Semantic Modeling of Cohort Descriptions in Research Studies
type: Ontology
version IRI: https://purl.org/heals/sco/1.1.0
imports: chearexternal.ttl
abstract: The Study Cohort Ontology (SCO) is developed to model overall structure and patterns of cohort variables and control/intervention groups defined within the structured population descriptions (commonly referred to as Table1's or Cohort Summary Tables)of observational case studies and clinical trials. We maintain only domain agnostic and commonly occuring subject variables and interventions in SCO, and we have a suite of ontologies (Diseases, Medications, LabResults etc) to encode Diabetes related terminology. We have adopted a bottom-up approach to modeling and we have revised the structure of SCO upon investigation of a few research studies (11 to be precise) from the Pharmacological Interventions (Chapter 8) and Cardiovascular Complications (Chapter 9) of the American Diabetes Association (ADA)’s Standards of Medical Care 2018 CPG. We enable deep drive visualizations driven off queries to knowledge graphs modeled on SCO, to help assist physician visualize the similarity of a patient to a study group, at a quick glance. We welcome contributions and suggestions to extend SCO to represent cohort descriptions of publications targeted to other diseases, and we plan to release set of tools to make this process seamless.
contributor: Deborah L. McGuinness
contributor: James P. McCusker
contributor: Oshani Seneviratne
creator: Shruthi Chari
description: The Study Cohort Ontology encodes the vocabulary to represent population desriptions in research studies, and provides the ability to model the aggregative descriptive statistical measures defined on the variables of subjects who are participants in the study population. We make it possible to represent a study component considered for determining the patient alignment to a research study, and we assist physicians in evaluating the fit of their patient population to the study population. In SCO, we are building a world-view inspired by the upper level Ontology SemanticScience Integrated Ontology (SIO) to model the descriptive statistics of characteristics on a set of patients (patient group) administered a medical intervention, and studied for an outcome in a research study. Since we capture the various definitions of patient groups (ie. by interventional measures or by control mechanisms), we provide the basic framework for filtering searches and to define cohort similarity at different granularities. ( cohort level and the study group levels ). For researchers who wish to contribute to the expansion of our ontology, we advise that they refer to our ontology documentation to familiarize themselves with the structure and term annotations ( such as definitions and labels).
label: Study Cohort Ontology

Demographic
type: Class
subclass of: subject characteristic
source: Miller-Keane Encyclopedia and Dictionary of Medicine, Nursing, and Allied Health, Seventh Edition
definition: the science dealing with populations, including matters of health, disease, births, and mortality

medical therapy
type: Class
subclass of: study intervention
source: https://en.wikipedia.org/wiki/Therapy
definition: the attempted remediation of a health problem, usually following a diagnosis

UnderweightOrNormal
has exact synonym: Normal or Underweight
has exact synonym: Underweight or Normal

research study
type: Class
subclass of: Study
subclass of: Restriction
  on property: hasAttribute
  some values from: cohort description
subclass of: Restriction
  on property: hasParticipant
  some values from: study subject
type: NamedIndividual
has attribute: definition
  was attributed to: https://researcher.watson.ibm.com/researcher/view.php
  has value: A scientific investigation that involves testing a hypothesi
has attribute: definition
  has value: A scientific study of nature that sometimes includes processes involved in health and disease
  source: clinical-measurement
label: study

anatomical entity
type: Class
subclass of: biological entity
IAO_0000412: hp.owl

connected anatomical structure
type: Class
subclass of: material anatomical entity
IAO_0000412: caro.owl
IAO_0000412: hp.owl
label: anatomical structure

material anatomical entity
type: Class
subclass of: anatomical entity
IAO_0000412: caro.owl
IAO_0000412: hp.owl

multicellular anatomical structure
type: Class
subclass of: connected anatomical structure
IAO_0000412: caro.owl
IAO_0000412: hp.owl

biological entity
type: Class
IAO_0000412: hp.owl

cell
type: Class
subclass of: connected anatomical structure
IAO_0000412: cl.owl
IAO_0000412: hp.owl

disease or condition
type: Class
subclass of: BiologicalQuality
IAO_0000412: doid.owl
source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
definition: A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism

Obesity
type: Class
IAO_0000115: Accumulation of substantial excess body fat.
IAO_0000412: hp.owl
has db xref: MSH:D009765
has db xref: SNOMEDCT_US:414915002
has db xref: SNOMEDCT_US:414916001
has db xref: UMLS:C0028754
has exact synonym: Having too much body fat
has exact synonym: Obesity
has OBO namespace: human_phenotype
id: HP:0001513

Truncal obesity
type: Class
subclass of: Obesity
IAO_0000115: Obesity located preferentially in the trunk of the body as opposed to the extremities.
IAO_0000412: hp.owl
has alternative id: HP:0008885
has db xref: MSH:D056128
has db xref: SNOMEDCT_US:248311001
has db xref: UMLS:C0311277
has exact synonym: Centripetal obesity
has exact synonym: Truncal obesity
has OBO namespace: human_phenotype
id: HP:0001956

Increased body weight
type: Class
IAO_0000115: Abnormally increased body weight.
IAO_0000412: hp.owl
created by: peter
creation date: 2008-02-27T03:21:00Z
has alternative id: HP:0045083
has db xref: MSH:D015430
has db xref: SNOMEDCT_US:161831008
has db xref: SNOMEDCT_US:262286000
has db xref: SNOMEDCT_US:8943002
has db xref: UMLS:C0043094
has exact synonym: Increased body weight
has OBO namespace: human_phenotype
has related synonym: Weight gain
id: HP:0004324

