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 example of usage definition alternative term definition source has_alternative_id has_broad_synonym has_exact_synonym has_narrow_synonym has_related_synonym comment see also physiological measurements circulation and respiration blood pressure weight anthropometry height heart rate (HR) An information content entity indicating the cause of death for a participant in the study. Penn Group cause of participant death cause of death 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 routine clincial visits an information content entity that is about a part of a health care encounter that occurs in a hospital facility EuPathDB hospitalization information hospitalizations An information content entity that is about an activity that realizes a social role and is often performed for payment. occupation occupation 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 marital status An information content entity about healthcare that is private or public. healthcare information healthcare information environmental system associated with the dwelling used by humans. Penn Group environment associated with human dwelling physical environment basic cohort attributes A directive information entity that specifies the sequence in which a series of events occurred or will occur. timeline timeline A data item that is about a population of organisms. population data item population data A population data item that is about the geographical location of a population of organisms. population location location A sample size that is about the count of individual organisms in a population. population size num. participants A quality which inheres in a population of organisms. population quality demographic data A population quality concerning the sex or sexes of the population. population sex or sexes sex(es) studied in cohort A population quality concerning the gender or genders of the population. population gender or genders gender(s) studied in cohort A population quality concerning the age range of a population. population age range age range A planned process that is a part of an investigation in which raw data is collected. data collection data collection events biosample Blood that is collected from an organism which has been fasting for a given amount of time. blood collected from fasting subject fasting or non-fasting A storage process for a biosample collected from an organism. biosample storage storage method laboratory measures An assay that investigates the genome or genomes of an individual organism or population of organisms. genomic assay Merged GECKO 'data type' into 'genomics'. genomics A genomic assay that profiles the microorganisms present in a sample. microbiome sequencing assay Potential new OBI request Microbiome markers (rRNA, etc) A genomic assay that identifies genetic loci and candidate genes correlated with phenotypes. PMID:27964730 eQTL analysis Potential new OBI request eQTL (Cis eQTLs and/or Trans eQTLs) A count of the number of biosamples collected for an investigation. biosample size sample size A material processing which prepares a biosample for investigation. biosample processing processing method survey administration An identifier that is guaranteed to be unique among all identifiers in a particular domain. Wikipedia:Unique_identifier unique identifier unique identifiers questionnaire/survey data 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 gender 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 ethnicity/race A geographical location in which an individual was born. birthplace location birthplace A geographical location in which an individual currently resides. residence location residence An organismal quality inhering in a bearer by virute of the bearer's highest level of formal education completed. education level education Information that is about the structure of an individual's family and/or household. family and household structure family and household structure A clinical history that is about the lifestyle and behaviors of an individual which may impact health outcomes. lifestyle history lifestyle and behaviours A lifestyle history that is about the tobacco use or exposure of an individual. tobacco use history tobacco use history A lifestyle history that is about the alcohol consumption of an individual. alcohol use history alcohol use history A lifestyle history that is about the sleep quality and duration of an individual. sleep history sleep history A lifestyle history that is about the diet and nutrition of an individual. nutritional history dietary history A textual entity that contains contact details for an individual's physician, which may include: name, phone number, address, etc. physician contact textual entity physician/practitioner info A treatment history that is about any non-pharamacological treatments such as surgery or physical therapy. non-pharmacological treatment history non-pharmacological interventions A clinical history that is about surgical operations performed on an individual. surgical history surgical interventions A clinical history that is about the prescription drugs taken by an individual. prescription drug history medication Information that is about the disease treated by a drug prescribed to an individual. disease treated by prescription drug associated disease(s) A biological process that results from a drug stimulus. response to medication drug response(s) statistics A statistic that summarizes a set of federated data. summary statistic for 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. recreational drug history recreational drug history A lifestyle history that is about the typical physical activity of an individual. physical activity history physical activity history other other biosample type An availability textual entity that is about a substance from an organism (a biosample). biosample availability textual entity availability A clinical history that is about pregnancy, maternity, fertility, menses, and any other reproductive aspect. reproductive history reproduction other questionnaire/survey data perception of health and quality of life A measurement datum of some aspect of human psychology. EFO:0009095 psychological measurement See also EFO:0009095 cognitive and psychological measurements A psychological measurement of some aspect of intellectual functions such as memory, problem solving, and comprehension. Wikipedia:Cognition cognitive measurement cognitive functioning A psychological measurement of a person's individual sets of behaviours, cognitions, and emotional patterns. Wikipedia:Personality personality measurement personality A biological process that results from neurophysiological changes in response to internal and external events. Wikipedia:Emotion emotion psychological distress and emotions A lifestyle history that is about oral health and hygiene. oral health history oral health history A non-pharmacological treatment history that is about psychological treatments such