Clinical Metadata Exploration Ontology
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Clinical Metadata Exploration Ontology

Release: 10-08-2025

This version:
https://w3id.org/cmeo#v2
Latest version:
https://w3id.org/cmeo#
Revision:
version 2
Authors:
Komal Gilani
Contributors:
Michel Dumontier
Imported Ontologies:
SIO
STATO
OBI
OBCS
DUO
Download serialization:
JSON-LD RDF/XML N-Triples TTL
License:
https://creativecommons.org/licenses/by/4.0/
Visualization:
Visualize with WebVowl
Cite as:
Komal Gilani. Clinical Metadata Exploration Ontology. Revision: version 2. Retrieved from: https://w3id.org/cmeo#v2
Provenance of this page
Alpha – still in experimental testing for coverage.

Abstract

Integrating clinical research data across institutions is challenged by heterogeneity in variable definitions, inconsistent use of terminologies, and limited support for interoperable metadata. Biomedical ontologies offer important resources for structuring clinical data, yet their integration for comprehensive metadata descriptors (such as variable semantics, statistical summaries, and governance elements) is not yet well established. These descriptors are critical for data discovery and harmonization. We introduce the Clinical Metadata Exploration Ontology (CMEO), a semantic framework that extends established ontologies including OBI, STATO, and DUO to provide a unified representation of study designs, data element properties (e.g., value sets, units), exploratory statistics, and data reuse permissions. CMEO enables semantic querying, cross-study comparison, and harmonization planning in settings where individual-level data cannot be shared.

Introduction back to ToC

This is a place holder text for the introduction. The introduction should briefly describe the ontology, its motivation, state of the art and goals.

Namespace declarations

Table 1: Namespaces used in the document
[Ontology NS Prefix]<https://w3id.org/cmeo#>
cmeo: <https://w3id.org/cmeo>
dc<http://purl.org/dc/elements/1.1/>
foaf<http://xmlns.com/foaf/0.1/>
obo<http://purl.obolibrary.org/obo/>
oboInOwl<http://www.geneontology.org/formats/oboInOwl#>
owl<http://www.w3.org/2002/07/owl#>
protege<http://protege.stanford.edu/plugins/owl/protege#>
rdf<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
rdfs<http://www.w3.org/2000/01/rdf-schema#>
sio<http://semanticscience.org/resource/>
skos<http://www.w3.org/2004/02/skos/core#>
swrl<http://www.w3.org/2003/11/swrl#>
swrlb<http://www.w3.org/2003/11/swrlb#>
terms<http://purl.org/dc/terms/>
xml<http://www.w3.org/XML/1998/namespace>
xsd<http://www.w3.org/2001/XMLSchema#>

CMEO: Overview back to ToC

This ontology has the following classes and properties.

Classes

Object Properties

Data Properties

Named Individuals

SWRL Rules

CMEO: Description back to ToC

An ontology for representing clinical studies, including study designs, the collection and preparation of the targets of investigation, as well as the data generated and the types of analysis performed on the data to reach conclusions, and their documentation. It further extends to represent metadata of each data element in the study and related statatistics.

Cross-reference for CMEO classes, object properties and data properties back to ToC

This section provides details for each class and property defined by CMEO.

Classes

accuracyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000049

A data item that refers to the number of true positives and true negatives divided by the total number of observations.
Source
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
has super-classes
derived data from inferential statistical analysis c

adverse drug reactionc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#adverse_drug_reaction

Is defined by
https://w3id.org/cmeo#
has super-classes
adverse event c

adverse eventc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#CMEO_00000002

Is defined by
https://w3id.org/cmeo#
has super-classes
clinical event c
has sub-classes
adverse drug reaction c, allergic reaction c, device adverse event c

age category researchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/DUO_0000034

An investigation concerning specific age categories.
Should be paired with the an ontology term representing this population (e.g., xxx).
has super-classes
investigation c

age of majority inclusion criterionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002423

An inclusion criterion that uses the age of majority for a state or institution, where one is generally considered to be an adult, which if met, makes an individual suitable for a given task or participation in a given process.
Source
NCI BBRB, OBIB
Term status
http://purl.obolibrary.org/obo/IAO_0000120
has super-classes
inclusion criterion c

agentc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#agent

has super-classes
object c

all-cause hospitalizationc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#all-cause_hospitalization

Is defined by
https://w3id.org/cmeo#
has super-classes
hospitalization c

all-cause mortalityc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#all-cause_mortality

Is defined by
https://w3id.org/cmeo#
has super-classes
death c

allergic reactionc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#allergic_reaction

Is defined by
https://w3id.org/cmeo#
has super-classes
adverse event c

analyte rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000275

A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role.
Source
OBI
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
Glucose in blood (measured in an assay to determine the concentration of glucose).
has super-classes
measurand role c

ancestry researchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/DUO_0000033

An investigation concerning ancestry or population origins.
has super-classes
investigation c

anthropometric measurementc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#anthropometric_measurement

Is defined by
https://w3id.org/cmeo#
has super-classes
measurement c

author rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000442

A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name.
Term status
http://purl.obolibrary.org/obo/IAO_0000125
has super-classes
role c

bar chartc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/STATO_0000166

the bart chart is a graph resulting from plotting rectangular bars with lengths proportional to the values that they represent.
has super-classes
graph c
has sub-classes
grouped bar chart c, stacked bar chart c

biasc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000080

A quantitative confidence value that is a general statistical term meaning a systematic (not random) deviation from the true value
Source
WEB: http://www.statistics.com
has super-classes
quantitative confidence value c

binary class variablec back to ToC or Class ToC

IRI: https://w3id.org/cmeo#dischotomous_variable

variable with only two categories
Is defined by
https://w3id.org/cmeo#
has super-classes
categorical variable c

biological attributec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBA_0000001

has super-classes
quality c

biomedical researchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/DUO_0000037

An investigation concerning health, medical, or biomedical research.
has super-classes
investigation c
has sub-classes
disease category research c, drug development research c, genetic research c

bleeding eventc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#bleeding_event

Is defined by
https://w3id.org/cmeo#
has super-classes
clinical event c

blood biomarkerc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#blood_biomarker

Is defined by
https://w3id.org/cmeo#
has super-classes
blood measurement c

blood measurementc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#blood_measurement

Is defined by
https://w3id.org/cmeo#
has super-classes
measurement c
has sub-classes
blood biomarker c, protein biomarker c

BMI range inclusion criterionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002428

An inclusion criterion that defines and states a Body Mass Index range, which if met, makes an individual suitable for a given task or participation in a given process.
Source
NCI BBRB, OBIB
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Example 
An important inclusion criterion is for for the individual to have a BMI between 18.5 and 35.0
has super-classes
inclusion criterion c

cardiac signc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#cardiac_sign

Is defined by
https://w3id.org/cmeo#
has super-classes
sign c

cardiovascular eventc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#cardiovascular_event

Is defined by
https://w3id.org/cmeo#
has super-classes
clinical event c

cardiovascular measurementc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#cardiovascular_measurement

Is defined by
https://w3id.org/cmeo#
has super-classes
measurement c

case-control study designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002624

A study design that entails the creation of two types of roles, such that each participant under investigation bears one or the other. What distinguishes the two types of roles is an 'outcome', which is associated with participants that have the case role but not associated with participants that have the control role. A case-control study examines the hypothesis that the presence of the outcome in case participants is associated with an 'exposure' that is not associated with control participants.
Source
Wikipedia, OBI
Term status
http://purl.obolibrary.org/obo/IAO_0000120
has super-classes
study design c

categorical labelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000963

A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
Source
Bjoern Peters
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Example 
The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.
has super-classes
datum label c
has members
ambidexterous ni, left handed ni, right handed ni

categorical value specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001930

A value specification that is specifies one category out of a fixed number of nominal categories
Term status
http://purl.obolibrary.org/obo/IAO_0000123
has super-classes
value specification c

categorical variablec back to ToC or Class ToC

IRI: https://w3id.org/cmeo#categorical_variable

Is defined by
https://w3id.org/cmeo#
has super-classes
variable c
has sub-classes
binary class variable c, multi class variable c

cause-specific hospitalizationc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#cause-specific_hospitalization

Is defined by
https://w3id.org/cmeo#
has super-classes
hospitalization c

cause-specific mortalityc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#cause-specific_mortality

Is defined by
https://w3id.org/cmeo#
has super-classes
death c

centrally registered identifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000578