Decreased body weight
type: Class
subclass of: UnderweightOrNormal
IAO_0000115: Abnormally low body weight.
IAO_0000412: hp.owl
created by: peter
creation date: 2008-02-27T03:22:00Z
has alternative id: HP:0001823
has alternative id: HP:0001826
has db xref: MSH:D013851
has db xref: MSH:D015431
has db xref: SNOMEDCT_US:161832001
has db xref: SNOMEDCT_US:248342006
has db xref: SNOMEDCT_US:262285001
has db xref: SNOMEDCT_US:89362005
has db xref: UMLS:C0041667
has db xref: UMLS:C1262477
has db xref: UMLS:C1844806
has exact synonym: Decreased body weight
has exact synonym: Decreased weight
has exact synonym: Low body weight
has exact synonym: Low weight
has exact synonym: Underweight
has exact synonym: Weight less than 3rd percentile
has OBO namespace: human_phenotype
id: HP:0004325

Childhood-onset truncal obesity
type: Class
subclass of: Truncal obesity
IAO_0000115: Truncal obesity with onset during childhood, defined as between 2 and 10 years of age.
IAO_0000412: hp.owl
has alternative id: HP:0008874
has db xref: UMLS:C1859846
has exact synonym: Truncal obesity apparent in childhood
has OBO namespace: human_phenotype
id: HP:0008915

Abdominal obesity
type: Class
subclass of: Obesity
IAO_0000115: Excessive fat around the stomach and abdomen.
IAO_0000412: hp.owl
created by: peter
creation date: 2014-03-23T05:00:05Z
has db xref: MSH:D056128
has db xref: SNOMEDCT_US:248311001
has db xref: UMLS:C0311277
has exact synonym: Abdominal obesity
has exact synonym: Central obesity
has OBO namespace: human_phenotype
id: HP:0012743

Class I obesity
type: Class
subclass of: Obesity
IAO_0000115: Obesity with a body mass index of 30 to 34.9 kg per square meter.
IAO_0000412: hp.owl
creator: HPO:probinson
date: 2017-05-14T20:06:40Z
has exact synonym: Class 1 obesity
has exact synonym: Obesity grade 1

Class II obesity
type: Class
subclass of: Obesity
IAO_0000115: Obesity with a body mass index of 35 to 39.9 kg per square meter.
IAO_0000412: hp.owl
creator: HPO:probinson
date: 2017-05-14T20:08:43Z
has exact synonym: Class 2 obesity
has exact synonym: Obesity grade 2

Class III obesity
type: Class
subclass of: Obesity
IAO_0000115: Obesity with a body mass index of 40 kg per square meter or higher.
IAO_0000412: hp.owl
creator: HPO:probinson
date: 2017-05-14T20:09:17Z
has exact synonym: Class 3 obesity
has exact synonym: Obesity grade 3

Overweight
type: Class
IAO_0000115: Increased body weight with a body mass index of 25-29.9 kg per square meter.
IAO_0000412: hp.owl
creator: HPO:probinson
date: 2017-05-14T20:12:36Z

Decreased body mass index
type: Class
IAO_0000115: Abnormally decreased weight-to-height squared ratio, calculated by dividing the individual's weight in kilograms by the square of the individual's height in meters and used as an indicator of underweight compared to averages.
IAO_0000412: hp.owl
has exact synonym: Decreased BMI

data monitoring
type: Class
subclass of: monitoring
IAO_0000115: Review of clinical information to determine veracity, thoroughness, and dependability.
IAO_0000412: ncit.owl
NCIT NHC0: C142488
NCIT P106: Activity
NCIT P108: Data Monitoring
NCIT P322: CDISC-GLOSS
NCIT P325: Process by which clinical data are examined for completeness, consistency, and accuracy.
has exact synonym: Data Monitoring
has exact synonym: data monitoring
in subset: NCIT C61410
in subset: NCIT C67497

electronic clinical trial
type: Class
subclass of: clinical trial
IAO_0000115: A clinical trial in which computerized systems are used to plan, collect, access, exchange, and archive data.
IAO_0000412: ncit.owl
NCIT NHC0: C142526
NCIT P106: Research Activity
NCIT P108: Electronic Clinical Trial
NCIT P322: CDISC-GLOSS
NCIT P325: Clinical trial in which primarily electronic processes are used to plan, collect (acquire), access, exchange, and archive data required for conduct, management, analysis, and reporting of the trial. NOTE: FDA has recently drawn a distinction between studies and trials. Both words refer to systematic efforts to obtain evidence relevant to regulatory authorities, but, depending on regulatory context and particularly in the case of postmarketing commitments, a study might not be the appropriate word for a clinical trial (prospective, controlled, randomized), but should be reserved instead for surveillance, structured gathering of information, epidemiological studies, or even animal studies [DRAFT Guidance for industry Postmarketing studies and Clinical Trials-implementation of section 505(o) of the Federal Food, Drug, and Cosmetic act]. Synonyms: eClinical study, eClinical investigation.
has exact synonym: Electronic Clinical Trial
has exact synonym: eClinical Trial
has exact synonym: eclinical trial
in subset: NCIT C61410
in subset: NCIT C67497

equivalence trial
type: Class
subclass of: clinical trial
IAO_0000115: A clinical trial with the objective of demonstrating clinical insignificance between the responses to two or more treatments.
IAO_0000412: ncit.owl
NCIT NHC0: C142539
NCIT P106: Research Activity
NCIT P108: Equivalence Trial
NCIT P322: CDISC-GLOSS
NCIT P325: A trial with the primary objective of showing that the response to two or more treatments differs by an amount that is clinically unimportant. NOTE: This is usually demonstrated by showing that the true treatment difference is likely to lie between a lower and an upper equivalence margin of clinically acceptable differences.
has exact synonym: Equivalence Trial
has exact synonym: equivalence trial
in subset: NCIT C61410
in subset: NCIT C67497

