An ontology to represent genomics cohort attributes.
Genomics Cohorts Knowledge Ontology
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
IHCC browser label
example of usage
definition
alternative term
definition source
has_alternative_id
has_broad_synonym
has_exact_synonym
has_narrow_synonym
has_related_synonym
comment
label
see also
part of
is about
inheres in
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
process
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
realizable entity
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
quality
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
site
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
material entity
immaterial entity
questionnaire/survey data
physiological measurements
clinical measurement data item
physiological measurements
circulation and respiration
cardiovascular measurement data item
circulation and respiration
blood pressure
blood pressure measurement data item
anthropometry
weight
body weight data item
physiological measurements
anthropometry
body morphological measurement data item
anthropometry
height
body height data item
circulation and respiration
heart rate (HR)
pulse data item
other questionnaire/survey data
cause of death
An information content entity indicating the cause of death for a participant in the study.
Penn Group
cause of participant death
healthcare information
routine clincial visits
a data item that is about an investigation and is the specified output of a data transformation that has only clinical visit data as input
EuPathDB
aggregated clinical visit information
healthcare information
hospitalizations
an information content entity that is about a part of a health care encounter that occurs in a hospital facility
EuPathDB
hospitalization information
socio-demographic and economic characteristics
occupation
An information content entity that is about an activity that realizes a social role and is often performed for payment.
occupation
socio-demographic and economic characteristics
marital status
a categorical value specification that is about a human being and specifies whether that human being is joined to another human being in marriage
EuPathDB, BFO's 'relational quality' examples
marital status
questionnaire/survey data
healthcare information
An information content entity about healthcare that is private or public.
healthcare information
questionnaire/survey data
physical environment
environmental system associated with the dwelling used by humans.
Penn Group
environment associated with human dwelling
basic cohort attributes
timeline
A directive information entity that specifies the sequence in which a series of events occurred or will occur.
timeline
basic cohort attributes
population data
A data item that is about a population of organisms.
population data item
population data
location
A population data item that is about the geographical location of a population of organisms.
population location
population data
num. participants
A sample size that is about the count of individual organisms in a population.
population size
basic cohort attributes
demographic data
A quality which inheres in a population of organisms.
population quality
demographic data
sex(es) studied in cohort
A population quality concerning the sex or sexes of the population.
population sex or sexes
demographic data
gender(s) studied in cohort
A population quality concerning the gender or genders of the population.
population gender or genders
demographic data
age range
A population quality concerning the age range of a population.
population age range
basic cohort attributes
data collection events
A planned process that is a part of an investigation in which raw data is collected.
data collection
blood
fasting or non-fasting
Blood that is collected from an organism which has been fasting for a given amount of time.
blood collected from fasting subject
biosample
storage method
A storage process for a biosample collected from an organism.
biosample storage
laboratory measures
genomics
An assay that investigates the genome or genomes of an individual organism or population of organisms.
Merged GECKO 'data type' into 'genomics'.
genomic assay
genomics
Microbiome markers (rRNA, etc)
A genomic assay that profiles the microorganisms present in a sample.
Potential new OBI request
microbiome sequencing assay
genomics
eQTL (Cis eQTLs and/or Trans eQTLs)
A genomic assay that identifies genetic loci and candidate genes correlated with phenotypes.
PMID:27964730
Potential new OBI request
eQTL analysis
biosample
sample size
A count of the number of biosamples collected for an investigation.
biosample size
biosample
processing method
A material processing which prepares a biosample for investigation.
biosample processing
survey administration
unique identifiers
An identifier that is guaranteed to be unique among all identifiers in a particular domain.
Wikipedia:Unique_identifier
unique identifier
socio-demographic and economic characteristics
gender
An organismal quality inhering in a bearer by virtue of the bearer's preference towards a range of characteristics pertaining to, and differentiating between, masculinity and femininity.
Wikipedia:Gender|PATO:0000047
gender
socio-demographic and economic characteristics
ethnicity/race
An organismal quality inhering in a bearer by virtue of the bearer's identification with a group of other individuals on the basis of presumed similarities such as language or common ancestry.