An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
Source
Original proposal from Bjoern, discussions at IAO calls
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Example 
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
has super-classes
identifier c
has sub-classes
OMOP identifier c, ORCID identifier c

clinical eventc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#clinical_event

Is defined by
https://w3id.org/cmeo#
has super-classes
data element c
has sub-classes
ER visits c, adverse event c, bleeding event c, cardiovascular event c, death c, hospitalization c

clinical exposure exclusion criterionc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#clinical_exposure_exclusion_criterion

Is defined by
https://w3id.org/cmeo#
has super-classes
exclusion criterion c

clinical history designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001337

A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.
Source
MO_832 clinical_history_design
Term status
http://purl.obolibrary.org/obo/IAO_0000120
has super-classes
study design c

clinical study designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500001

Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach]
Source
Clinical Research Glossary Version 4.0 CDICS glossary group
Term status
http://purl.obolibrary.org/obo/IAO_0000125
Example 
PMID: 17655677.J Cardiovasc Electrophysiol. 2007 Aug;18(9):965-71.Biventricular versus right ventricular pacing in patients with AV block (BLOCK HF): clinical study design and rationale.
has super-classes
study design c

cluster study group rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002898

A study group role that is the result of the allocation of a cluster of study-defined groupings of people in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol.
Source
ClinEpiDB
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Example 
A cluster study group consisting of eight pregnant women who lived close enough to each other so that a community promoter could readily walk to each compound.
has super-classes
study group role c

codec back to ToC or Class ToC

IRI: https://w3id.org/cmeo#code

A unique identifier assigned to a concept in a standardized vocabulary (e.g., LOINC, SNOMED).
Is defined by
https://w3id.org/cmeo#
has super-classes
identifier c

cohort study designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000106

A study design that starts with an exposure and moves forward to the outcome of interest, even if the data are collected retrospectively. As an example, a group of patients who have variable exposure to a risk factor of interest can be followed over time for an outcome.
Source
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
has super-classes
observational design c

completedc back to ToC or Class ToC

IRI: http://semanticscience.org/resource/SIO_000034

completed is that status of a process that successfully unfolds.
has super-classes
process status c

compliancec back to ToC or Class ToC

IRI: https://w3id.org/cmeo#compliance

has super-classes
disposition c

compliance or adherencec back to ToC or Class ToC

IRI: https://w3id.org/cmeo#compliance_or_adherence

Is defined by
https://w3id.org/cmeo#
has super-classes
observation c

compound study group rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002899

A study group role that is the result of the allocation of a compound of geographically-proximate households with a shared component in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol.
Source
ClinEpiDB
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Example 
A compound study group consisting of geographically proximate households that share a common water source.
has super-classes
study group role c

compound treatment designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000951

an intervention design in which the treatment is the administration of a compound
Source
MO_555 compound_treatment_design
Term status
http://purl.obolibrary.org/obo/IAO_0000120
has super-classes
intervention design c
has sub-classes
dose response design c

consumption measurementc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#consumption_measurement

The quantification of any morphological or physiological parameter related to intake or ingestion, especially of food or drink, or a value resulting from such a quantification.
Is defined by
https://w3id.org/cmeo#
has super-classes
measurement c

contact representative rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001687

A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent.
Term status
http://purl.obolibrary.org/obo/IAO_0000123
has super-classes
role c

continuantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000002

An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
has super-classes
entity c
has sub-classes
generically dependent continuant c, independent continuant c, specifically dependent continuant c
is in domain of
participates in op
is in range of
has participant op
is disjoint with
occurrent c

continuant fiat boundaryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000140

b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
has super-classes
immaterial entity c
has sub-classes
one-dimensional continuant fiat boundary c, two-dimensional continuant fiat boundary c, zero-dimensional continuant fiat boundary c
is disjoint with
spatial region c, spatial region c, site c

continuous variablec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/STATO_0000251

A continuous variable over a particular range of the real numbers is one whose value in that range must be such that, if the variable can take values a and b in that range, then it can also take any value between a and b.
Source
WEB: https://en.wikipedia.org/wiki/Continuous_and_discrete_variables
has super-classes
variable c

contour plotc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000057

Source
OBI_0000246
group:Flow Cytometry community
Example 
Contour plot of SSC-H, FSC-H, and FL1-H.
has super-classes
graph c

correlation coefficientc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/STATO_0000142

The correlation coefficient of two variables in a data sample is their covariance divided by the product of their individual standard deviations. It is a normalized measurement of how the two are linearly related.
has super-classes
quantitative confidence value c
has sub-classes
Kendall's correlation coefficient c, Matthews correlation coefficient c, Pearson's correlation coefficient c, Spearman's rank correlation coefficient c, polychoric correlation coefficient c, r2 measure of linkage desequilibrium c

country of residence inclusion criteriac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002562

An inclusion criterion that defines and states one or more countries of residence which, if met, makes a human being suitable for a given task or participation in a given process.
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Example 
"include US residents"
has super-classes
inclusion criterion c

credible intervalc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000071

A quantitative confidence value that is used in Bayesian analysis to describe the range in which a posterior probability estimate is likely to reside.
Source
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
has super-classes
quantitative confidence value c

cross over designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500003

a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control
Source
(source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html)
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Example 
PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity.
has super-classes
repeated measure design c
has sub-classes
n-to-1 design c, single arm cross over design c

data about an ontology partc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000102

Data about an ontology part is a data item about a part of an ontology, for example a term
has super-classes
data item c

data acquisitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000002

A planned process that gathers and measures information on variables of interest, in an established systematic fashion that enables one to answer stated research questions, test hypotheses, and evaluate outcomes. Data acquistion results in a collection of data.
Source
WEB: http://en.wikipedia.org/wiki/Data_collection
has super-classes
planned process c

data categorizationc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#data_categorization

Is defined by
https://w3id.org/cmeo#
has super-classes
planned process c

data collection designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000137

A plan specification that provides a detailed outline of how data is collected.
has super-classes
plan specification c

data coordinating center rolec back to ToC or Class ToC

IRI: https://w3id.org/cmeo#data_coordinating_center_role

Organization responsible for managing, coordinating, and analyzing study data.
has super-classes
role c

data elementc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#data_element

A basic unit of information that has a unique meaning and instances (data items) of distinct value. Examples of data elements include gender, race, and geographic location in data dictionary(ref. https://cde.nlm.nih.gov/). It provides classification of data elements
A grouping or label that provides a semantic interpretation of a data element.
has super-classes
data item c
has sub-classes
clinical event c, identifier c, measurement c, medical history c, medications and therapies c, observation c, procedure c, sign or symptom c

data format specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000098

A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
Source
OBI branch derived
OBI_0000187
Term status
http://purl.obolibrary.org/obo/IAO_0000123
has super-classes
directive information entity c

data itemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000027

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.
Term status
http://purl.obolibrary.org/obo/IAO_0000125
Example 
Data items include counts of things, analyte concentrations, and statistical summaries.
has super-classes
information content entity c
has sub-classes
data about an ontology part c, data element c, data matrix c, data set c, data type c, data use modifier c, data use permission c, derived data from statistical analysis c, variable c

data matrixc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000120

A data item that is more specifically a rectangular array of numbers, symbols, or expressions, arranged in rows and columns.
Source
WEB: https://en.wikipedia.org/wiki/Matrix_(mathematics)
is equivalent to
data item c and (has member op only data set c) and (has member op min 2 data set c)
has super-classes
data item c

data setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000100

A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
Source
OBI_0000042
group:OBI
Term status
http://purl.obolibrary.org/obo/IAO_0000125
Example 
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
has super-classes
data item c, information content entity c

data standardizationc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#data_standardization

Is defined by
https://w3id.org/cmeo#
has super-classes
planned process c

data typec back to ToC or Class ToC

IRI: https://w3id.org/cmeo#data_type

data type of variables such as int, float, str, datetime etc.
Is defined by
https://w3id.org/cmeo#
has super-classes
data item c

data use modifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/DUO_0000017

Data use modifiers indicate additional conditions for use.
has super-classes
data item c

data use permissionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/DUO_0000001

