Genomics Cohorts Knowledge Ontology (IHCC View)
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
An information content entity indicating the cause of death for a participant in the study.
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
an information content entity that is about a part of a health care encounter that occurs in a hospital facility
An information content entity that is about an activity that realizes a social role and is often performed for payment.
a categorical value specification that is about a human being and specifies whether that human being is joined to another human being in marriage
EuPathDB, BFO's 'relational quality' examples
An information content entity about healthcare that is private or public.
environmental system associated with the dwelling used by humans.
environment associated with human dwelling
A directive information entity that specifies the sequence in which a series of events occurred or will occur.
A data item that is about a population of organisms.
A population data item that is about the geographical location of a population of organisms.
A sample size that is about the count of individual organisms in a population.
A quality which inheres in a population of organisms.
A population quality concerning the sex or sexes of the population.
A population quality concerning the gender or genders of the population.
A population quality concerning the age range of a population.
A planned process that is a part of an investigation in which raw data is collected.
Blood that is collected from an organism which has been fasting for a given amount of time.
A storage process for a biosample collected from an organism.
An assay that investigates the genome or genomes of an individual organism or population of organisms.
Merged GECKO 'data type' into 'genomics'.
A genomic assay that profiles the microorganisms present in a sample.
A genomic assay that identifies genetic loci and candidate genes correlated with phenotypes.
A count of the number of biosamples collected for an investigation.
A material processing which prepares a biosample for investigation.
An identifier that is guaranteed to be unique among all identifiers in a particular domain.
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.
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.
A geographical location in which an individual was born.
A geographical location in which an individual currently resides.
An organismal quality inhering in a bearer by virute of the bearer's highest level of formal education completed.
Information that is about the structure of an individual's family and/or household.
A clinical history that is about the lifestyle and behaviors of an individual which may impact health outcomes.
A lifestyle history that is about the tobacco use or exposure of an individual.
A lifestyle history that is about the alcohol consumption of an individual.
A lifestyle history that is about the sleep quality and duration of an individual.
A lifestyle history that is about the diet and nutrition of an individual.
A textual entity that contains contact details for an individual's physician, which may include: name, phone number, address, etc.
A treatment history that is about any non-pharamacological treatments such as surgery or physical therapy.
A clinical history that is about surgical operations performed on an individual.
A clinical history that is about the prescription drugs taken by an individual.
Information that is about the disease treated by a drug prescribed to an individual.
A biological process that results from a drug stimulus.
A statistic that summarizes a set of federated data.
summary statistics for additional data from federated sources
A lifestyle history that is about the use of unprescribed and/or non-prescription drugs.
A lifestyle history that is about the typical physical activity of an individual.
An availability textual entity that is about a substance from an organism (a biosample).
A clinical history that is about pregnancy, maternity, fertility, menses, and any other reproductive aspect.
perception of health and quality of life
A measurement datum of some aspect of human psychology.
cognitive and psychological measurements
A psychological measurement of some aspect of intellectual functions such as memory, problem solving, and comprehension.
A psychological measurement of a person's individual sets of behaviours, cognitions, and emotional patterns.
A biological process that results from neurophysiological changes in response to internal and external events.
A lifestyle history that is about oral health and hygiene.
A non-pharmacological treatment history that is about psychological treatments such as counselling.
A non-pharmacological treatment history that is about use of radiology for treatment of disease, disorder, or symptom.
A non-pharmacological treatment history that is about physical therapy treatments such as physical rehabilitation.
A psychological measurement of an individual's subjective perception of health.
A psychological measurement of an individual's perception of their quality of life.
Information that is about an individual's limitations in activities that involve caring for an moving the body.
Information about an individual's use of assistive devices in performing daily activities.
Information about an individual's association with a religion, denomiation, or sub- or non-denominational religious group.
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.
A clinical history that is about any family history of disease.
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.
A cognitive measurement that is an output (score) from the Alzheimer's Disease Assessment Scale.
Alzheimer's Disease Assessment Scale score
A cognitive measurement that is an output (score) from the Mini-Mental State Exam.
Information about the language an individual has been exposed to from birth and is their first language.
A cognitive measurement that is the output (score) from the Montreal Cognitive Assessment Test (MoCA) for Dementia
Montreal Cognitive Assessment Test score
A cognitive measurement that is the output (score) from the CERAD Neurophyschological Battery.
A cognitive measurement that is the output (score) from the Penn Computerized Neurocognitive Battery.
Penn Computerized Neurocognitive Battery score
A disorder that is present at birth due to genetics or environmental factors during development.
A cognitive measurement that is the output (score) from the Severe Impairment Battery.
A cognitive measurement that is the output (score) from the Neuropsychiatric Inventory.
A cognitive measurement that is the output (score) from the Clinical Dementia Rating Scale.
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
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.
A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
A disease involving the integumental system.
disease or disorder of integumental system
A disease involving the musculoskeletal system.
disease or disorder of musculoskeletal system
musculoskeletal system disease or disorder
A disease or disorder that involves the digestive system.
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.
A disease involving the cardiovascular system.
cardiovascular system disease or disorder
disease of subdivision of hemolymphoid system
disease or disorder of cardiovascular system
A disease involving the reproductive system.
disease or disorder of reproductive system
A disorder resulting from an abnormality in the immune system.
A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves.
A disease that has its basis in the disruption of mental process.
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 or disorder of respiratory system
A disease involving the endocrine system.
A disorder resulting from the presence and activity of a microbial, viral, or parasitic agent. It can be transmitted by direct or indirect contact.
Replaces 'infection' in disease hierarchy. OBI imported term infection is moved to pathologic process. This class is a container class for infectious diseases, not the process of infection itself.
A disease involving the hematopoietic system.
disease of the blood and blood-forming organs
disease or disorder of hematopoietic system
hematopoietic system disease or disorder
hematological disorders and malignancies
Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity.
A disease that involves the visual system.
Pathological processes of the ear, the nose, and the throat, also known as the ENT diseases.
diseases of the ear, nose, and/or throat
A condition or physical state produced by the ingestion, injection, inhalation of or exposure to a deleterious agent.
An assay that produces a picture of an entity.
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.
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
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
An assay that identifies the organism species in a specimen.
An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation.
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.
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).
A information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment.
exposure to environmental and workplace carcinogens history
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.
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
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
criteria for enrollment and recruitment procedures
A process experienced by the patient, which can only be experienced by the patient, that is hypothesized to be clinically relevant.
A time quality inhering in a bearer by virtue of how long the bearer has existed.
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.
A quality that inheres in an entire organism or part of an organism.
socio-demographic and economic characteristics
"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.
'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
Information about a calendar date or timestamp indicating day, month, year and time of an event.
STATO
A spatiotemporal region encompassing some part of the life cycle of an organism.
A fluid that is composed of blood plasma and erythrocytes.
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.
Excretion that is the output of a kidney
A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
Portion of semisolid bodily waste discharged through the anus[MW,modified]