An ontology to represent genomics cohort attributes.
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
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])
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
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
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
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)
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
body morphological measurement data item
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
socio-demographic and economic characteristics
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.
summary statistics for additional data from federated sources
A statistic that summarizes a set of federated data.
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.
A count which represents the subset of a collection chosen for an investigation, survey, or assay.
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.
A clinical history that is about any treatment (surgical, prescription, etc.) for disease, disorder, or symptom.
cognitive and psychological measurements
A measurement datum of some aspect of human psychology.
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.
perception of health and quality of life
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.
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.
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.
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
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
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
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
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
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.
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
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
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.
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.
An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
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.
diseases of the ear, nose, and/or throat
Pathological processes of the ear, the nose, and the throat, also known as the ENT diseases.
A condition or physical state produced by the ingestion, injection, inhalation of or exposure to a deleterious agent.
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.
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
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
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.
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
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
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
A series of statements representing health-relevant qualities of a patient and of a patient's family.
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.
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.
May be of the same or different species.
"Prescription for John Smith : Ativan 2mg tablets, take 1 tablet twice daily by mouth as needed if anxious, dispense 60 tablets, renew 12 times. Signed by Dr Hazard. Date: 15/10/29"
A health care prescription specifying the initiation, modification or cessation of a drug administration.
'take Aspirin 81 mg oral tablet, 1 tablet once daily by mouth, start today' or the synonymous abbreviated version 'Aspirin 81 mg tablet PO DIE'
A drug administration description that specifies a drug administration prescribed or reported by an healthcare provider. It specifies: - The drug product - The posology It may also specify a starting drug administration condition
a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data.
STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/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
Information about a calendar date or timestamp indicating day, month, year and time of an event.
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]