A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used.
has super-classes
data item c

data use permission assignment processc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#data_use_permission_assignment_process

has super-classes
informed consent process c

data visualizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200111

A planned process with the objective to graphically represent some data by inputing the data and outputting images, diagrams or animations.
Source
PERSON: Elisabetta Manduchi
PERSON: James Malone
PERSON: Melanie Courtot
PERSON: Tina Boussard
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
Generation of a heatmap from a microarray dataset
has super-classes
planned process c

datum labelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000009

A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
Term status
http://purl.obolibrary.org/obo/IAO_0000123
has super-classes
information content entity c
has sub-classes
categorical label c, measurement unit label c

deathc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#death

Is defined by
https://w3id.org/cmeo#
has super-classes
clinical event c
has sub-classes
all-cause mortality c, cause-specific mortality c

demographicsc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#demographics

Is defined by
https://w3id.org/cmeo#
has super-classes
observation c
has sub-classes
socioeconomic status c

dendrogramc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000183

A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
Source
WEB: http://en.wikipedia.org/wiki/Dendrogram
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
Dendrograms are often used in computational biology to
illustrate the clustering of genes.
has super-classes
graph c

density plotc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000079

A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.
Source
OBI_0000179
group:Flow Cytometry community
Example 
Density plot of SSC-H and FSC-H.
has super-classes
graph c

derived data from descriptive statistical analysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000219

has super-classes
derived data from statistical analysis c

derived data from inferential statistical analysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000220

A data item that is derived from an inferential statistical data analysis.
Source
WEB: http://psc.dss.ucdavis.edu/sommerb/sommerdemo/stat_inf/intro.htm
WEB: http://www.ask.com/question/what-is-numerical-data
has super-classes
derived data from statistical analysis c
has sub-classes
accuracy c, odds ratio c, prevalence rate c, quantitative confidence value c, rank order c, relative risk c, reliability c, sensitivity c, specificity c, standardized mortality ratio c, test statistic c, validity c, weighted data c

derived data from statistical analysisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000218

A data item that is derived from a statistical data analysis.
Source
WEB: http://en.wikipedia.org/wiki/Statistic
WEB: http://www.ask.com/question/what-is-numerical-data
has super-classes
data item c
has sub-classes
derived data from descriptive statistical analysis c, derived data from inferential statistical analysis c

devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000968

device is modelled as processed material in OBI which refers to material entities that can alter and modified under certain process. however device is a material object and it doesnot change it course. We dont not consider blood samples as device but only material entities such as needle, MRI scan, wearable smart watch etc.
has super-classes
object c
has sub-classes
wearable device c

device adverse eventc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#device_adverse_event

Is defined by
https://w3id.org/cmeo#
has super-classes
adverse event c

device identifierc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#device_identifier

Is defined by
https://w3id.org/cmeo#
has super-classes
identifier c

device settingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000654

a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Example 
Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification
has super-classes
quality c

diagnostic measurementc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#diagnostic_measurement

Is defined by
https://w3id.org/cmeo#
has super-classes
measurement c

diagnostic validityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000138

A validity that refers to the validity of a diagnosis, and associated diagnostic tests or screening tests in a clinical field such as medicine.
Source
http://en.wikipedia.org/wiki/Validity_(statistics)
has super-classes
validity c

diagramc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000309

A figure that expresses one or more propositions
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Example 
A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
has super-classes
figure c
has sub-classes
graph c

directive information entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000033

An information content entity whose concretizations indicate to their bearer how to realize them in a process.
Term status
http://purl.obolibrary.org/obo/IAO_0000122
has super-classes
information content entity c
has sub-classes
data format specification c, objective specification c, plan specification c, selection criterion c, study design variable specification c, study outcome specification c, timeline specification c

disease category researchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/DUO_0000040

Biomedical research research concerning specific disease/s
has super-classes
biomedical research c

disease or disorderc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0000001

A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
has super-classes
disposition c

disease test sensitivityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000094

A sensitivity that refers to the number of patients with a positive test who have a disease divided by all patients who have the disease. A test with high sensitivity will not miss many patients who have the disease (i.e., few false negative results).
Source
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
has super-classes
sensitivity c

disease test specificityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000095

A specificity that refers to the number of patients who have a negative test and do not have the disease divided by the number of patients who do not have the disease. A test with high specificity will infrequently identify patients as having a disease when they do not (i.e., few false positive results).
Source
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
has super-classes
specificity c

dispositionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000016

Example 
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
has super-classes
realizable entity c
has sub-classes
compliance c, disease or disorder c, function c, uncertainty c
is in range of
has disposition op
is disjoint with
role c

donor rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110087

A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro.
Source
IEDB
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Example 
A T cell line from a PPD(+) donor.
has super-classes
role c

dose response designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001418

A study design that examines the relationship between the size of the administered dose and the extent of the response.
Source
MO_485 dose_response_design
Term status
http://purl.obolibrary.org/obo/IAO_0000120
has super-classes
compound treatment design c

dot plotc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000037

A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
Source
OBI_0000123
group:OBI
Example 
Dot plot of SSC-H and FSC-H.
has super-classes
graph c

drug development researchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/DUO_0000039

Biomedical research concerning drug development.
has super-classes
biomedical research c

drug rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000040

a role borne by a molecular entity and is realized in a process of absorption by an organism alters, or effects (or is assumed to effect) a function(s) which inhere in an organism
Source
OBI, CDISC
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Example 
http://www.answers.com/topic/drug
   1. A substance used in the diagnosis, treatment, or prevention of a disease or as a component of a medication.
   2. Such a substance as recognized or defined by the U.S. Food, Drug, and Cosmetic Act.
has super-classes
role c

ecological validityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000154

An external validity that refers to the extent to which research results can be applied to real life situations outside of research settings.
Source
http://en.wikipedia.org/wiki/Validity_(statistics)
has super-classes
external validity c

eligibility criterionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500026

an eligibility criterion (rule) is_a selection criterion which defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process.
Source
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3.
has super-classes
selection criterion c
has sub-classes
exclusion criterion c, inclusion criterion c

email addressc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000429

Term status
http://purl.obolibrary.org/obo/IAO_0000123
has super-classes
information content entity c, textual entity c

entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000001

Example 
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
has super-classes
Thing c
has sub-classes
continuant c, occurrent c
is in domain of
denoted by op, exists at op
is in range of
denotes op

ER visitsc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#ER_visits

Is defined by
https://w3id.org/cmeo#
has super-classes
clinical event c

ethnicity inclusion criterionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002563

An inclusion criteria that defines and states one or more ethnicities which, if met, makes an entity suitable for a given task or participation in a given process.
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Example 
"include only Hispanic individuals"
has super-classes
inclusion criterion c

ETL processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000650

A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second.
Source
WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load
has super-classes
planned process c

exclusion criterionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500028

an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study
Source
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
Term status
http://purl.obolibrary.org/obo/IAO_0000125
Example 
PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months.
has super-classes
eligibility criterion c
has sub-classes
clinical exposure exclusion criterion c, history of metastatic cancer exclusion criterion c, intravenous drug use exclusion criterion c, radiation treatment exclusion criteria c, surgical procedure history exclusion criterion c

experimental validityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000143

A validity that refers to whether an experiment (or a study) is able to scientifically answer the questions it is intended to answer.
Source
http://en.wikipedia.org/wiki/Validity_(statistics)
has super-classes
validity c
has sub-classes
external validity c, internal validity c, statistical conclusion validity c

external validityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000153

An experimental validity that refers to the extent to which the (internally valid) results of a study can be held to be true for other cases, for example to different people, places or times. In other words, it is about whether findings can be validly generalized. If the same research study was conducted in those other cases, would it get the same results?
Source
http://en.wikipedia.org/wiki/Validity_(statistics)
has super-classes
experimental validity c
has sub-classes
ecological validity c

family historyc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#family_history

Is defined by
https://w3id.org/cmeo#
has super-classes
medical history c

family status inclusion criterionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002560

An inclusion criterion that defines and states one or more family statuses, which, if met, makes a human being suitable for a given task or participation in a given process.
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Example 
"included married and unmarried patients", "included divorced individuals"
has super-classes
inclusion criterion c

fiat object partc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000024

Example 
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
has super-classes
material entity c

figurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000308

An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Example 
Any picture, diagram or table
has super-classes
information content entity c
has sub-classes
diagram c, image c

formulac back to ToC or Class ToC

IRI: https://w3id.org/cmeo#formula

Is defined by
https://w3id.org/cmeo#
has super-classes
information content entity c

functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000034

Example 
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
has super-classes
disposition c
has sub-classes
measure function c, record function c, transfer function c
is in domain of
function of op
is in range of
has function op

functional and behavioral assesment scorec back to ToC or Class ToC

IRI: https://w3id.org/cmeo#functional_and_behavioral_assesment_score

Is defined by
https://w3id.org/cmeo#
has super-classes
measurement c

gender category researchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/DUO_0000035