Wikipedia:Ethnic_group
ethnicity
socio-demographic and economic characteristics
birthplace
A geographical location in which an individual was born.
birthplace location
socio-demographic and economic characteristics
residence
A geographical location in which an individual currently resides.
residence location
socio-demographic and economic characteristics
education
An organismal quality inhering in a bearer by virute of the bearer's highest level of formal education completed.
education level
socio-demographic and economic characteristics
family and household structure
Information that is about the structure of an individual's family and/or household.
family and household structure
questionnaire/survey data
lifestyle and behaviours
A clinical history that is about the lifestyle and behaviors of an individual which may impact health outcomes.
lifestyle history
lifestyle and behaviours
tobacco use history
A lifestyle history that is about the tobacco use or exposure of an individual.
tobacco use history
lifestyle and behaviours
alcohol use history
A lifestyle history that is about the alcohol consumption of an individual.
alcohol use history
lifestyle and behaviours
sleep history
A lifestyle history that is about the sleep quality and duration of an individual.
sleep history
lifestyle and behaviours
dietary history
A lifestyle history that is about the diet and nutrition of an individual.
nutritional history
healthcare information
physician/practitioner info
A textual entity that contains contact details for an individual's physician, which may include: name, phone number, address, etc.
physician contact textual entity
questionnaire/survey data
non-pharmacological interventions
A treatment history that is about any non-pharamacological treatments such as surgery or physical therapy.
non-pharmacological treatment history
non-pharmacological interventions
surgical interventions
A clinical history that is about surgical operations performed on an individual.
surgical history
questionnaire/survey data
medication
A clinical history that is about the prescription drugs taken by an individual.
prescription drug history
medication
associated disease(s)
Information that is about the disease treated by a drug prescribed to an individual.
disease treated by prescription drug
medication
drug response(s)
A biological process that results from a drug stimulus.
response to medication
statistics
summary statistics for additional data from federated sources
A statistic that summarizes a set of federated data.
summary statistic for federated data
lifestyle and behaviours
recreational drug history
A lifestyle history that is about the use of unprescribed and/or non-prescription drugs.
recreational drug history
lifestyle and behaviours
physical activity history
A lifestyle history that is about the typical physical activity of an individual.
physical activity history
A count which represents the subset of a collection chosen for an investigation, survey, or assay.
sample size
biosample
availability
An availability textual entity that is about a substance from an organism (a biosample).
biosample availability textual entity
other questionnaire/survey data
reproduction
A clinical history that is about pregnancy, maternity, fertility, menses, and any other reproductive aspect.
reproductive history
A clinical history that is about any treatment (surgical, prescription, etc.) for disease, disorder, or symptom.
treatment history
questionnaire/survey data
cognitive and psychological measurements
A measurement datum of some aspect of human psychology.
EFO:0009095
See also EFO:0009095
psychological measurement
cognitive and psychological measurements
cognitive functioning
A psychological measurement of some aspect of intellectual functions such as memory, problem solving, and comprehension.
Wikipedia:Cognition
cognitive measurement
cognitive and psychological measurements
personality
A psychological measurement of a person's individual sets of behaviours, cognitions, and emotional patterns.
Wikipedia:Personality
personality measurement
cognitive and psychological measurements
psychological distress and emotions
A biological process that results from neurophysiological changes in response to internal and external events.
Wikipedia:Emotion
emotion
lifestyle and behaviours
oral health history
A lifestyle history that is about oral health and hygiene.
oral health history
non-pharmacological interventions
psychological interventions
A non-pharmacological treatment history that is about psychological treatments such as counselling.
psychological treatment history
non-pharmacological interventions
radiological interventions
A non-pharmacological treatment history that is about use of radiology for treatment of disease, disorder, or symptom.
radiological treatment history
non-pharmacological interventions
physical therapy interventions
A non-pharmacological treatment history that is about physical therapy treatments such as physical rehabilitation.
physical therapy history
perception of health and quality of life
perception of health
A psychological measurement of an individual's subjective perception of health.
perception of health measurement
perception of health and quality of life
quality of life
A psychological measurement of an individual's perception of their quality of life.
quality of life measurement
perception of health and quality of life
functional limitations
Information that is about an individual's limitations in activities that involve caring for an moving the body.