exploratory investigational new drug study
type: Class
subclass of: clinical trial
IAO_0000115: A type of clinical trial that involves low dosage and short duration of drug exposure for a limited number of study participants with the intent of gathering preliminary data on the mechanism of action, pharmacodynamics, pharmacokinetics, or bioavailability of promising therapeutic candidate agents in human subjects.
IAO_0000412: ncit.owl
NCIT NHC0: C142547
NCIT P106: Research Activity
NCIT P108: Exploratory Investigational New Drug Study
NCIT P322: CDISC-GLOSS
NCIT P325: A clinical study that is conducted early in Phase 1; involves very limited human exposure and has no therapeutic or diagnostic intent (e.g., screening studies, microdose studies) [FDA Guidance for industry, investigators, and Reviewers: exploratory IND studies, January 2006] See also Phase 0.
has exact synonym: Exploratory IND Study
has exact synonym: Exploratory Investigational New Drug Study
has exact synonym: exploratory IND study
in subset: NCIT C61410
in subset: NCIT C67497

low-interventional clinical trial
type: Class
subclass of: clinical trial
IAO_0000115: A clinical trial that is non-interventional by design but includes diagnostic or monitoring procedures that carry minimal risk or impact on patients.
IAO_0000412: ncit.owl
NCIT NHC0: C142601
NCIT P106: Research Activity
NCIT P108: Low-interventional Clinical Trial
NCIT P322: CDISC-GLOSS
NCIT P325: A clinical trial which fulfills all of the following conditions: (a) the investigational medicinal products, excluding placebos, are authorized; (b) according to the protocol of the clinical trial, (i) the investigational medicinal products are used in accordance with the terms of the marketing authorization; or (ii) the use of the investigational medicinal products is evidence-based and supported by published scientific evidence on the safety and efficacy of those investigational medicinal products in any of the Member States concerned; and (c) the additional diagnostic or monitoring procedures do not pose more than minimal additional risk or burden to the safety of the subjects compared to normal clinical practice in any Member State concerned. [REGULATION (EU) No 536/2014 Article 2.2.(3)]
has exact synonym: Low-interventional Clinical Trial
has exact synonym: low-interventional clinical trial
in subset: NCIT C61410
in subset: NCIT C67497

marketing support trials
type: Class
subclass of: clinical trial
IAO_0000115: A type of clinical trial in which the therapeutic benefits of a marketed product are either clarified or preferentially compared to another marketed product.
IAO_0000412: ncit.owl
NCIT NHC0: C142603
NCIT P106: Research Activity
NCIT P108: Marketing Support Trials
NCIT P322: CDISC-GLOSS
NCIT P325: Clinical studies that are designed to clarify therapeutic benefits of a marketed product or to show potential decision-makers the rationale for preferring one therapy over another.
has exact synonym: Marketing Support Trials
has exact synonym: marketing support trials
in subset: NCIT C61410
in subset: NCIT C67497

mega-trial
type: Class
subclass of: clinical trial
IAO_0000115: A type of clinical trial in which 10,000 or more subjects are enrolled.
IAO_0000412: ncit.owl
NCIT NHC0: C142609
NCIT P106: Research Activity
NCIT P108: Mega-Trial
NCIT P322: CDISC-GLOSS
NCIT P325: Massive trials that test the advantages of therapeutic interventions by enrolling 10,000 or more subjects.
has exact synonym: Mega-Trial
has exact synonym: large sample trial
has exact synonym: mega-trials
in subset: NCIT C61410
in subset: NCIT C67497

pragmatic trial
type: Class
subclass of: clinical trial
IAO_0000115: A study designed to test the effectiveness of an intervention in a broad routine clinical practice.
IAO_0000412: ncit.owl
NCIT NHC0: C142641
NCIT P106: Research Activity
NCIT P108: Pragmatic Trial
NCIT P322: CDISC-GLOSS
NCIT P325: Term used to describe a clinical study designed to examine the benefits of a product under real world conditions.
has exact synonym: Pragmatic Trial
has exact synonym: pragmatic trial
in subset: NCIT C61410
in subset: NCIT C67497

superiority trial
type: Class
subclass of: clinical trial
IAO_0000115: A trial with the primary objective of showing that the response to the investigational product is superior to a comparative agent (active or placebo control). (ICH)
IAO_0000412: ncit.owl
NCIT NHC0: C142722
NCIT P106: Research Activity
NCIT P108: Superiority Trial
NCIT P322: CDISC-GLOSS
NCIT P325: A trial with the primary objective of showing that the response to the investigational product is superior to a comparative agent (active or placebo control). [ICH E9]
has exact synonym: Superiority Trial
has exact synonym: superiority trial
in subset: NCIT C61410
in subset: NCIT C67497

clinical study
type: Class
subclass of: study
IAO_0000115: Research conducted with human subjects or on material of human origin in which an investigator directly interacts with human subjects; includes development of new technologies, study of mechanisms of human diseases, therapy, clinical trials, epidemiologic, behavior, and health services research.
IAO_0000412: ncit.owl
NCIT NHC0: C15206
NCIT P106: Research Activity
NCIT P108: Clinical Study
NCIT P207: C0008972
NCIT P322: CDISC
NCIT P322: CDISC-GLOSS
NCIT P322: FDA
NCIT P325: A clinical study involves research using human volunteers (also called participants) that is intended to add to medical knowledge. There are two main types of clinical studies: clinical trials (also called interventional studies) and observational studies. [ClinicalTrials.gov] See also clinical trial.
NCIT P325: A clinical study involves research using human volunteers (also called participants) that is intended to add to medical knowledge. There are two main types of clinical studies: clinical trials (also called interventional studies) and observational studies. [ClinicalTrials.gov] See also clinical trial. (CDISC Glossary)
NCIT P366: Clinical_Study
has exact synonym: CLINICAL STUDY
has exact synonym: Clinical Research
has exact synonym: Clinical Studies
has exact synonym: Clinical Study
has exact synonym: Study
has exact synonym: clinical study
in subset: NCIT C132298
in subset: NCIT C132310
in subset: NCIT C54447
in subset: NCIT C54587
in subset: NCIT C61410
in subset: NCIT C67497