as counselling. psychological treatment history psychological interventions A non-pharmacological treatment history that is about use of radiology for treatment of disease, disorder, or symptom. radiological treatment history radiological interventions A non-pharmacological treatment history that is about physical therapy treatments such as physical rehabilitation. physical therapy history physical therapy interventions A psychological measurement of an individual's subjective perception of health. perception of health measurement perception of health A psychological measurement of an individual's perception of their quality of life. quality of life measurement quality of life 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 functional limitations Information about an individual's use of assistive devices in performing daily activities. Maelstrom:Use_devices information on use of assistive devices use of assistive devices 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 religion 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 social environment A clinical history that is about any family history of disease. family history of disease family history of disease A non-pharmacological treatment history that is about diagnostic procedures to determine a condition or disease. diagnostic procedure history Includes procedures such as colonoscopies, ultrasounds, etc., but excludes laboratory tests. diagnostic interventions A cognitive measurement that is an output (score) from the Alzheimer's Disease Assessment Scale. Alzheimer's Disease Assessment Scale score ADAS A cognitive measurement that is an output (score) from the Mini-Mental State Exam. Mini-Mental State Exam score MMSE 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 native language A cognitive measurement that is the output (score) from the Montreal Cognitive Assessment Test (MoCA) for Dementia Montreal Cognitive Assessment Test score MoCA A cognitive measurement that is the output (score) from the CERAD Neurophyschological Battery. CERAD Neuropsychological Battery score CERAD Battery A cognitive measurement that is the output (score) from the Penn Computerized Neurocognitive Battery. Penn Computerized Neurocognitive Battery score Penn CNB A disorder that is present at birth due to genetics or environmental factors during development. congenital disorder congenital and genetic disorders A cognitive measurement that is the output (score) from the Severe Impairment Battery. Severe Impairment Battery score SIB A cognitive measurement that is the output (score) from the Neuropsychiatric Inventory. Neuropsychiatric Inventory score NPI A cognitive measurement that is the output (score) from the Clinical Dementia Rating Scale. Clinical Dementia Rating Scale score CDR 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 aims and objectives 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 consent/accessibility personal beliefs and values 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 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 integumentary system disease disorder of integument disorder of integumental system skin and subcutaneous tissue 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 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 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 diseases 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 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 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 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 immune system disease or disorder immune system disorder disorder of immune system immune disorder, NOS immune system diseases 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 disorders A disease that has its basis in the disruption of mental process. disorder of mental process mental disorder mental or behavioural disorder mental process disease disorder of mental process mental and behaviour disorders 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 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 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 diseases 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 disease 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 blood-related disorders https://github.com/monarch-initiative/mondo/issues/254 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 injuries 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 visual system diseases 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 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. poisoning Poisonings intoxication poisoning syndrome poisoning An assay that produces a picture of an entity. OBI branch derived imaging assay imaging 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 DNA/Genotyping 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 Sequence variants (CNV, SNP arrays) 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 RNAseq/gene expression An assay that identifies the organism species in a specimen. NIAID GSCID-BRC metadata working group organism identification assay microbiology An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation. Penn group epigenetic modification assay Epigenetics 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 WGS 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 WES 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 exposure to carcinogens 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 Metagenomics 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 study 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 inclusion criterion 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. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf symptom signs and symptoms income and possessions A time quality inhering in a bearer by virtue of how long the bearer has existed. age age/birthdate 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 biological sex A quality that inheres in an entire organism or part of an organism. organismal quality 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. drug prescription prescription '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 administration Information about a calendar date or timestamp indicating day, month, year and time of an event. STATO date date and time-related information A spatiotemporal region encompassing some part of the life cycle of an organism. life cycle stage developmental stage stage life stage/time point A fluid that is composed of blood plasma and erythrocytes. blood portion of blood vertebrate blood whole blood blood 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 sample type Excretion that is the output of a kidney urine urine A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. saliva salivary gland secretion sailva normalis saliva atomaris saliva molecularis saliva Portion of semisolid bodily waste discharged through the anus[MW,modified] excreta faeces fecal material fecal matter feces 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 stool