Maelstrom:Act_daily_living
information on functional limitations
perception of health and quality of life
use of assistive devices
Information about an individual's use of assistive devices in performing daily activities.
Maelstrom:Use_devices
information on use of assistive devices
socio-demographic and economic characteristics
religion
Information about an individual's association with a religion, denomiation, or sub- or non-denominational religious group.
url:http://archive.stats.govt.nz/methods/classifications-and-standards/classification-related-stats-standards/religious-affiliation/definition.aspx
religious affiliation
other questionnaire/survey data
social environment
An immaterial entity that encompasses the domain made up of interactions between the individual's physical environment, social processes, and relationships with other individuals and groups.
PMID:10352860
human social environment
other questionnaire/survey data
family history of disease
A clinical history that is about any family history of disease.
family history of disease
non-pharmacological interventions
diagnostic interventions
A non-pharmacological treatment history that is about diagnostic procedures to determine a condition or disease.
Includes procedures such as colonoscopies, ultrasounds, etc., but excludes laboratory tests.
diagnostic procedure history
cognitive functioning
ADAS
A cognitive measurement that is an output (score) from the Alzheimer's Disease Assessment Scale.
Alzheimer's Disease Assessment Scale score
cognitive functioning
MMSE
A cognitive measurement that is an output (score) from the Mini-Mental State Exam.
Mini-Mental State Exam score
socio-demographic and economic characteristics
native language
Information about the language an individual has been exposed to from birth and is their first language.
url:https://en.wikipedia.org/wiki/First_language
native language of individual
cognitive functioning
MoCA
A cognitive measurement that is the output (score) from the Montreal Cognitive Assessment Test (MoCA) for Dementia
Montreal Cognitive Assessment Test score
cognitive functioning
CERAD Battery
A cognitive measurement that is the output (score) from the CERAD Neurophyschological Battery.
CERAD Neuropsychological Battery score
cognitive functioning
Penn CNB
A cognitive measurement that is the output (score) from the Penn Computerized Neurocognitive Battery.
Penn Computerized Neurocognitive Battery score
diseases
congenital and genetic disorders
A disorder that is present at birth due to genetics or environmental factors during development.
congenital disorder
cognitive functioning
SIB
A cognitive measurement that is the output (score) from the Severe Impairment Battery.
Severe Impairment Battery score
cognitive functioning
NPI
A cognitive measurement that is the output (score) from the Neuropsychiatric Inventory.
Neuropsychiatric Inventory score
cognitive functioning
CDR
A cognitive measurement that is the output (score) from the Clinical Dementia Rating Scale.
Clinical Dementia Rating Scale score
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
GO:0000004
GO:0007582
GO:0044699
biological process
physiological process
single organism process
single-organism process
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
biological_process
basic cohort attributes
aims and objectives
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
goal specification
OBI Plan and Planned Process/Roles Branch
OBI_0000217
objective specification
Data items include counts of things, analyte concentrations, and statistical summaries.
An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
data
data item
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
OBI_0000142
information content entity
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
directive information entity
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
OBI Plan and Planned Process branch
OBI_0000344
2/3/2009 Comment from OBI review.
Action specification not well enough specified.
Conditional specification not well enough specified.
Question whether all plan specifications have objective specifications.
Request that IAO either clarify these or change definitions not to use them
plan specification
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
OBI_0000305
group:OBI
measurement datum
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
text
textual entity
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
document
From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/):
Project home page:http://krux.googlecode.com
A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained.
availability textual entity
survey administration
consent/accessibility
From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/):
Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal.
A textual entity that documents the consenting process used to enroll patients in a study.
consent textual entity
An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
identifier
other questionnaire/survey data
personal beliefs and values
belief
questionnaire/survey data
diseases
A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
condition
disease
disease or disorder
disease or disorder, non-neoplastic
diseases
diseases and disorders
disorder
disorders
medical condition
other disease
disease or disorder
diseases
skin and subcutaneous tissue diseases
A disease involving the integumental system.