case study
type: Class
subclass of: research study
IAO_0000115: An uncontrolled observational study containing a detailed report of the diagnosis, treatment, and follow-up of an individual patient. Case reports also contain some demographic information about the patient (for example, age, gender, ethnic origin).
IAO_0000412: ncit.owl
NCIT NHC0: C15362
NCIT P106: Research Activity
NCIT P108: Case Study
NCIT P207: C0085973
NCIT P322: CDISC
NCIT P325: A detailed report of the diagnosis, treatment, and follow-up of an individual patient. Case reports also contain some demographic information about the patient (for example, age, gender, ethnic origin).
NCIT P325: A study in which the subject with the condition under study (the case) is compared against a theoretical/historical model of distribution that serves as a control.
NCIT P366: Case_Study
has exact synonym: CASE ONLY
has exact synonym: Case Report
has exact synonym: Case Study
has exact synonym: case report
in subset: NCIT C127259
in subset: NCIT C132298
in subset: NCIT C61410
in subset: NCIT C66830

research activity
type: Class
subclass of: clinical or research activity
IAO_0000115: Systematic investigation into a subject in order to discover facts, establish or revise a theory, or develop a plan of action based on the facts discovered.
IAO_0000412: ncit.owl
NCIT NHC0: C15429
NCIT P106: Research Activity
NCIT P108: Research Activity
NCIT P207: C0242481
NCIT P325: A scientific study of nature that sometimes includes processes involved in health and disease. For example, clinical trials are research studies that involve people. These studies may be related to new ways to screen, prevent, diagnose, and treat disease. They may also study certain outcomes and certain groups of people by looking at data collected in the past or future.
NCIT P366: Research_Activity
has exact synonym: Research
has exact synonym: Research Activity
has exact synonym: research study

phase III trial
type: Class
subclass of: clinical study by phase
IAO_0000115: A clinical research protocol designed to investigate the efficacy of the biomedical or behavioral intervention in large groups of human subjects (from several hundred to several thousand), to confirm efficacy, to monitor adverse reactions to the new medication or treatment regimen with respect to long-term use and by comparing the intervention to other standard or experimental interventions as well as to a placebo.
IAO_0000412: ncit.owl
NCIT NHC0: C15602
NCIT P106: Research Activity
NCIT P108: Phase III Trial
NCIT P207: C0282461
NCIT P322: CDISC
NCIT P322: CDISC-GLOSS
NCIT P325: A study to compare the results of people taking a new treatment with the results of people taking the standard treatment (for example, which group has better survival rates or fewer side effects). In most cases, studies move into phase III only after a treatment seems to work in phases I and II. Phase III trials may include hundreds of people.
NCIT P325: Phase 3. Studies are expanded controlled and uncontrolled trials. They are performed after preliminary evidence suggesting effectiveness of the drug has been obtained, and are intended to gather the additional information about effectiveness and safety that is needed to confirm efficacy and evaluate the overall benefit-risk relationship of the drug and to provide an adequate basis for physician labeling. NOTE: Phase 3 studies usually include from several hundred to several thousand subjects. [After FDA CDER Handbook, ICH E8] (CDISC glossary)
NCIT P325: Studies are expanded controlled and uncontrolled trials. They are performed after preliminary evidence suggesting effectiveness of the drug has been obtained and are intended to gather the additional information about effectiveness and safety that is needed to confirm efficacy and evaluate the overall benefit-risk relationship of the drug and to provide an adequate basis for physician labeling. NOTE: Phase 3 studies usually include from several hundred to several thousand subjects. [after FDA CDER handbook, ICH E8]
NCIT P366: Phase_III_Trial
has exact synonym: 3
has exact synonym: Clinical Trials, Phase III
has exact synonym: PHASE III TRIAL
has exact synonym: Phase 3 Study
has exact synonym: Phase III Clinical Trial
has exact synonym: Phase III Protocol
has exact synonym: Phase III Study
has exact synonym: Phase III Trial
has exact synonym: Phase III Trials
has exact synonym: Trial Phase 3
has exact synonym: phase 3
has exact synonym: phase III trial
in subset: NCIT C132298
in subset: NCIT C61410
in subset: NCIT C66737
in subset: NCIT C66830
in subset: NCIT C67497

phase I/II trial
type: Class
subclass of: clinical study by phase
IAO_0000115: A clinical research protocol designed to study the safety, dosage levels and response to new treatment. Phase I/II trials combine a Phase I and a Phase II trial of the same treatment into a single protocol.
IAO_0000412: ncit.owl
NCIT NHC0: C15693
NCIT P106: Research Activity
NCIT P108: Phase I/II Trial
NCIT P207: C1519043
NCIT P322: CDISC
NCIT P325: A class of clinical study that combines elements characteristic of traditional Phase I and Phase II trials. See also Phase I, Phase II.
NCIT P325: A trial to study the safety, dosage levels, and response to a new treatment.
NCIT P366: Phase_I_II_Trial
has exact synonym: 1-2
has exact synonym: PHASE I/II TRIAL
has exact synonym: Phase I/II Trial
has exact synonym: Phase I/II trial
has exact synonym: Trial Phase 1-2
has exact synonym: Trial Phase 1/2
in subset: NCIT C132298
in subset: NCIT C61410
in subset: NCIT C66737
in subset: NCIT C66830

phase I and II Vaccine trial
type: Class
subclass of: phase I/II trial
subclass of: vaccine clinical trial
IAO_0000115: Select candidate vaccines or concepts suitable for Phase I and Phase II trials and conduct these trials.
IAO_0000412: ncit.owl
NCIT NHC0: C15835
NCIT P106: Research Activity
NCIT P108: Phase I and II Vaccine Trials
NCIT P207: C1519044
NCIT P366: Phase_I_and_II_Vaccine_Trials
has exact synonym: Phase I and II Vaccine Trials

