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 inheres in BFO:0000015 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 BFO:0000016 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 BFO:0000017 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 BFO:0000019 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 BFO:0000029 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 BFO:0000040 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 BFO:0000141 immaterial entity CMO:0000000 questionnaire/survey data physiological measurements clinical measurement data item CMO:0000001 physiological measurements circulation and respiration cardiovascular measurement data item CMO:0000003 circulation and respiration blood pressure blood pressure measurement data item CMO:0000012 anthropometry weight body weight data item CMO:0000021 physiological measurements anthropometry body morphological measurement data item CMO:0000106 anthropometry height body height data item CMO:0000294 circulation and respiration heart rate (HR) pulse data item EUPATH:0000147 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 EUPATH:0000305 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 EUPATH:0000308 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 EUPATH:0000359 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 EUPATH:0000374 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 EUPATH:0000451 questionnaire/survey data healthcare information An information content entity about healthcare that is private or public. healthcare information EUPATH:0010032 questionnaire/survey data physical environment environmental system associated with the dwelling used by humans. Penn Group environment associated with human dwelling GECKO:0000003 basic cohort attributes timeline A directive information entity that specifies the sequence in which a series of events occurred or will occur. timeline GECKO:0000005 basic cohort attributes population data A data item that is about a population of organisms. population data item GECKO:0000006 population data location A population data item that is about the geographical location of a population of organisms. population location GECKO:0000008 population data num. participants A sample size that is about the count of individual organisms in a population. population size GECKO:0000009 basic cohort attributes demographic data A quality which inheres in a population of organisms. population quality GECKO:0000010 demographic data sex(es) studied in cohort A population quality concerning the sex or sexes of the population. population sex or sexes GECKO:0000011 demographic data gender(s) studied in cohort A population quality concerning the gender or genders of the population. population gender or genders GECKO:0000012 demographic data age range A population quality concerning the age range of a population. population age range GECKO:0000013 basic cohort attributes data collection events A planned process that is a part of an investigation in which raw data is collected. data collection GECKO:0000019 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 GECKO:0000026 biosample storage method A storage process for a biosample collected from an organism. biosample storage GECKO:0000032 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 GECKO:0000040 genomics Microbiome markers (rRNA, etc) A genomic assay that profiles the microorganisms present in a sample. Potential new OBI request microbiome sequencing assay GECKO:0000042 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 GECKO:0000044 biosample sample size A count of the number of biosamples collected for an investigation. biosample size GECKO:0000047 biosample processing method A material processing which prepares a biosample for investigation. biosample processing GECKO:0000055 survey administration unique identifiers An identifier that is guaranteed to be unique among all identifiers in a particular domain. Wikipedia:Unique_identifier unique identifier GECKO:0000060 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 GECKO:0000061 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 GECKO:0000063 socio-demographic and economic characteristics birthplace A geographical location in which an individual was born. birthplace location GECKO:0000064 socio-demographic and economic characteristics residence A geographical location in which an individual currently resides. residence location GECKO:0000065 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 GECKO:0000066 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 GECKO:0000067 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 GECKO:0000068 lifestyle and behaviours tobacco use history A lifestyle history that is about the tobacco use or exposure of an individual. tobacco use history GECKO:0000069 lifestyle and behaviours alcohol use history A lifestyle history that is about the alcohol consumption of an individual. alcohol use history GECKO:0000071 lifestyle and behaviours sleep history A lifestyle history that is about the sleep quality and duration of an individual. sleep history GECKO:0000072 lifestyle and behaviours dietary history A lifestyle history that is about the diet and nutrition of an individual. nutritional history GECKO:0000073 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 GECKO:0000091 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 GECKO:0000092 non-pharmacological interventions surgical interventions A clinical history that is about surgical operations performed on an individual. surgical history GECKO:0000093 questionnaire/survey data medication A clinical history that is about the prescription drugs taken by an individual. prescription drug history GECKO:0000094 medication associated disease(s) Information that is about the disease treated by a drug prescribed to an individual. disease treated by prescription drug GECKO:0000096 medication drug response(s) A biological process that results from a drug stimulus. response to medication GECKO:0000102 statistics summary statistics for additional data from federated sources A statistic that summarizes a set of federated data. summary statistic for federated data GECKO:0000103 lifestyle and behaviours recreational drug history A lifestyle history that is about the use of unprescribed and/or non-prescription drugs. recreational drug history GECKO:0000104 lifestyle and behaviours physical activity history A lifestyle history that is about the typical physical activity of an individual. physical activity history GECKO:0000106 A count which represents the subset of a collection chosen for an investigation, survey, or assay. sample size GECKO:0000113 biosample availability An availability textual entity that is about a substance from an organism (a biosample). biosample availability textual entity GECKO:0000114 other questionnaire/survey data reproduction A clinical history that is about pregnancy, maternity, fertility, menses, and any other reproductive aspect. reproductive history GECKO:0000115 A clinical history that is about any treatment (surgical, prescription, etc.) for disease, disorder, or symptom. treatment history GECKO:0000118 questionnaire/survey data cognitive and psychological measurements A measurement datum of some aspect of human psychology. EFO:0009095 See also EFO:0009095 psychological measurement GECKO:0000119 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 GECKO:0000120 cognitive and psychological measurements personality A psychological measurement of a person's individual sets of behaviours, cognitions, and emotional patterns. Wikipedia:Personality personality measurement GECKO:0000121 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 GECKO:0000122 lifestyle and behaviours oral health history A lifestyle history that is about