MONDO:0045027
disease of integumental system
disease or disorder of integumental system
disorder of integumental system
integumental system disease
integumental system disease or disorder
integumentary disease
disorder of integument
disorder of integumental system
integumentary system disease
diseases
musculoskeletal system diseases
A disease involving the musculoskeletal system.
disease of musculoskeletal system
disease or disorder of musculoskeletal system
disorder of musculoskeletal system
musculoskeletal disease
musculoskeletal system disease
musculoskeletal system disease or disorder
musculoskeletal system disorder
disorder of musculoskeletal system
musculoskeletal disorder
musculoskeletal system disease
diseases
urinary system diseases
A disease involving the renal system.
disease of renal system
disease or disorder of renal system
disorder of renal system
disorder of the urinary system
disorder of urinary system
non-neoplastic urinary tract disease
renal disease
renal system disease
renal system disease or disorder
urinary system disease
urinary tract disease
urinary tract disorder
urologic disorder
urological disorders
disease, urinary tract
disease, urologic
disease, urological
diseases, urinary tract
diseases, urologic
diseases, urological
disorder of renal system
urinary disease
urinary system disorder
urinary tract diseases
urologic disease
urological disease
urological diseases
urological disorder
urinary system disease
diseases
digestive system diseases
A disease or disorder that involves the digestive system.
alimentary system disease
digestive disease
digestive system disease
digestive system disease or disorder
digestive system disorder
disease of digestive system
disease or disorder of digestive system
disorder of digestive system
gastroenterological system disease
gastroenterological system disorder
gastroenteropathy
gastrointestinal disease
gastrointestinal disorder
gastrointestinal system disease
gastrointestinal system disorder
git disease
stomach or intestinal disorder
disorder of digestive system
digestive system disease
diseases
cancer
A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas.
CA
cancer
cell type cancer
malignancy
malignant Growth
malignant neoplasm
malignant neoplasm (disease)
malignant neoplastic disease
malignant tumor
neoplasm (disease), malignant
neoplasm, malignant
organ system cancer
primary cancer
MT
cancer
diseases
cardiovascular diseases
A disease involving the cardiovascular system.
cardiovascular disease
cardiovascular disease (CVD)
cardiovascular disorder
cardiovascular system disease
cardiovascular system disease or disorder
disease of cardiovascular system
disease of subdivision of hemolymphoid system
disease or disorder of cardiovascular system
disorder of cardiovascular system
circulatory system disease
disorder of cardiovascular system
cardiovascular disease
diseases
reproductive system diseases
A disease involving the reproductive system.
disease of reproductive system
disease or disorder of reproductive system
disorder of reproductive system
genital disorders
genital system disease
reproductive disease
reproductive system disease
reproductive system disease or disorder
reproductive system disorder
disorder of reproductive system
reproductive system disease
diseases
immune system diseases
A disorder resulting from an abnormality in the immune system.
disease of immune system
disease or disorder of immune system
disorder of immune system
immune disease
immune disorder
immune dysfunction
immune system disease or disorder
immune system disorder
disorder of immune system
immune disorder, NOS
immune system disease
diseases
nervous system disorders
A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves.
disease of nervous system
disease or disorder of nervous system
disorder of nervous system
nervous system disease
nervous system disease or disorder
nervous system disorder
neurologic disease
neurologic disorder
neurological disease
neurological disorder
disorder of nervous system
nervous system disorder
diseases
mental and behaviour disorders
A disease that has its basis in the disruption of mental process.
disorder of mental process
mental or behavioural disorder
mental process disease
disorder of mental process
mental disorder
diseases
respiratory system diseases
A non-neoplastic or neoplastic disorder that affects the respiratory system. Representative examples include pneumonia, chronic obstructive pulmonary disease, pulmonary failure, lung adenoma, lung carcinoma, and tracheal carcinoma.
disease of respiratory system
disease or disorder of respiratory system
disorder of respiratory system
respiratory disease
respiratory disorder
respiratory system disease
respiratory system disease or disorder
respiratory system disorder
disorder of respiratory system
respiratory system disease
diseases
endocrine system diseases
A disease involving the endocrine system.
disease of endocrine system
disease or disorder of endocrine system
disorder of endocrine system
endocrine disease
endocrine disorder
endocrine system disease
endocrine system disease or disorder
endocrine system disorder
endocrinopathy
thyroid or other glandular disorders
disorder of endocrine system
endocrine system disease
diseases
infectious diseases
A disorder resulting from the presence and activity of a microbial, viral, or parasitic agent. It can be transmitted by direct or indirect contact.