vaccine clinical trial
type: Class
subclass of: clinical trial
IAO_0000412: ncit.owl
NCIT NHC0: C15864
NCIT P106: Research Activity
NCIT P108: Vaccine Clinical Trial
NCIT P207: C1519888
NCIT P366: Vaccine_Clinical_Trial
has exact synonym: Vaccine Clinical Trial

phase III large scale vaccine trial
type: Class
subclass of: phase III trial
subclass of: vaccine clinical trial
IAO_0000115: Select suitable vaccine candidates and support efficacy trials when appropriate criteria are met.
IAO_0000412: ncit.owl
NCIT NHC0: C15873
NCIT P106: Research Activity
NCIT P108: Phase III Large Scale Vaccine Trial
NCIT P207: C1519902
NCIT P366: Vaccine_Trial-Phase_III_Large_Scale
has exact synonym: Phase III Large Scale Vaccine Trial
has exact synonym: Vaccine Trial-Phase III Large Scale

multi-institutional clinical trial
type: Class
subclass of: clinical study by organizational parameters
subclass of: clinical trial
IAO_0000412: ncit.owl
NCIT NHC0: C16104
NCIT P106: Research Activity
NCIT P108: Multi-Institutional Clinical Trial
NCIT P207: C0206012
NCIT P322: CDISC-GLOSS
NCIT P325: A clinical trial that is carried out at more than one medical institution.
NCIT P325: Clinical trial conducted according to a single protocol but at more than one site and, therefore, carried out by more than one investigator. [ICH E9 Glossary] See investigator/ institution.
NCIT P366: Multi-Institutional_Clinical_Trial
has exact synonym: Multi-Institutional Clinical Trial
has exact synonym: multicenter study
has exact synonym: multicenter trial
in subset: NCIT C61410
in subset: NCIT C67497

clinical trial, other
type: Class
subclass of: clinical trial
IAO_0000115: A clinical trial that is not therapeutic, preventive or diagnostic.
IAO_0000412: ncit.owl
NCIT NHC0: C16123
NCIT P106: Research Activity
NCIT P108: Clinical Trial, Other
NCIT P207: C1516648
NCIT P366: Clinical_Trials_Other
has exact synonym: Clinical Trial, Other
has exact synonym: Clinical Trials, Other
has exact synonym: Other Clinical Trial

clinical or research activity
type: Class
subclass of: activity
IAO_0000115: Any specific activity undertaken during the course of a clinical study or research protocol.
IAO_0000412: ncit.owl
NCIT NHC0: C16203
NCIT P106: Activity
NCIT P108: Clinical or Research Activity
NCIT P207: C1516654
NCIT P366: Clinical_or_Research_Activity
has exact synonym: Clinical or Research Activity

Alaska Native
type: Class
subclass of: NCIT C41259
IAO_0000115: Denotes a person having origins in any indigenous people of Alaska and their descendants and who maintains tribal affiliation, or community or cultural attachment. The concept refers to population subgroups such as Eskimos, Aleuts, Inupiat, Yupik, Alutiiq, Egegik,and Pribilovian, Alaskan Athabascan, Tlingit, and Haida. The concept refers also to individuals who classify themselves as such.
IAO_0000412: ncit.owl
NCIT NHC0: C18237
NCIT P106: Population Group
NCIT P108: Alaska Native
NCIT P207: C0682125
NCIT P325: The native people of Alaska.
NCIT P366: Alaska_Native
has exact synonym: ALASKA NATIVE
has exact synonym: Alaska Indian
has exact synonym: Alaska Indians
has exact synonym: Alaska Native
has exact synonym: Alaska Natives
has exact synonym: Alaskan Native

adjunct clinical trial
type: Class
subclass of: clinical trial
IAO_0000115: A clinical trial that uses materials from some other clinical trial.
IAO_0000412: ncit.owl
NCIT NHC0: C18707
NCIT P106: Governmental or Regulatory Activity
NCIT P108: Adjunct Clinical Trial
NCIT P207: C1516638
NCIT P366: Clinical_Trials_Adjunct
has exact synonym: Adjunct Clinical Trial
has exact synonym: Clinical Trial, Adjunct
has exact synonym: Clinical Trials, Adjunct

percentage
type: Class
subclass of: statistical measure
IAO_0000115: A fraction or ratio with 100 understood as the denominator.
IAO_0000412: ncit.owl
NCIT NHC0: C25613
NCIT P106: Conceptual Entity
NCIT P108: Percentage
NCIT P207: C0439165
NCIT P322: CDISC
NCIT P322: NCPDP
NCIT P325: One hundred times the quotient of one quantity divided by another, with the same units of measurement.
NCIT P366: Percentage
has exact synonym: %
has exact synonym: Percentage
in subset: NCIT C61410
in subset: NCIT C66770
in subset: NCIT C66830
in subset: NCIT C71620
in subset: NCIT C77526
in subset: NCIT C85494
in subset: NCIT C89415
in subset: NCIT C89509
in subset: NCIT C91101

NCIT C41259
has exact synonym: AMERICAN INDIAN OR ALASKA NATIVE
has exact synonym: American Indian or Alaska Native
has exact synonym: First Nations
has exact synonym: Native American
has exact synonym: Native Americans
has exact synonym: american indian or alaska native

activity
type: Class
subclass of: Thing
IAO_0000115: An active process; excludes processes and mechanisms which fulfill biological functions.
IAO_0000412: ncit.owl
NCIT NHC0: C43431
NCIT P106: Activity
NCIT P108: Activity
NCIT P207: C0441655
NCIT P322: BRIDG
NCIT P325: Any action that can, in the context of a study or a post-marketing investigation, be defined, planned, scheduled or performed. EXAMPLE(S): surgical procedure, laboratory test, administration of a drug.
NCIT P366: Activity
has exact synonym: Activity
has exact synonym: General activity
in subset: NCIT C105551