An investigation concerning specific gender categories.
Should be paired with the an ontology term representing this population (e.g., xxx).
has super-classes
investigation c

general signc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#general_sign

Is defined by
https://w3id.org/cmeo#
has super-classes
sign c

generically dependent continuantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000031

b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
Example 
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
has super-classes
continuant c
has sub-classes
information content entity c
is in domain of
is concretized as op
is in range of
concretizes op
is disjoint with
independent continuant c, specifically dependent continuant c, independent continuant c, specifically dependent continuant c

genetic researchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/DUO_0000038

Biomedical research concerning genetics (i.e., the study of genes, genetic variations and heredity).
has super-classes
biomedical research c

geographic locationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GAZ_00000448

has super-classes
site c

graphc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000038

A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
Source
OBI_0000240
group:OBI
Term status
http://purl.obolibrary.org/obo/IAO_0000125
has super-classes
diagram c
has sub-classes
Venn diagram c, bar chart c, contour plot c, dendrogram c, density plot c, dot plot c, heatmap c, histogram c, line graph c, scatter plot c

grouped bar chartc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/STATO_0000267

grouped bar chart is a kind of bar chart which juxtaposes the discrete values for each of the possible value of a given categorical variable, thus providing within group comparison. Grouped bar charts are good for comparing between each element in the categories, and comparing elements across categories. However, the grouping can make it harder to tell the difference between the total of each group.
has super-classes
bar chart c

health care provider rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OMRSE_00000012

A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism.
has super-classes
role c

health status inclusion criterionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002453

An inclusion criterion that defines and states one or more clinically significant bodily components, dispositions, and/or bodily processes of an entity that are inferred from relevant clinical findings or self-reported, which, if met, makes the entity suitable for a given task or participation in a given process.
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Example 
‘diagnosed with Type 2 diabetes mellitus’, ‘E11.4’, ’not finding of hypertension'
has super-classes
inclusion criterion c

healthy volunteer criterionc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#healthy_volunteer_criterion

A type of eligibility criteria that indicates whether people who do not have the condition/disease being studied can participate in that clinical study. Indication that participants who do not have a disease or condition, or related conditions or symptoms, under study in the clinical study are permitted to participate in the clinical study.
Is defined by
https://w3id.org/cmeo#
has super-classes
inclusion criterion c

heatmapc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000180

A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
Source
GROUP:OBI
Term status
http://purl.obolibrary.org/obo/IAO_0000122
has super-classes
graph c

histogramc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000179

A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
Source
GROUP:OBI
Term status
http://purl.obolibrary.org/obo/IAO_0000122
has super-classes
graph c

historyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000182

has super-classes
process c

history of metastatic cancer exclusion criterionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002430

An exclusion criterion defined as whether an individual has ever been diagnosed with metastatic cancer (cancer that spread beyond the initial site such as to other organs like brain bone or liver), which if met, makes the individual unsuitable for a given task or participation in a given process.
Source
NCI BBRB, OBIB
Term status
http://purl.obolibrary.org/obo/IAO_0000120
has super-classes
exclusion criterion c

Homo sapiensc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_9606

has super-classes
organism c

hospital patient inclusion criterionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002559

An inclusion criterion defines that a human being has to be a hospital patient to be suitable for a given task or participation in a given process.
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Example 
"included hospital patients"
has super-classes
inclusion criterion c

hospital rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OMRSE_00000054

A healthcare provider role that inheres in an organization and is realized by providing inpatient care.
has super-classes
role c

hospitalizationc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#hospitalization

Is defined by
https://w3id.org/cmeo#
has super-classes
clinical event c
has sub-classes
all-cause hospitalization c, cause-specific hospitalization c, procedure related hospitalization c, readmission c

human subject enrollmentc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#human_subject_enrollment

Is defined by
https://w3id.org/cmeo#
has super-classes
planned process c

hypothesis driven investigationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000355

is an investigation with the goal to test one or more hypothesis
Source
OBI branch derived
Term status
http://purl.obolibrary.org/obo/IAO_0000125
has super-classes
investigation c

hypothesis generating investigationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000356

is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis
Source
OBI branch derived
Term status
http://purl.obolibrary.org/obo/IAO_0000125
has super-classes
investigation c

identifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0020000

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.
Sep 29, 2016: The current definition has been amended from the previous version: "A proper name 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." to more accuratly reflect the necessary and sufficient condition on the class. (MB)
Authors:
Mathias Brochhausen
has super-classes
data element c, symbol c
has sub-classes
centrally registered identifier c, code c, device identifier c, participant identifier c

imagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000101

An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
Source
OBI_0000030
group:OBI
Term status
http://purl.obolibrary.org/obo/IAO_0000122
has super-classes
figure c
has sub-classes
photograph c

image acquisition functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000397

An image acquisition function is a function to acquire an image of a material
Term status
http://purl.obolibrary.org/obo/IAO_0000122
has super-classes
measure function c

immaterial entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000141

has super-classes
independent continuant c
has sub-classes
continuant fiat boundary c, site c, spatial region c
is disjoint with
material entity c

inclusion criterionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500027

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.
Source
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
Term status
http://purl.obolibrary.org/obo/IAO_0000125
Example 
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) .
has super-classes
eligibility criterion c
has sub-classes
BMI range inclusion criterion c, age of majority inclusion criterion c, country of residence inclusion criteria c, ethnicity inclusion criterion c, family status inclusion criterion c, health status inclusion criterion c, healthy volunteer criterion c, hospital patient inclusion criterion c, sex inclusion criterion c, use of medication inclusion criterion c

independent continuantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000004

b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
Example 
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
has super-classes
continuant c
has sub-classes
immaterial entity c, material entity c
is in domain of
capable of op, has disposition op, has function op, has role op, located in op
is in range of
located in op, occurs in op
is disjoint with
specifically dependent continuant c, generically dependent continuant c, specifically dependent continuant c, generically dependent continuant c

information carrierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000015

A quality of an information bearer that imparts the information content
Source
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
Term status
http://purl.obolibrary.org/obo/IAO_0000125
Example 
In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
is equivalent to
quality c and (concretizes op some information content entity c)
has super-classes
quality c

information content entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000030

A generically dependent continuant that is about some thing.
Source
OBI_0000142
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has super-classes
generically dependent continuant c
has sub-classes
data item c, data set c, datum label c, directive information entity c, email address c, figure c, formula c, process status c, symbol c, textual entity c, value specification c
is in domain of
denotes op, has value specification op, is about op
is in range of
denoted by op

informed consent processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000810

A planned process with the objective to inform a person or their legal representative of legally and ethically relevant facts about a process that the person in question is asked to participate in, and which results in a documented decision as to whether the person in question will participate.
Source
http://clinicaltrials.gov/ct2/info/glossary#informed
Term status
http://purl.obolibrary.org/obo/IAO_0000122
has super-classes
planned process c
has sub-classes
data use permission assignment process c, informing investigator of subject study arm c, informing subject of study arm c

informing investigator of subject study armc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000804

A planned process with the objective to make the investigator aware of which study arm a patient is participating in.
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Example 
Informing the investigator whether a patient is receiving a placebo or a treatment with an investigational compound.
has super-classes
informed consent process c

informing subject of study armc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000842

A planned process with the objective to make the subject aware of which study arm they are participating in.
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Example 
Informing participants whether they are receiving a placebo or a treatment with an investigational compound.
has super-classes
informed consent process c

internal validityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000152

An experimental validity that refers to the degree to which conclusions about causal relationships can be made (e.g. cause and effect), based on the measures used, the research setting, and the whole research design.
Source
http://en.wikipedia.org/wiki/Validity_(statistics)
has super-classes
experimental validity c

intervention designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000115

An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
Source
OBI branch derived
Term status
http://purl.obolibrary.org/obo/IAO_0000125
Example 
PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.
has super-classes
study design c
has sub-classes
compound treatment design c, randomized complete block design c, repeated measure design c

intraclass correlation coefficientc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000084