ID
clinical infection
communicable disease
infection
infectious
infectious disease
infectious diseases and manifestations
infectious disorder
transmissible disease
disease by infectious agent
Replaces 'infection' in disease hierarchy. OBI imported term infection is moved to pathologic process. This class is a container class for infectious diseases, not the process of infection itself.
infectious disease
diseases
blood-related disorders
A disease involving the hematopoietic system.
blood disease
blood disorder
blood dyscrasia
disease of hematopoietic system
disease of the blood and blood-forming organs
disease or disorder of hematopoietic system
disorder of hematopoietic system
hematologic and lymphocytic disorder
hematologic disorder
hematological disease
hematological disorder
hematological system disease
hematopoietic disease
hematopoietic system disease
hematopoietic system disease or disorder
rare hematologic disease
blood dyscrasia NOS
disorder of hematopoietic system
hematological disorders and malignancies
placeholder for lymphoid disease
hematologic disease
https://github.com/monarch-initiative/mondo/issues/254
diseases
injuries
Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity.
injury
trauma
traumatic injury
wound
injury
diseases
visual system diseases
A disease that involves the visual system.
disease of visual system
disease or disorder of visual system
disorder of visual system
visual system disease
visual system disease or disorder
visual system disorder
disorder of visual system
disease of visual system
diseases
diseases of the ear, nose, and/or throat
Pathological processes of the ear, the nose, and the throat, also known as the ENT diseases.
ear, nose and throat disorder
ear, nose or throat disorder
ear/nose/throat disease
otolaryngologic disorder
otorhinolaryngologic disease
ENT disease
ENT diseases
disease, ENT
disease, otolaryngologic
disease, otolaryngological
disease, otorhinolaryngologic
disease, otorhinolaryngological
diseases, ENT
diseases, otolaryngologic
diseases, otolaryngological
diseases, otorhinolaryngologic
diseases, otorhinolaryngological
otolaryngologic disease
otolaryngologic diseases
otolaryngological disease
otolaryngological diseases
otorhinolaryngological disease
otorhinolaryngological diseases
Editor note: consider uberon class
otorhinolaryngologic disease
diseases
poisoning
A condition or physical state produced by the ingestion, injection, inhalation of or exposure to a deleterious agent.
Poisonings
intoxication
poisoning syndrome
poisoning
Injecting mice with a vaccine in order to test its efficacy
A process that realizes a plan which is the concretization of a plan specification.
branch derived
planned process
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
measuring
scientific observation
OBI branch derived
assay
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
material transformation
OBI branch derived
material processing
laboratory measures
imaging
An assay that produces a picture of an entity.
OBI branch derived
imaging assay
genomics
DNA/Genotyping
High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923
An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions.
SNP analysis
genotype profiling
OBI Biomaterial
genotyping assay
genomics
Sequence variants (CNV, SNP arrays)
Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. PMID:18058796
An assay that determines lost or amplified genomic regions of DNA by comparing genomic DNA originating from tissues from the same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping
CNV analysis
copy number variation profiling assay
genomics
RNAseq/gene expression
An transcription profiling assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance.
transcription profiling by high throughput sequencing
EFO:0002770
RNA-seq assay
laboratory measures
microbiology
An assay that identifies the organism species in a specimen.
NIAID GSCID-BRC metadata working group
organism identification assay
genomics
Epigenetics
An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation.
Penn group
epigenetic modification assay
genomics
WGS
WGS permits comprehensive sequencing of introns and exons, whereas whole exome sequencing (WES) allows deeper sequencing of exonic regions at a lower cost. Due to the large number of genetic variants found in each genome, it is necessary to use filtering approaches to distinguish deleterious from benign variants. WES has been used successfully to identify novel genetic causes of primary immunodeficiency. Complex structural variations and non-Mendelian disorders remain challenges for WGS.
A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism.