American Indian
type: Class
subclass of: NCIT C41259
IAO_0000115: Denotes a person having origins in one of the indigenous peoples of North America, who lived on the continent prior to the European colonization. The term includes individuals belonging to a large number of tribes, states, and ethnic groups, many of them still enduring as communities.
IAO_0000412: ncit.owl
NCIT NHC0: C43877
NCIT P106: Population Group
NCIT P108: American Indian
NCIT P207: C0002460
NCIT P325: The native people of North America.
NCIT P366: American_Indian
has exact synonym: AMERICAN INDIAN
has exact synonym: American Indian

ratio
type: Class
subclass of: statistical measure
IAO_0000115: Quotient of quantities of the same kind for different components within the same system.
IAO_0000412: ncit.owl
NCIT NHC0: C44256
NCIT P106: Quantitative Concept
NCIT P108: Ratio
NCIT P207: C0456603
NCIT P322: CDISC
NCIT P322: UCUM
NCIT P325: The quotient of one quantity divided by another, with the same units of measurement.
NCIT P366: Ratio
has exact synonym: RATIO
has exact synonym: Ratio
has exact synonym: ratio
has exact synonym: {RATIO}
has exact synonym: {Ratio}
in subset: NCIT C19752
in subset: NCIT C61410
in subset: NCIT C66770
in subset: NCIT C66830
in subset: NCIT C67567
in subset: NCIT C71620
in subset: NCIT C77526
in subset: NCIT C85494

monitoring
type: Class
IAO_0000115: The act of observing something (and sometimes keeping a record of it).
IAO_0000412: ncit.owl
NCIT NHC0: C61256
NCIT P106: Activity
NCIT P108: Monitoring
NCIT P208: CL415337
NCIT P325: In medicine, to regularly watch and check a person or condition to see if there is any change. Also refers to a device that records and/or displays patient data, such as for an electrocardiogram (EKG).
NCIT P366: Monitoring
has exact synonym: Monitoring
has exact synonym: monitor

study
type: Class
subclass of: research activity
IAO_0000115: A detailed examination, analysis, or critical inspection of a subject designed to discover facts about it.
IAO_0000412: ncit.owl
NCIT NHC0: C63536
NCIT P106: Research Activity
NCIT P108: Study
NCIT P207: C0947630
NCIT P366: Study
has exact synonym: Study

clinical study by phase
type: Class
subclass of: clinical study
IAO_0000412: ncit.owl
NCIT NHC0: C70820
NCIT P106: Research Activity
NCIT P108: Clinical Study by Phase
NCIT P207: C2347801
NCIT P366: Clinical_Study_by_Phase
has exact synonym: Clinical Study by Phase

clinical study by organizational parameters
type: Class
subclass of: clinical study
IAO_0000412: ncit.owl
NCIT NHC0: C70824
NCIT P106: Research Activity
NCIT P108: Clinical Study by Organizational Parameters
NCIT P207: C2347800
NCIT P366: Clinical_Study_by_Organizational_Parameters
has exact synonym: Clinical Study by Organizational Parameters

clinical trial
type: Class
subclass of: research study
subclass of: clinical study
type: NamedIndividual
has attribute: definition
  was attributed to: https://researcher.watson.ibm.com/researcher/view.php
  has value: A prospective study designed to evaluate whether one or more interventions are associated with an outcome
has attribute: definition
  was attributed to: https://researcher.watson.ibm.com/researcher/view.php
  has value: A prospective study designed to evaluate whether one or more interventions are associated with an outcome
NCIT P322: CDISC-GLOSS
NCIT P106: Research Activity
NCIT P325: 1) A research investigation involving human subjects that is designed to answer specific questions about the safety and efficacy of a biomedical intervention (drug, treatment, device) or new ways of using a known drug, treatment, or device). 2) A research study in which one or more human subjects are prospectively assigned to one or more interventions (which may include placebo or other control) to evaluate the effects of those interventions on health-related biomedical or behavioral outcomes.(1. modified from ICH E6 Glossary, Directive 2001/20/EC. 2. NIH revised definition 2015) (CDISC Glossary)
has exact synonym: Clinical Trial
has exact synonym: clinical trial
in subset: NCIT C132310
NCIT P325: A type of research study that tests how well new medical approaches work in people. These studies test new methods of screening, prevention, diagnosis, or treatment of a disease.
in subset: NCIT C132298
in subset: NCIT C67497
IAO_0000412: ncit.owl
has exact synonym: Clinical Trials
NCIT NHC0: C71104
NCIT P322: CDISC
IAO_0000115: A research study that prospectively assigns human participants or groups of humans to one or more health-related interventions to evaluate the effects on health outcomes.
NCIT P207: C0008976
NCIT P325: A research investigation involving human subjects that is designed to answer specific questions about the safety and efficacy of a biomedical intervention (drug, treatment, device) or new ways of using a known drug, treatment, or device). NOTE: NIH Office of Science Policy further specifies that a clinical trial is a type of research study that prospectively assigns subjects to interventions, and the EU clinical trial regulations set forth 3 specific conditions, any one of which qualifies a study as a clinical trial. These conditions include applying diagnostic or monitoring procedures not used in normal clinical practice to subjects. [after ICH E6 [R2], EU CTR 2014] See also clinical study, clinical investigation.
in subset: NCIT C61410
has exact synonym: Clinical Trials, Unspecified
has exact synonym: Trial
NCIT P366: Clinical_Trial_Generic
NCIT P108: Clinical Trial

quality
type: Class
IAO_0000412: hp.owl
IAO_0000589: quality (PATO)

qualitative
type: Class
subclass of: quality
IAO_0000412: hp.owl

deviation(from_normal)
type: Class
subclass of: qualitative
IAO_0000412: hp.owl

weight
type: Class
subclass of: force
IAO_0000412: hp.owl
IAO_0000412: uo.owl

abnormal
type: Class
subclass of: deviation(from_normal)
IAO_0000412: hp.owl

increased weight
type: Class
subclass of: weight
subclass of: increased force
IAO_0000412: hp.owl