A quantitative confidence value that is a descriptive statistic and can be used to describe how strongly units in the same group resemble each other; unlike other correlation measures it operates on data structured as groups, rather than data structured as paired observations.
Source
WEB: http://en.wikipedia.org/wiki/Intraclass_correlation
has super-classes
quantitative confidence value c

intravenous drug use exclusion criterionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002431

An exclusion criterion defined as when an individual has a history of intravenous drug abuse for a specific timeframe, which if met, makes the individual unsuitable for a given task or participation in a given process.
Source
NCI BBRB, OBIB
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Example 
Donor eligibility based on history of intravenous drug abuse in the last 5 years.
has super-classes
exclusion criterion c

investigationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000066

a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
Source
OBI branch derived
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
has super-classes
planned process c
has sub-classes
age category research c, ancestry research c, biomedical research c, gender category research c, hypothesis driven investigation c, hypothesis generating investigation c, method development c, population research c, research control c, surveillance process c

investigation agent rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000202

A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing.
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)
Source
OBI
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
has super-classes
role c

kappa statisticc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000109

A statistic test for several similar measures of agreement used with categorical data; typically used in assessing the degree to which two or more raters, examining the same data, agree on assigning data to categories
Source
WEB: http://www.statistics.com
has super-classes
test statistic c

Kendall's correlation coefficientc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/STATO_0000240

Kendall's correlation coefficient is a correlation coefficient between 2 ordinal variables (natively or following a ranking procedure) and may be used when the conditions for computing Pearson's correlation are not met (e.g linearity, normality of the 2 continuous variables)
has super-classes
correlation coefficient c

laboratory-based populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0003086

A population where the collection of individuals is located and maintained in a laboratory, research, or production facility.
Source
VEuPathDB
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Example 
Refers to whether the mosquitoes used in the analysis of insecticide resistance were collected from an established strain or any other population kept in a laboratory under controlled conditions. (per MIRO_30000033)
has super-classes
population c

lack of fit errorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000099

A statistical error that occurs when the analysis omits one or more important terms or factors from the model.
Source
WEB: http://www.itl.nist.gov/div898/handbook/pri/section7/pri7.htm
has super-classes
statistical error c

lengthc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000122

A 1-D extent quality which is equal to the distance between two points.
has super-classes
morphology c

lifestyle and behaviorc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#lifestyle_and_behavior

Is defined by
https://w3id.org/cmeo#
has super-classes
observation c

likelihood ratioc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000118

A quantitative confidence value that expresses how many times more likely the data are under one model than the other.
Source
WEB: http://en.wikipedia.org/wiki/Likelihood-ratio_test
has super-classes
quantitative confidence value c
has sub-classes
negative likelihood ratio c, positive likelihood ratio c

line graphc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000573

A line graph is a type of graph created by connecting a series of data points together with a line.
Source
GROUP:OBI
WEB: http://en.wikipedia.org/wiki/Line_chart
Term status
http://purl.obolibrary.org/obo/IAO_0000122
has super-classes
graph c

massc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000125

A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
has super-classes
physical quality c

material anatomical entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000465

Anatomical entity that has mass.
has super-classes
object c

material entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000040

An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
Example 
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
has super-classes
independent continuant c
has sub-classes
fiat object part c, object c, object aggregate c
is disjoint with
immaterial entity c

Matthews correlation coefficientc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/STATO_0000524

Matthews Correlation Coefficient (or MCC) is a correlation coefficient which is a measure of the quality of binary (two-class) classifications, introduced by biochemist Brian W. Matthews in 1975.
has super-classes
correlation coefficient c

measurand rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002444

A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role.
Source
https://en.wiktionary.org/wiki/measurand
Term status
http://purl.obolibrary.org/obo/IAO_0000120
has super-classes
role c
has sub-classes
analyte role c

measure functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000453

Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
A glucometer measures blood glucose concentration, the glucometer has a measure function.
has super-classes
function c
has sub-classes
image acquisition function c

measurement unit labelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000003

A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
Term status
http://purl.obolibrary.org/obo/IAO_0000125
Example 
Examples of measurement unit labels are liters, inches, weight per volume.
has super-classes
datum label c
is in range of
has measurement unit label op

medical historyc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#medical_history

Is defined by
https://w3id.org/cmeo#
has super-classes
data element c
has sub-classes
family history c

medications and therapiesc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#medications_and_therapies

Prescriptions, over-the-counter meds, hormonal therapy, treatment history
Is defined by
https://w3id.org/cmeo#
has super-classes
data element c

method developmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/DUO_0000031

An investigation concerning development of methods, algorithms, software or analytical tools.
has super-classes
investigation c

missing value specificationc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#missing_value_specification

to indicate the missing value indicator for a data element in its dataset
has super-classes
value specification c

mixed sexc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#mixed_sex

has super-classes
population quality c

morbidityc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#morbidity

has super-classes
population quality c

morphologyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000051

A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
has super-classes
physical object quality c
has sub-classes
length c, shape c, size c, weight c

multi class variablec back to ToC or Class ToC

IRI: https://w3id.org/cmeo#polychotomous_variable

variable with more than two categories
Is defined by
https://w3id.org/cmeo#
has super-classes
categorical variable c

n-to-1 designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500004

N-of-1 design is a cross-over design in which the same patient is repeatedly randomised to receive either the experimental treatment or its control (Senn, 1993).
Source
Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm)
Term status
http://purl.obolibrary.org/obo/IAO_0000125
has super-classes
cross over design c

negative likelihood ratioc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000046

A likelihood ratio that is calculated by dividing 1 minus sensitivity by specificity ((1-sensitivity)/specificity).
Source
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
has super-classes
likelihood ratio c

neurological signc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#neurological_sign

Is defined by
https://w3id.org/cmeo#
has super-classes
sign c

not startedc back to ToC or Class ToC

IRI: http://semanticscience.org/resource/SIO_000963

not started is the status of a process that is predicted to exist but has not yet begun.
has super-classes
process status c

objectc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#object

Example 
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
has super-classes
material entity c
has sub-classes
agent c, device c, material anatomical entity c, organism c, specimen c

object aggregatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000027

Source
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
Example 
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
has super-classes
material entity c
has sub-classes
organization c, population c

objective specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000005

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.
Source
OBI Plan and Planned Process/Roles Branch
OBI_0000217
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
has super-classes
directive information entity c

observationc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#observation

has super-classes
data element c
has sub-classes
compliance or adherence c, demographics c, lifestyle and behavior c, risk factor c

observational designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0300311

observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.
Source
OBI branch derived
Term status
http://purl.obolibrary.org/obo/IAO_0000125
Example 
PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.
has super-classes
study design c
has sub-classes
cohort study design c

obsolete B cell epitope competitive binding assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001715

A competitive inhibition of binding assay using a assay
Source
IEDB (QTT)
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Is deprecated
true

obsolete B cell epitope direct binding assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001712

A direct binding assay using a assay
Source
IEDB (QTT)
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Is deprecated
true

obsolete biological vector rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000109

a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission.
Source
OBI and Wikipedia
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Is deprecated
true
Example 
1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria.
Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280

obsolete cell bound MHC direct binding assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001582

direct binding assay measuring MHC ligand binding using MHC derived from a cell
Source
IEDB (QTT)
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Is deprecated
true

obsolete consent code primary categoryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/DUO_0000002

A categorical data item indicating the primary category the consent code belongs to according to Dyke et al. 2016.
Is deprecated
true

obsolete consent code secondary categoryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/DUO_0000003

A categorical data item indicating the secondary category the consent code belongs to according to Dyke et al. 2016.
Is deprecated
true

obsolete intracellular cytokine staining assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000665

The measurement of cytokines within the cytoplasm of a cell by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer.
Source
IEDB
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Is deprecated
true
Example 
Permeabilizing T cells and staining them with fluorescent labeled anti-IFN-gamma antibodies

obsolete intracellular material detection by flow cytometry assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000856

An assay in which the presence of a material inside a cell is measured by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer.
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true

obsolete MHC multimer staining assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000667

An MHC multimer assay is an assay that detects T cells capable of binding the MHC:ligand complexes present in the multimer. The multimer is fluorescently labelled. The T cells bound to multimers are counted in a flow cytometer
Source
IEDB
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Is deprecated
true
Example 
Measuring T cells that are specific for the SYFPEITHI peptide when presented by the murine MHC molecule H-2 Kd by staining them with a tetramer of peptide loaded MHC complexes.

