Genomics Cohorts Knowledge Ontology (IHCC View)
type: Ontology
version IRI: ihcc-gecko.owl
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

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

see also
type: AnnotationProperty

physiological measurements
type: Class
subclass of: questionnaire/survey data

circulation and respiration
type: Class
subclass of: physiological measurements

blood pressure
type: Class
subclass of: circulation and respiration

weight
type: Class
subclass of: anthropometry

anthropometry
type: Class
subclass of: physiological measurements

height
type: Class
subclass of: anthropometry

heart rate (HR)
type: Class
subclass of: circulation and respiration

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

routine clincial visits
type: Class
subclass of: healthcare information
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
has_exact_synonym: aggregated clinical visit information

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

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

marital status
type: Class
subclass of: socio-demographic and economic characteristics
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
has_exact_synonym: marital status

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

physical environment
type: Class
subclass of: questionnaire/survey data
definition: environmental system associated with the dwelling used by humans.
definition source: Penn Group
has_exact_synonym: environment associated with human dwelling

basic cohort attributes
type: Class

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

population data
type: Class
subclass of: basic cohort attributes
definition: A data item that is about a population of organisms.
has_exact_synonym: population data item

location
type: Class
subclass of: population data
definition: A population data item that is about the geographical location of a population of organisms.
has_exact_synonym: population location

num. participants
type: Class
subclass of: population data
definition: A sample size that is about the count of individual organisms in a population.
has_exact_synonym: population size

demographic data
type: Class
subclass of: basic cohort attributes
definition: A quality which inheres in a population of organisms.
has_exact_synonym: population quality

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

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

age range
type: Class
subclass of: demographic data
definition: A population quality concerning the age range of a population.
has_exact_synonym: population age range

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

biosample
type: Class

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

storage method
type: Class
subclass of: biosample
definition: A storage process for a biosample collected from an organism.
has_exact_synonym: biosample storage

laboratory measures
type: Class

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

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

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

sample size
type: Class
subclass of: biosample
definition: A count of the number of biosamples collected for an investigation.
has_exact_synonym: biosample size

processing method
type: Class
subclass of: biosample
definition: A material processing which prepares a biosample for investigation.
has_exact_synonym: biosample processing

survey administration
type: Class

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

questionnaire/survey data
type: Class

gender
type: Class
subclass of: socio-demographic and economic characteristics
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
has_exact_synonym: gender

ethnicity/race
type: Class
subclass of: socio-demographic and economic characteristics
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
has_exact_synonym: ethnicity

birthplace
type: Class
subclass of: socio-demographic and economic characteristics
definition: A geographical location in which an individual was born.
has_exact_synonym: birthplace location

residence
type: Class
subclass of: socio-demographic and economic characteristics
definition: A geographical location in which an individual currently resides.
has_exact_synonym: residence location

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

family and household structure
type: Class
subclass of: socio-demographic and economic characteristics
definition: Information that is about the structure of an individual's family and/or household.
has_exact_synonym: family and household structure

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

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

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

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

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

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

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

surgical interventions
type: Class
subclass of: non-pharmacological interventions
definition: A clinical history that is about surgical operations performed on an individual.
has_exact_synonym: surgical history

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

associated disease(s)
type: Class
subclass of: medication
definition: Information that is about the disease treated by a drug prescribed to an individual.
has_exact_synonym: disease treated by prescription drug

drug response(s)
type: Class
subclass of: medication
definition: A biological process that results from a drug stimulus.
has_exact_synonym: response to medication

statistics
type: Class

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

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

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

other
type: Class
subclass of: genomics

other biosample type
type: Class
subclass of: sample type

availability
type: Class
subclass of: biosample
definition: An availability textual entity that is about a substance from an organism (a biosample).
has_exact_synonym: biosample availability textual entity

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

other questionnaire/survey data
type: Class
subclass of: questionnaire/survey data

perception of health and quality of life
type: Class
subclass of: questionnaire/survey data

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

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

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

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

oral health history
type: Class
subclass of: lifestyle and behaviours
definition: A lifestyle history that is about oral health and hygiene.
has_exact_synonym: oral health history

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

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

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

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

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

functional limitations
type: Class
subclass of: perception of health and quality of life
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
has_exact_synonym: information on functional limitations

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

religion
type: Class
subclass of: socio-demographic and economic characteristics
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
has_exact_synonym: religious affiliation

social environment
type: Class
subclass of: other questionnaire/survey data
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
has_exact_synonym: human social environment

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

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

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

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

native language
type: Class
subclass of: socio-demographic and economic characteristics
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
has_exact_synonym: native language of individual

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

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

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

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

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

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

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

aims and objectives
type: Class
subclass of: basic cohort attributes
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
has_exact_synonym: objective specification

consent/accessibility
type: Class
subclass of: survey administration
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.
has_exact_synonym: consent textual entity

personal beliefs and values
type: Class
subclass of: other questionnaire/survey data

diseases
type: Class
subclass of: questionnaire/survey data
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

skin and subcutaneous tissue diseases
type: Class
subclass of: 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_exact_synonym: integumentary system disease
has_related_synonym: disorder of integument
has_related_synonym: disorder of integumental system

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

respiratory system diseases
type: Class
subclass of: 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 diseases
type: Class
subclass of: 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 diseases
type: Class
subclass of: 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.

blood-related disorders
type: Class
subclass of: diseases
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 disease
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

injuries
type: Class
subclass of: diseases
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

visual system diseases
type: Class
subclass of: 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

diseases of the ear, nose, and/or throat
type: Class
subclass of: diseases
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: diseases
definition: A condition or physical state produced by the ingestion, injection, inhalation of or exposure to a deleterious agent.
has_exact_synonym: poisoning
has_related_synonym: Poisonings
has_related_synonym: intoxication
has_related_synonym: poisoning syndrome

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

DNA/Genotyping
type: Class
subclass of: genomics
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
has_exact_synonym: genotyping assay

Sequence variants (CNV, SNP arrays)
type: Class
subclass of: genomics
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
has_exact_synonym: copy number variation profiling assay

RNAseq/gene expression
type: Class
subclass of: genomics
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
has_exact_synonym: RNA-seq assay

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

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

WGS
type: Class
subclass of: genomics
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
has_exact_synonym: whole genome sequencing assay

WES
type: Class
subclass of: genomics
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
has_exact_synonym: exome sequencing assay

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

Metagenomics
type: Class
subclass of: genomics
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
has_exact_synonym: whole metagenome sequencing assay

study design
type: Class
subclass of: basic cohort attributes
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
has_exact_synonym: study design

criteria for enrollment and recruitment procedures
type: Class
subclass of: population data
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
has_exact_synonym: inclusion criterion

signs and symptoms
type: Class
subclass of: other questionnaire/survey data
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
has_exact_synonym: symptom

income and possessions
type: Class
subclass of: socio-demographic and economic characteristics

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

biological sex
type: Class
subclass of: socio-demographic and economic characteristics
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.
has_exact_synonym: biological sex

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

prescription
type: Class
subclass of: medication
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.
has_exact_synonym: drug prescription

administration
type: Class
subclass of: medication
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
has_exact_synonym: drug administration specification

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

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

blood
type: Class
subclass of: sample type
definition: A fluid that is composed of blood plasma and erythrocytes.
has_exact_synonym: blood
has_exact_synonym: portion of blood
has_exact_synonym: vertebrate blood
has_related_synonym: whole blood

sample type
type: Class
subclass of: biosample
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: sample type
definition: Excretion that is the output of a kidney
has_exact_synonym: urine

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

stool
type: Class
subclass of: sample type
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: feces
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