physical quality
type: Class
subclass of: physical object quality
IAO_0000412: hp.owl

force
type: Class
subclass of: physical quality
IAO_0000412: hp.owl

physical object quality
type: Class
subclass of: quality
IAO_0000412: hp.owl

duration
type: Class
subclass of: statistical measure
IAO_0000115: A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point.
IAO_0000412: pato.owl
has alternative id: PATO:0000081
has exact synonym: period
has OBO namespace: quality
has related synonym: time
id: PATO:0001309
in subset: attribute slim
in subset: hpo slim

pathological
type: Class
subclass of: abnormal
IAO_0000412: hp.owl

increased force
type: Class
subclass of: force
subclass of: increased object quality
IAO_0000412: hp.owl

increased quality
type: Class
subclass of: deviation(from_normal)
IAO_0000412: hp.owl

increased object quality
type: Class
subclass of: physical object quality
subclass of: increased quality
IAO_0000412: hp.owl

study group population
type: Class
IAO_0000114: IAO_0000122
IAO_0000115: is a population whose individual members realize (may be expressed as) a combination of inclusion rule values specifications or resulting from a sampling process (e.g. recruitment followed by randomization to group) on which a number of measurements will be carried out, which may be used as input to statistical tests and statistical inference.
IAO_0000117: Alejandra Gonzalez-Beltran
IAO_0000117: Orlaith Burke
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: STATO
IAO_0000412: stato.owl
STATO_0000032: statistical sample

cohort
type: Class
subclass of: study group population
subclass of: Restriction
  on property: hasAttribute
  some values from: population size
type: NamedIndividual
has attribute: definition
  was attributed to: https://researcher.watson.ibm.com/researcher/view.php
  has value: A cohort is the group of subjects enrolled in a study"
has attribute: definition
  was attributed to: JamesMcCusker
  has value: "Top-level group of subjects participating in a study"
IAO_0000119: STATO
IAO_0000115: a cohort is a study group population where the members are human beings which meet inclusion criteria and undergo a longitudinal design
IAO_0000117: Orlaith Burke
IAO_0000117: Philippe Rocca-Serra
IAO_0000412: stato.owl
IAO_0000116: possibly submit to 'Population and Community Ontology'
IAO_0000114: IAO_0000122
IAO_0000117: Alejandra Gonzalez-Beltran

anatomical structure
type: Class
subclass of: connected anatomical structure
IAO_0000412: hp.owl

anatomical entity
type: Class
IAO_0000412: hp.owl

length unit
type: Class
IAO_0000115: A unit which is a standard measure of the distance between two points.
IAO_0000412: uo.owl
created by: george gkoutos
has OBO namespace: unit.ontology
id: UO:0000001
in subset: unit group slim

mass unit
type: Class
IAO_0000115: A unit which is a standard measure of the amount of matter/energy of a physical object.
IAO_0000412: uo.owl
created by: george gkoutos
has OBO namespace: unit.ontology
id: UO:0000002
in subset: unit group slim

kilogram
type: Class
subclass of: mass unit
subclass of: base unit
subclass of: unit of measurement
IAO_0000115: A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
IAO_0000412: uo.owl
created by: george gkoutos
has exact synonym: kg
has OBO namespace: unit.ontology
id: UO:0000009
in subset: unit slim

centimeter
type: Class
subclass of: length unit
subclass of: unit of measurement
IAO_0000115: A length unit which is equal to one hundredth of a meter or 10^[-2] m.
IAO_0000412: uo.owl
created by: george gkoutos
has exact synonym: centimetre
has exact synonym: cm
has OBO namespace: unit.ontology
id: UO:0000015
in subset: unit slim

base unit
type: Class
IAO_0000115: A unit which is one of a particular measure to which all measures of that type can be related.
IAO_0000412: uo.owl
created by: george gkoutos
has OBO namespace: unit.ontology
id: UO:0000045
in subset: unit group slim

mean
type: Class
subclass of: CentralTendencyMeasure
source: Mean
definition: the central value of a discrete set of numbers: specifically, the sum of the values divided by the number of values

patient
type: Class
subclass of: Restriction
  on property: hasAttribute
  some values from: electronic health record
subclass of: Restriction
  on property: hasProperty
  some values from: disease or condition
source: https://www.tititudorancea.com/z/patient_en.htm
definition: a person who receives medical attention, care, or treatment, or who is registered with medical professional or institution with the purpose to receive medical care when necessary

standard deviation
type: Class
subclass of: DispersionMeasure
source: Standard deviation
definition: a measure that is used to quantify the amount of variation or dispersion of a set of data values

study subject
type: Class
subclass of: Restriction
  on property: hasProperty
  some values from: disease or condition
subclass of: Restriction
  on property: hasProperty
  some values from: study intervention
subclass of: Restriction
  on property: hasProperty
  some values from: enrollment status
subclass of: Restriction
  on property: isParticipantIn
  some values from: research study
source: https://en.wikipedia.org/wiki/Research_participant
definition: A research participant, also called a human subject or an experiment, trial, or study participant or subject, is a person who participates in human subject research by being the target of observation by researchers

unit of measurement
type: Class

CentralTendencyMeasure
type: Class
subclass of: statistical measure
comment: Statistical measure describing the distribution of single variable

DispersionMeasure
type: Class
subclass of: statistical measure
comment: Statistical measure characterizing the distribution of single variable

study intervention
type: Class
subclass of: StudyMethod
comment: Capturing the interventions variables in research studies
comment: The intervention type used in a research study (corresponding to I in the PICO(T) model )
synonym: Study intervention

statistical measure
type: Class
subclass of: DataAnalysisInstrument
subclass of: Restriction
  on property: hasAttribute
  all values from: unit of measurement
subclass of: Restriction
  on property: hasValue
  some values from: decimal
source: Measure
definition: a standard unit used to express the size, amount, or degree of something