WGS
PMID:23095910
PMID:25827230
whole genome sequencing assay
genomics
WES
DNA was extracted from the Ficoll pellet of blood taken from congenital asplenia patients. Unamplified, high-molecular weight, RNase-treated genomic DNA (4_6 _g) was used for whole exome sequencing (WES) with the use of Agilent 71 Mb (V4 + UTR) singlesample capture and an Illumina HiSeq 2000. Sequencing was carried out so as to obtain 30_ coverage from 2 _ 100-bp paired-end reads. We used the Annovar tool (25) to annotate the resulting highquality (HQ) variants. In the regions targeted by WES capture (81.5% of the consensus coding genome), the mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected per sample were 84,192 and13,325, respectively. After filtering, a mean of 74,398 (95.3%) high-quality (HQ) SNVs and 9,033 (70.6%) HQ indels were called. A mean of 105 coding HQ SNVs and 32 indels was identified.
A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons).
WES
PMID:25827230
exome sequencing assay
physical environment
exposure to carcinogens
A information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment.
OBIB
exposure to environmental and workplace carcinogens history
genomics
Metagenomics
A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample.
WMS
Bjoern Peters
Michelle Giglio
whole metagenome sequencing assay
PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability
OBI-Branch
storage
basic cohort attributes
study design
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
experimental design
study design
population data
criteria for enrollment and recruitment procedures
PMID: 23979341-The major inclusion criterion was patients in whom severe cerebral embolism was diagnosed at age 75 or younger (more than 9 in the NIHSS score on day 7 after the onset of stroke) .
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.
inclusion condition
inclusion rule
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
inclusion criterion
A series of statements representing health-relevant qualities of a patient and of a patient's family.
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
clinical history
other questionnaire/survey data
signs and symptoms
A process experienced by the patient, which can only be experienced by the patient, that is hypothesized to be clinically relevant.
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
symptom
socio-demographic and economic characteristics
income and possessions
income data
socio-demographic and economic characteristics
age/birthdate
A time quality inhering in a bearer by virtue of how long the bearer has existed.
age
socio-demographic and economic characteristics
biological sex
An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
biological sex
questionnaire/survey data
socio-demographic and economic characteristics
A quality that inheres in an entire organism or part of an organism.
organismal quality
Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family.
A material entity that consists of two or more organisms, viruses, or viroids.
group of organism
organism collection
May be of the same or different species.
collection of organisms
medication
prescription
"Prescription for John Smith : Ativan 2mg tablets, take 1 tablet twice daily by mouth as needed if anxious, dispense 60 tablets, renew 12 times. Signed by Dr Hazard. Date: 15/10/29"
A health care prescription specifying the initiation, modification or cessation of a drug administration.
drug prescription
medication
administration
'take Aspirin 81 mg oral tablet, 1 tablet once daily by mouth, start today' or the synonymous abbreviated version 'Aspirin 81 mg tablet PO DIE'
A drug administration description that specifies a drug administration prescribed or reported by an healthcare provider.
It specifies:
- The drug product
- The posology
It may also specify a starting drug administration condition
drug administration specification
a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data.
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic).
statistic
a count of 4 resulting from counting limbs in humans
a count is a data item denoted by an integer and represented the number of instances or occurences of an entity
STATO
count
survey administration
date and time-related information
Information about a calendar date or timestamp indicating day, month, year and time of an event.
STATO
date
other questionnaire/survey data
life stage/time point
A spatiotemporal region encompassing some part of the life cycle of an organism.
developmental stage
stage
life cycle stage
sample type
blood
A fluid that is composed of blood plasma and erythrocytes.
portion of blood
vertebrate blood
whole blood
blood
biosample
sample type
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
body fluid or substance
body substance
organism substance
portion of body substance
portion of organism substance
organism substance
sample type
urine
Excretion that is the output of a kidney
urine
sample type
saliva
A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
salivary gland secretion
sailva normalis
saliva atomaris
saliva molecularis
saliva
sample type
stool
Portion of semisolid bodily waste discharged through the anus[MW,modified]
excreta
faeces
fecal material
fecal matter
matières fécales@fr
merde@fr
partie de la merde@fr
piece of shit
porción de mierda@es
portion of excrement
portion of faeces
portion of fecal material
portion of fecal matter
portion of feces
portionem cacas
stool
teil der fäkalien@de
cow dung
cow pat
dung
fewmet
frass
guano
portion of dung
portion of guano
portion of scat
scat
spraint
droppings
excrement
ordure
spoor
feces