obsolete molecular labelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/REO_0000280

A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay
Source
OBI developer call, 3-12-12
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Is deprecated
true

obsolete molecular label rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/REO_0000171

A reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay.
Source
OBI developer call, 3-12-12
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Is deprecated
true

obsolete performing a diagnosisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000988

The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true
Example 
Diagnosing that a patient has pneumonia based on information on measurements of temperature, sound of breathing, and patient complaining about a headache.

obsolete T cell recognition of eluted MHC ligand assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001540

An assay that identifies an MHC ligand using a T cell response assay as a readout
Source
IEDB
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Is deprecated
true
Example 
Using proliferation of a T cell line specific for SIINFEKL in response to material eluted from a cell as evidence that SIINFEKL was presented by MHC on that cell.

obsolete2_binary digital entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000019

A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters.
Source
group:OBI
OBI_0000244
Is deprecated
true
Example 
MS Word document, ZIP file, DICOM file, JPEG file

obsolete2_binary executablec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000093

Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)
Source
group:OBI
OBI_0000222
Is deprecated
true

obsolete2_digital entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000012

A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical.
Source
group:OBI
OBI_0000261
Is deprecated
true

obsolete2_report figurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000059

A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements
Source
group:OBI
OBI_0000027
Term status
http://purl.obolibrary.org/obo/IAO_0000124
Is deprecated
true

obsolete_anatomical entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100015

An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue'
Source
MO
Term status
http://purl.obolibrary.org/obo/IAO_0000121
Is deprecated
true
Example 
Tissue, organ, system, sperm, blood or body location (arm).

obsolete_blinded medication rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000223

Is a role which inheres in a material entity which is manufactured to be similar in appearance to a test material entity in e.g. a clinical trial to prevent participants from detecting which is the active and inactive substance
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Is deprecated
true
Example 
115 patients received ipilimumab and blinded medication
Inert pill shaped like aspirin tablet

obsolete_cell linec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100062

A secondary cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (ie has been successively passaged together in culture).
Source
OBI-CLO Alignment Working Group (Spring 2013)
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Is deprecated
true
Example 
A split of HeLa cells in active culture, or stored in frozen aliquots. Populations of HEK 293 cells used in experiments such as those documented in Changes in ultrastructure and endogenous ionic channels activity during culture of HEK 293 cell line. Eur J Pharmacol. 2007 Jul 12;567(1-2):10-8. PMID: 17482592.
He, Tong-Chuan, et al. Identification of c-MYC as a target of the APC pathway. Science 281.5382 (1998): 1509-1512. - To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene. Note that common usage in the literature is often of the form a human colorectal cancer cell line, as seen above. But such references to studies in a line refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells.  It is these discrete populations that we refer to as 'cell lines'.

obsolete_cell line cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100055

A material entity that represents generations of a primary culture.
Source
GROUP: OBI Biomaterial Branch
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Is deprecated
true

obsolete_defined processesc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600065

Place holder class, see editor note
Source
OBI branch derived
Term status
http://purl.obolibrary.org/obo/IAO_0000121
Is deprecated
true

obsolete_diethyl pyrocarbonatec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000851

Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true

obsolete_DNA ligasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000698

A DNA ligase is an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true

obsolete_DNA sequencing training servicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000986

A training process with the objective to provide a trainee with the skill to run DNA sequencing experiments
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true

obsolete_documentingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000340

Source
wikipedia http://en.wikipedia.org/wiki/Documenting
Term status
http://purl.obolibrary.org/obo/IAO_0000125
Is deprecated
true
Example 
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.

obsolete_electrically powered devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000972

a processed material created to have a function and which requires electrical power to execute
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true

obsolete_enrollmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000296

enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules
Source
IEDB
Term status
http://purl.obolibrary.org/obo/IAO_0000125
Is deprecated
true
Example 
Enrollment of patients in a study. Short-term outcome of neuropsychiatric events in systemic lupus erythematosus upon enrollment into an international inception cohort study. Arthritis Rheum. 2008 May 15;59(5):721-9. PMID: 18438902

obsolete_establishing a CRID registryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000576

a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID.
Is deprecated
true

obsolete_general scalar measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000987

Term status
http://purl.obolibrary.org/obo/IAO_0000124
Is deprecated
true

obsolete_immortal cell line culturec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100056

A cell line that is expected to be capable of indefinite propagation in an vitro culture.
Source
PERSON:Matthew Brush
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Is deprecated
true

obsolete_label rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000140

Label role is a role which inheres in a material entity and which is realized in a detection of label assay
Source
OBI
Is deprecated
true

obsolete_left handednessc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000937

Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true

obsolete_material access provider rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000936

a service provider role which is realized by a servicer provider organization performing access to some material
Source
OBI
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true
Example 
A person or organization who provides access to a DNA sequencer.

obsolete_material_entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000018

Is deprecated
true

obsolete_molecular concentrationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000577

A concentration is a relational quality that inheres in a material entity towards molecular scattered aggregate that is part of it by virtue of some ratio of masses of the two or the counts of the grains of the two or volume occupied by the larger material entity.
Source
Discussion in Karslruhe, Oct 2008, with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg.
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true
Example 
the phosphate concentration should be 0.1M

obsolete_protocol service provider rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000980

a service provider role which is realized by a servicer provider organization performing a protocol execution
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Is deprecated
true
Example 
DNA sequencing of a sample by a core lab which returns data to the consumer

obsolete_report elementc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000091

A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page).
Source
GROUP:OBI
OBI_0000001
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Is deprecated
true

obsolete_report tablec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000097

A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content
Source
group:OBI
OBI_0000265
Is deprecated
true

obsolete_right handednessc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000974

Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true

obsolete_role of being first subject treatedc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000100

First subject treated role is a study subject role borne by the subject realized in the application of the process specified in intervention study design with no previous study subject realizing the role prior in the study
Source
OBI
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Is deprecated
true
Example 
Rat 1A; first enrolled patient to receive treatment

obsolete_sample populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000264

A sample population is an object aggregate that is selected from the population, e.g. the fish in the net that were sampled from the lake, the people that responded to the call for volunteers.
Source
GROUP: OBI Biomaterial Branch
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Is deprecated
true
Example 
Patterns of benzylpiperazine/trifluoromethylphenylpiperazine party pill use and adverse effects in a population sample in New Zealand. Drug Alcohol Rev. 2008 Mar 31:1-7.  PMID: 18608458

obsolete_specimen fixation functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001037

A specimen fixation function is a function that holds or fastens an entity in a fixed position.
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true

obsolete_survival curvec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000182

A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
Source
WEB: http://www.graphpad.com/www/book/survive.htm
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Is deprecated
true

obsolete_trypsinized materialc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000420

A material entity that has undergone a process of digestion with trypsin
Is deprecated
true
Example 
A trypsinized suspension of cells

occurrentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000003

An entity that has temporal parts and that happens, unfolds or develops through time.
has super-classes
entity c
has sub-classes
process c, process boundary c, spatiotemporal region c, temporal region c
is in domain of
has participant op, occurs in op, precedes op
is in range of
participates in op, precedes op
is disjoint with
continuant c

odds ratioc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000054

A data item that refers to the odds that an individual with a specific condition has been exposed to a risk factor divided by the odds that a control has been exposed. The odds ratio is used in case-control studies. The odds ratio provides a reasonable estimate of the relative risk for uncommon conditions.
Source
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
has super-classes
derived data from inferential statistical analysis c

OMOP identifierc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#observational_medical_outcome_partnership_identifier

Is defined by
https://w3id.org/cmeo#
has super-classes
centrally registered identifier c

one-dimensional continuant fiat boundaryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000142

Example 
The Equator
all geopolitical boundaries
all lines of latitude and longitude
the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
the median sulcus of your tongue
has super-classes
continuant fiat boundary c
is disjoint with
two-dimensional continuant fiat boundary c, zero-dimensional continuant fiat boundary c, two-dimensional continuant fiat boundary c, zero-dimensional continuant fiat boundary c

one-dimensional spatial regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000026

Example 
an edge of a cube-shaped portion of space.
has super-classes
spatial region c
is disjoint with
three-dimensional spatial region c, two-dimensional spatial region c, zero-dimensional spatial region c, three-dimensional spatial region c

one-dimensional temporal regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000038