Clinical Trials Protocol Template - NIH Office of Science Policy
type: Class
subclass of: enrollment status
adapted from: https://osp.od.nih.gov/wp-content/uploads/2014/01/Protocol_Template_05Feb2016_508.pdf
label: active
definition: participants following clinical trial protocol

cohort description
type: Class
subclass of: Dataset
subclass of: Restriction
  on property: hasDataItem
  some values from: study intervention
subclass of: Restriction
  on property: hasDataItem
  some values from: statistical measure
subclass of: Restriction
  on property: hasDataItem
  some values from: study arm
subclass of: Restriction
  on property: hasDataItem
  some values from: subject characteristic
comment: All typical components that constitute the description of study populations, captured in the first table of a research study, and hence called Table 1s
synonym: Table 1

control arm
type: Class
subclass of: study arm
type: NamedIndividual
has attribute: definition
  has value: An arm type that can receive an intervention that is considered effective (the standard), a placebo, or no intervention
  adapted from: https://aidsinfo.nih.gov/understanding-hiv-aids/glossary/3392/control-arm

Clinical Trials Protocol Template - NIH Office of Science Policy
type: Class
subclass of: enrollment status
adapted from: https://osp.od.nih.gov/wp-content/uploads/2014/01/Protocol_Template_05Feb2016_508.pdf
label: discontinued
definition: participants no longer, following clinical trial protocol

electronic health record
type: Class
subclass of: Dataset
subclass of: Restriction
  on property: hasAttribute
  some values from: Anthropometry
subclass of: Restriction
  on property: hasAttribute
  some values from: Demographic
subclass of: Restriction
  on property: hasAttribute
  some values from: laboratory test result
subclass of: Restriction
  on property: hasProperty
  some values from: study intervention
source: what-electronic-health-record-ehr
definition: a digital version of a patient’s paper chart

enrollment status
type: Class
subclass of: StatusDescriptor
adapted from: https://research-compliance.umich.edu/sites/default/files/resource-download/enrollmentdefinition_additionalhelp.pdf
definition: patients are consented and screened, with eligibility verified

intention to treat population
type: Class
subclass of: cohort
source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159210/
definition: every subject who is randomized according to randomized treatment assignment, ignoring noncompliance, protocol deviations, withdrawal, and anything that happens after randomization

intervention arm
type: Class
subclass of: study arm
subclass of: Restriction
  on property: subClassOf
  some values from: study subject
type: NamedIndividual
has attribute: definition
  has value: An arm type in which a group of participants receives the intervention/treatment that is the focus of the clinical trial
  source: https://clinicaltrials.gov/ct2/about-studies/glossary

meta-analysis
type: Class
subclass of: research study
type: NamedIndividual
has attribute: definition
  has value: A quantitative, formal, epidemiological study design used to systematically assess previous research studies to derive conclusions about that body of research
  source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3049418/

laboratory test result
type: Class
subclass of: subject characteristic

population size
type: Class
subclass of: statistical measure
subclass of: Restriction
  on property: hasValue
  some values from: integer
adapted from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296634/
definition: number of patients to which the study results could be reasonably generalized

randomized population
type: Class
subclass of: cohort
type: NamedIndividual
has attribute: definition
  has value: set of patients recruited for research studies, who are randomly assigned to different study groups, intending to ensure that all potential confounding factors are divided equally among the groups that will later be compared (structural equivalence)
  adapted from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3196997/

safety population
type: Class
subclass of: cohort
type: NamedIndividual
has attribute: definition
  has value: set of patients recruited for research studies, who are a part of the experimental treatment population, additionally patients receiving the experimental intervention is analyzed with the experimental group
  adapted from: https://www.dummies.com/education/science/biology/how-to-define-analytical-populations-for-a-clinical-study/
  adapted from: https://www.ncbi.nlm.nih.gov/books/NBK209903/

study arm
type: Class
subclass of: cohort
subclass of: Class
  intersection of: Restriction
    on property: hasAttribute
    some values from: Class
      union of: disease or condition
      union of: study intervention
      union of: subject characteristic
  intersection of: Restriction
    on property: hasAttribute
    some values from: Restriction
      on property: hasAttribute
      some values from: statistical measure
  intersection of: Restriction
    on property: hasAttribute
    some values from: Restriction
      on property: hasAttribute
      some values from: Restriction
        on property: hasValue
        some values from: decimal
type: NamedIndividual
has attribute: definition
  was attributed to: https://researcher.watson.ibm.com/researcher/view.php
  has value: An arm in a clinical trial is a group of subjects receiving the same therapeutic intervention (or none)
has attribute: definition
  has value: A group or subgroup of participants in a clinical trial that receives a specific intervention/treatment, or no intervention, according to the trial's protocol.
  source: https://clinicaltrials.gov/ct2/about-studies/glossary

subject characteristic
type: Class
subclass of: Restriction
  on property: hasAttribute
  some values from: DimensionalQuantity
subclass of: Restriction
  on property: hasAttribute
  some values from: unit of measurement
source: R. J. Little et al., "The prevention and treatment of missing data in clinical trials," New England J. Medicine, vol. 367, no. 14, pp. 1355{1360, 2012
definition: Property that summarizes important attributes of the participants enrolled in a study

NonHispanicOrLatino
has exact synonym: Non-Hispanic

UnknownRace
has exact synonym: Other Race

NCIT C16352
has exact synonym: Black

NCIT C17459
has exact synonym: Hispanic
has exact synonym: Hispanic Populations
has exact synonym: Hispanic or Latino
has exact synonym: Hispanics or Latinos
has exact synonym: Latino Population
has exact synonym: Spanish Origins

NCIT C41219
has exact synonym: Hawaiiaan
has exact synonym: Pacific Islander
has exact synonym: Hawaiian or Pacific Islander

http://purl.org/twc/ontologies/cmo.owl#0000105
has exact synonym: BMI