type: Class
subclass of: quality
IHCC category: questionnaire/survey data
IHCC browser label: socio-demographic and economic characteristics
definition: A quality that inheres in an entire organism or part of an organism.

collection of organisms
type: Class
subclass of: material entity
example of usage: Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family.
definition: A material entity that consists of two or more organisms, viruses, or viroids.
alternative term: group of organism
alternative term: organism collection
comment: May be of the same or different species.

drug prescription
type: Class
subclass of: document
IHCC category: medication
IHCC browser label: prescription
example of usage: "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"
definition: A health care prescription specifying the initiation, modification or cessation of a drug administration.

drug administration specification
type: Class
subclass of: directive information entity
IHCC category: medication
IHCC browser label: administration
example of usage: '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'
definition: 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

statistic
type: Class
subclass of: measurement datum
definition: a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data.
definition source: STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic).

count
type: Class
subclass of: measurement datum
example of usage: a count of 4 resulting from counting limbs in humans
definition: a count is a data item denoted by an integer and represented the number of instances or occurences of an entity
definition source: STATO

date
type: Class
subclass of: measurement datum
IHCC category: survey administration
IHCC browser label: date and time-related information
definition: Information about a calendar date or timestamp indicating day, month, year and time of an event.
definition source: STATO

life cycle stage
type: Class
subclass of: process
IHCC category: other questionnaire/survey data
IHCC browser label: life stage/time point
definition: A spatiotemporal region encompassing some part of the life cycle of an organism.
has_narrow_synonym: developmental stage
has_narrow_synonym: stage

blood
type: Class
subclass of: organism substance
IHCC category: sample type
IHCC browser label: blood
definition: A fluid that is composed of blood plasma and erythrocytes.
has_exact_synonym: portion of blood
has_exact_synonym: vertebrate blood
has_related_synonym: whole blood

organism substance
type: Class
subclass of: material entity
IHCC category: biosample
IHCC browser label: sample type
definition: 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.
has_exact_synonym: body fluid or substance
has_exact_synonym: body substance
has_exact_synonym: organism substance
has_exact_synonym: portion of body substance
has_exact_synonym: portion of organism substance

urine
type: Class
subclass of: organism substance
IHCC category: sample type
IHCC browser label: urine
definition: Excretion that is the output of a kidney

saliva
type: Class
subclass of: organism substance
IHCC category: sample type
IHCC browser label: saliva
definition: A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
has_exact_synonym: salivary gland secretion
has_related_synonym: sailva normalis
has_related_synonym: saliva atomaris
has_related_synonym: saliva molecularis

feces
type: Class
subclass of: organism substance
IHCC category: sample type
IHCC browser label: stool
definition: Portion of semisolid bodily waste discharged through the anus[MW,modified]
has_broad_synonym: excreta
has_exact_synonym: faeces
has_exact_synonym: fecal material
has_exact_synonym: fecal matter
has_exact_synonym: matières fécales@fr
has_exact_synonym: merde@fr
has_exact_synonym: partie de la merde@fr
has_exact_synonym: piece of shit
has_exact_synonym: porción de mierda@es
has_exact_synonym: portion of excrement
has_exact_synonym: portion of faeces
has_exact_synonym: portion of fecal material
has_exact_synonym: portion of fecal matter
has_exact_synonym: portion of feces
has_exact_synonym: portionem cacas
has_exact_synonym: stool
has_exact_synonym: teil der fäkalien@de
has_narrow_synonym: cow dung
has_narrow_synonym: cow pat
has_narrow_synonym: dung
has_narrow_synonym: fewmet
has_narrow_synonym: frass
has_narrow_synonym: guano
has_narrow_synonym: portion of dung
has_narrow_synonym: portion of guano
has_narrow_synonym: portion of scat
has_narrow_synonym: scat
has_narrow_synonym: spraint
has_related_synonym: droppings
has_related_synonym: excrement
has_related_synonym: ordure
has_related_synonym: spoor