Example 
the temporal region during which a process occurs.
has super-classes
temporal region c
is disjoint with
zero-dimensional temporal region c

ongoingc back to ToC or Class ToC

IRI: http://semanticscience.org/resource/SIO_000035

ongoing is the status of a process that is not yet complete.
has super-classes
process status c

ORCID identifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000708

A centrally registered identifier that is issued by ORCID (https://orcid.org/) and used to persistantly identify oneself as a human researcher or contributor.
Is defined by
https://w3id.org/cmeo#
Source
https://orcid.org/
Term status
http://purl.obolibrary.org/obo/IAO_0000125
has super-classes
centrally registered identifier c

organismc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100026

A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
Source
WEB: http://en.wikipedia.org/wiki/Organism
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
animal
fungus
plant
virus
has super-classes
object c
has sub-classes
Homo sapiens c

organizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000245

An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
Source
GROUP: OBI
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
has super-classes
object aggregate c
has members
Thermo Fisher Scientific ni

p-valuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000175

A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.
Source
WEB: http://en.wikipedia.org/wiki/P-value
Term status
http://purl.obolibrary.org/obo/IAO_0000121
Example 
PMID:19696660
in contrast to the in-vivo data AT-III increased significantly from
113.5% at baseline to 117% after 4 days (n = 10, P-value= 0.02; Table 2).
has super-classes
quantitative confidence value c

participant identifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0003071

A symbol that denotes a participant under investigation.
Is defined by
https://w3id.org/cmeo#
Source
VEuPathDB
Term status
http://purl.obolibrary.org/obo/IAO_0000120
is equivalent to
identifier c and (denotes op some has role op some participant under investigation role c)
has super-classes
identifier c

participant under investigation rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000097

A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
Source
OBI
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. 
Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study.
Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.
has super-classes
role c

patient rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000093

a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider
Source
OBI, CDISC
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Example 
a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
has super-classes
role c

Pearson's correlation coefficientc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/STATO_0000280

The Pearson's correlation coefficient is a correlation coefficient which evaluates two continuous variables for association strength in a data sample. It assumes that both variables are normally distributed and linearity exists. The coefficient is calculated by dividing their covariance with the product of their individual standard deviations. It is a normalized measurement of how the two are linearly related.
has super-classes
correlation coefficient c

period prevalence ratec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000064

A prevalence rate that occurs at a specific period of time.
Source
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
has super-classes
prevalence rate c

phenotypec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OGMS_0000023

A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
has super-classes
quality c

photographc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000185

A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
Source
WEB: http://en.wiktionary.org/wiki/photograph
Term status
http://purl.obolibrary.org/obo/IAO_0000122
has super-classes
image c

physical object qualityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001241

A quality which inheres in a continuant.
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
has super-classes
quality c
has sub-classes
morphology c, physical quality c, population quality c

physical qualityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001018

A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
has super-classes
physical object quality c
has sub-classes
mass c

planc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000260

A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process.
Source
branch derived
Term status
http://purl.obolibrary.org/obo/IAO_0000125
Example 
The plan of researcher X to perform an experiment according to a protocol.
has super-classes
realizable entity c

plan specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000104

A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
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
Source
OBI Plan and Planned Process branch
OBI_0000344
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
has super-classes
directive information entity c
has sub-classes
data collection design c, protocol c, study design c

planned processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000011

A process that realizes a plan which is the concretization of a plan specification.
Source
branch derived
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
Injecting mice with a vaccine in order to test its efficacy
is equivalent to
realizes op some concretizes op some plan specification c
has super-classes
process c
has sub-classes
ETL process c, data acquisition c, data categorization c, data standardization c, data visualization c, human subject enrollment c, informed consent process c, investigation c, study design execution c
is in domain of
has output op, has_input op
is in range of
is input of op, is output of op

point prevalence ratec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000065

A prevalence rate that occurs at a specific point of time.
Source
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
has super-classes
prevalence rate c

polychoric correlation coefficientc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/STATO_0000269

polychoric correlation coefficient is a correlation coefficient which is computed over 2 variables to characterise an association by proxy with 2 (latent) variables which are assumed to be continuous and normally distributed.
has super-classes
correlation coefficient c
has sub-classes
tetrachoric correlation coefficient c

populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000181

a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
Source
adapted from Oxford English Dictionnary
Term status
http://purl.obolibrary.org/obo/IAO_0000125
Example 
PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
has super-classes
object aggregate c
has sub-classes
laboratory-based population c

population based designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002945

A study design where the selection of the individuals that are included into the study are intended to be representative of all individuals in the a priori defined specific population and is done at the population level or among the population groups, generally to find the cause, incidence or spread of the disease or to see the response to the treatment, nutrition or environment.
Source
https://link.springer.com/referenceworkentry/10.1007%2F978-1-4419-1005-9_45, EFO_0001430 population based design
Term status
http://purl.obolibrary.org/obo/IAO_0000120
has super-classes
study design c

population qualityc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#population_quality

has super-classes
physical object quality c
has sub-classes
mixed sex c, morbidity c

population researchc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/DUO_0000032

An investigation concerning a specific population group.
Should be paired with the an ontology term representing this population (e.g., xxx).
has super-classes
investigation c

positive likelihood ratioc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000047

A likelihood ratio that is calculated by dividing sensitivity by 1 minus specificity (sensitivity/(1-specificity)).
Source
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
has super-classes
likelihood ratio c

powerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000074

A quantitative confidence value that refers to the ability of a study to detect a true difference. Negative findings may reflect that the study was underpowered to detect a difference.
Source
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
has super-classes
quantitative confidence value c

prevalence ratec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000055

A data item that refers to the number of individuals with a given disease at a given point in time divided by the population at risk at a specified point in time or over a specified period of time.
Source
WEB: http://health.mo.gov/training/epi/PrevalenceRates.html
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
has super-classes
derived data from inferential statistical analysis c
has sub-classes
period prevalence rate c, point prevalence rate c

primary outcome specificationc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#primary_outcome_specification

Is defined by
https://w3id.org/cmeo#
has super-classes
study outcome specification c

procedurec back to ToC or Class ToC

IRI: https://w3id.org/cmeo#procedure

Is defined by
https://w3id.org/cmeo#
has super-classes
data element c

procedure related hospitalizationc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#hospitalization_for_procedure

Is defined by
https://w3id.org/cmeo#
has super-classes
hospitalization c

processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000015

p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
Example 
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.
has super-classes
occurrent c
has sub-classes
history c, planned process c
is in domain of
concretizes op, realizes op
is in range of
capable of op, realized in op
is disjoint with
temporal region c, temporal region c, spatiotemporal region c, process boundary c

process boundaryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000035

p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
Example 
the boundary between the 2nd and 3rd year of your life.
has super-classes
occurrent c
is disjoint with
temporal region c, temporal region c, spatiotemporal region c, process c

process qualityc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#process_quality

A process quality is quality that is associated with a process.
has super-classes
quality c

process statusc back to ToC or Class ToC

IRI: http://semanticscience.org/resource/SIO_000033

process status is a process quality that describes the state of a process.
has super-classes
information content entity c
has sub-classes
completed c, not started c, ongoing c

protein biomarkerc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#protein_biomarker_data_element

Is defined by
https://w3id.org/cmeo#
has super-classes
blood measurement c

protocolc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000272

A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
Source
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
has super-classes
plan specification c

qualityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000019

Example 
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
has super-classes
specifically dependent continuant c
has sub-classes
biological attribute c, device setting c, information carrier c, phenotype c, physical object quality c, process quality c, relational quality c
is in range of
has quality op
is disjoint with
realizable entity c

quantitative confidence valuec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000071

A data item which is used to indicate the degree of uncertainty about a measurement.
Source
group:OBI
Term status
http://purl.obolibrary.org/obo/IAO_0000125
has super-classes
derived data from inferential statistical analysis c
has sub-classes
bias c, correlation coefficient c, credible interval c, intraclass correlation coefficient c, likelihood ratio c, p-value c, power c, random error c, standard error c, standardized coefficient c, statistical error c, type 1 error rate c, type 2 error rate c

r2 measure of linkage desequilibriumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/STATO_0000123

r2 is a correlation coefficient which is computed over the frequency of 2 dichotomous variable and is used as a measure of Linkage Disequilibrium and as input data item to the creation of an LD plot
has super-classes
correlation coefficient c

radiation treatment exclusion criteriac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002425