oral health and hygiene. oral health history GECKO:0000123 non-pharmacological interventions psychological interventions A non-pharmacological treatment history that is about psychological treatments such as counselling. psychological treatment history GECKO:0000124 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 GECKO:0000125 non-pharmacological interventions physical therapy interventions A non-pharmacological treatment history that is about physical therapy treatments such as physical rehabilitation. physical therapy history GECKO:0000126 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 GECKO:0000127 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 GECKO:0000128 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 GECKO:0000129 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 GECKO:0000130 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 GECKO:0000131 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 GECKO:0000132 other questionnaire/survey data family history of disease A clinical history that is about any family history of disease. family history of disease GECKO:0000133 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 GECKO:0000134 cognitive functioning ADAS A cognitive measurement that is an output (score) from the Alzheimer's Disease Assessment Scale. Alzheimer's Disease Assessment Scale score GECKO:0000135 cognitive functioning MMSE A cognitive measurement that is an output (score) from the Mini-Mental State Exam. Mini-Mental State Exam score GECKO:0000136 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 GECKO:0000137 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 GECKO:0000138 cognitive functioning CERAD Battery A cognitive measurement that is the output (score) from the CERAD Neurophyschological Battery. CERAD Neuropsychological Battery score GECKO:0000139 cognitive functioning Penn CNB A cognitive measurement that is the output (score) from the Penn Computerized Neurocognitive Battery. Penn Computerized Neurocognitive Battery score GECKO:0000140 diseases congenital and genetic disorders A disorder that is present at birth due to genetics or environmental factors during development. congenital disorder GECKO:0000141 cognitive functioning SIB A cognitive measurement that is the output (score) from the Severe Impairment Battery. Severe Impairment Battery score GECKO:0000142 cognitive functioning NPI A cognitive measurement that is the output (score) from the Neuropsychiatric Inventory. Neuropsychiatric Inventory score GECKO:0000143 cognitive functioning CDR A cognitive measurement that is the output (score) from the Clinical Dementia Rating Scale. Clinical Dementia Rating Scale score GO:0008150 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 IAO:0000005 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 IAO:0000027 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 IAO:0000030 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 IAO:0000033 An information content entity whose concretizations indicate to their bearer how to realize them in a process. directive information entity IAO:0000104 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 IAO:0000109 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 IAO:0000300 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 IAO:0000310 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 IAO:0000612 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 IAO:0000619 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 IAO:0020000 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 MF:0000041 other questionnaire/survey data personal beliefs and values belief MONDO:0000001 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 MONDO:0002051 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 MONDO:0002081 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 MONDO:0002118 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 MONDO:0004335 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 MONDO:0004992 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 MONDO:0004995 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 MONDO:0005039 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 MONDO:0005046 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 MONDO:0005071 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 MONDO:0005084 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 MONDO:0005087 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 MONDO:0005151 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 MONDO:0005550 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 MONDO:0005570 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 MONDO:0021178 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 MONDO:0024458 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 MONDO:0024623 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 MONDO:0029000 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 OBI:0000011 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 OBI:0000070 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 OBI:0000094 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 OBI:0000185 laboratory measures imaging An assay that produces a picture of an entity. OBI branch derived imaging assay OBI:0000435 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 OBI:0000537 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 OBI:0001271 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 OBI:0001624 laboratory measures microbiology An assay that identifies the organism species in a specimen. NIAID GSCID-BRC metadata working group organism identification assay OBI:0002020 genomics Epigenetics An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation. Penn group epigenetic modification assay OBI:0002117 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 OBI:0002118 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 OBI:0002415 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 OBI:0002623 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 OBI:0302893 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 OBI:0500000 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 OBI:0500027 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 OGMS:0000015 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 OGMS:0000020 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 OMRSE:00000501 socio-demographic and economic characteristics income and possessions income data PATO:0000011 socio-demographic and economic characteristics age/birthdate A time quality inhering in a bearer by virtue of how long the bearer has existed. age PATO:0000047 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 PATO:0001995 questionnaire/survey data socio-demographic and economic characteristics A quality that inheres in an entire organism or part of an organism. organismal quality PCO:0000000 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 PDRO:0000024 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 PDRO:0010022 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 STATO:0000039 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 STATO:0000047 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 STATO:0000093 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 UBERON:0000105 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 UBERON:0000178 sample type blood A fluid that is composed of blood plasma and erythrocytes. portion of blood vertebrate blood whole blood blood UBERON:0000463 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 UBERON:0001088 sample type urine Excretion that is the output of a kidney urine UBERON:0001836 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 UBERON:0001988 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 is about 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