An exclusion criterion that defines whether radiation was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process
Source
NCI BBRB, OBIB
Term status
http://purl.obolibrary.org/obo/IAO_0000120
has super-classes
exclusion criterion c

random errorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000075

A component of experimental error that occurs due to natural variation in the process.
Source
WEB: http://www.itl.nist.gov/div898/handbook/pri/section7/pri7.htm
has super-classes
quantitative confidence value c

random variablec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000126

A statistical variable whose value is subject to variations due to chance (i.e. randomness, in a mathematical sense).
Source
WEB: http://en.wikipedia.org/wiki/Random_variable
has super-classes
variable c

randomized complete block designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500007

A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups.
Source
http://www.tufts.edu/~gdallal/ranblock.htm
Term status
http://purl.obolibrary.org/obo/IAO_0000125
Example 
http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd))
has super-classes
intervention design c

randomized controlled trial designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000107

A study design in which patients are randomly assigned to two or more interventions.
Source
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
has super-classes
study design c

rank orderc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000117

A data item that represents an arrangement according to a rank, i.e., the position of a particular case relative to other cases on a defined scale.
Source
WEB: http://www.merriam-webster.com/dictionary/rank%20order
has super-classes
derived data from inferential statistical analysis c

readmissionc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#readmission

Is defined by
https://w3id.org/cmeo#
has super-classes
hospitalization c

realizable entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000017

A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
Example 
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
has super-classes
specifically dependent continuant c
has sub-classes
disposition c, plan c, role c
is in domain of
realized in op
is in range of
realizes op
is disjoint with
quality c

record functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000368

A record function is a function that registers or collects information in a particular format on a particular recording medium. For example on paper or a digital representation
Term status
http://purl.obolibrary.org/obo/IAO_0000122
has super-classes
function c

relational qualityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000145

b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
Example 
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
a marriage bond, an instance of love, an obligation between one person and another.
a marriage bond, an instance of requited love, an obligation between one person and another.
has super-classes
quality c

relative riskc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000056

A data item that equals the incidence in exposed individuals divided by the incidence in unexposed individuals. The relative risk can be calculated from studies in which the proportion of patients exposed and unexposed to a risk is known, such as a cohort study.
Source
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
has super-classes
derived data from inferential statistical analysis c

reliabilityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000057

A data item that refers to the extent to which repeated measurements of a relatively stable phenomenon fall closely to each other.
Source
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
has super-classes
derived data from inferential statistical analysis c

repeated measure designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500002

a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs
Source
http://www.holah.karoo.net/experimentaldesigns.htm
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Example 
PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations.
has super-classes
intervention design c
has sub-classes
cross over design c

research controlc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/DUO_0000036

An investigation concerning use of data as reference or control material.
has super-classes
investigation c

respiratory signc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#respiratory_sign

Is defined by
https://w3id.org/cmeo#
has super-classes
sign c

retrospective study designc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#retrospective_study_design

A study in which participants with known outcomes are assessed based on data collected before the study.
has super-classes
study design c

risk factorc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#risk_factor

Is defined by
https://w3id.org/cmeo#
has super-classes
observation c

rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000023

A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
Example 
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
has super-classes
realizable entity c
has sub-classes
author role c, contact representative role c, data coordinating center role c, donor role c, drug role c, health care provider role c, hospital role c, investigation agent role c, measurand role c, participant under investigation role c, patient role c, service provider role c, study group role c
is in range of
has role op
is disjoint with
disposition c

scalar value specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001931

A value specification that consists of two parts: a numeral and a unit label
Term status
http://purl.obolibrary.org/obo/IAO_0000123
has super-classes
value specification c

scatter plotc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000184

A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
Source
WEB: http://en.wikipedia.org/wiki/Scatterplot
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
Comparison of gene expression values in two samples can be displayed in a scatter plot
has super-classes
graph c

secondary outcome specificationc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#secondary_outcome_specification

Is defined by
https://w3id.org/cmeo#
has super-classes
study outcome specification c

selection criterionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001755

A directive information entity which defines and states a principle of standard by which selection process may take place.
Source
OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
rats should be aged between 6 and 8 weeks and weight between 180-250grams
has super-classes
directive information entity c
has sub-classes
eligibility criterion c

sensitivityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000058

A data item that measures the proportion of actual positives which are correctly identified as such (e.g. the percentage of sick people who are correctly identified as having the condition).
Source
WEB: http://en.wikipedia.org/wiki/Sensitivity_and_specificity
has super-classes
derived data from inferential statistical analysis c
has sub-classes
disease test sensitivity c

sensorc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#sensor

has super-classes
wearable device c

service provider rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000947

is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Example 
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
has super-classes
role c

sex inclusion criterionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002561

An inclusion criterion that defines and states one or more sexes which, if met, makes an entity suitable for a given task or participation in a given process.
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Example 
"included males and females", "included male patients"
has super-classes
inclusion criterion c

shapec back to ToC or Class ToC

IRI: https://w3id.org/cmeo#shape

has super-classes
morphology c

signc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#sign

Is defined by
https://w3id.org/cmeo#
has super-classes
sign or symptom c
has sub-classes
cardiac sign c, general sign c, neurological sign c, respiratory sign c

sign or symptomc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#sign_or_symptom

has super-classes
data element c
has sub-classes
sign c, symptom c, vital sign c

single arm cross over designc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#single_arm_cross_over_design

has super-classes
cross over design c

sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000029

Example 
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)
has super-classes
immaterial entity c
has sub-classes
geographic location c
is disjoint with
spatial region c, spatial region c, continuant fiat boundary c

sizec back to ToC or Class ToC

IRI: https://w3id.org/cmeo#size

has super-classes
morphology c

socioeconomic statusc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#socioeconomic_status

Is defined by
https://w3id.org/cmeo#
has super-classes
demographics c

spatial regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000006

has super-classes
immaterial entity c
has sub-classes
one-dimensional spatial region c, three-dimensional spatial region c, two-dimensional spatial region c, zero-dimensional spatial region c
is disjoint with
site c, continuant fiat boundary c, site c, continuant fiat boundary c

spatiotemporal regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000011

Example 
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
has super-classes
occurrent c
is disjoint with
temporal region c, temporal region c, process c, process boundary c

Spearman's rank correlation coefficientc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/STATO_0000201

Spearman's rank correlation coefficient is a correlation coefficient which is a nonparametric measure of statistical dependence between two ranked variables. It assesses how well the relationship between two variables can be described using a monotonic function. If there are no repeated data values, a perfect Spearman correlation of +1 or −1 occurs when each of the variables is a perfect monotone function of the other. Spearman's coefficient may be used when the conditions for computing Pearson's correlation are not met (e.g linearity, normality of the 2 continuous variables) but may require a ranking transformation of the variables
has super-classes
correlation coefficient c

specifically dependent continuantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000020

b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
Example 
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the role of being a doctor
the shape of this hole.
the smell of this portion of mozzarella
has super-classes
continuant c
has sub-classes
quality c, realizable entity c
is in domain of
concretizes op
is in range of
has characteristic op, is concretized as op
is disjoint with
independent continuant c, generically dependent continuant c, independent continuant c, generically dependent continuant c

specificityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000059

A data item that refers to the proportion of negatives in a binary classification test which are correctly identified
Source
WEB: http://en.wikipedia.org/wiki/Sensitivity_and_specificity
has super-classes
derived data from inferential statistical analysis c
has sub-classes
disease test specificity c

specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100051

A material entity that has the specimen role.
Source
GROUP: OBI Biomaterial Branch
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen; collecting a stone from a site.
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
has super-classes
object c

stacked bar chartc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/STATO_0000159

Stacked bar chart is a bar which is used to compare overall quantities across items while showing the contribution of category to the total amount. Stacked bar chart can be used for highlighting the total as they visually aggregate all of the categories in a group while indicating a part to whole relationship. The downside is that it becomes harder to compare the sizes of the individual categories.
has super-classes
bar chart c

stages and scalesc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#stages_and_scales

Is defined by
https://w3id.org/cmeo#
has super-classes
measurement c

standard errorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000235

A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution.
Source
group:OBI
Term status
http://purl.obolibrary.org/obo/IAO_0000125
has super-classes
quantitative confidence value c

standardized coefficientc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000085

A quantitative confidence value that has been standardized so that they have variances of 1.0; produces standardized regression coefficients (betas)
Source
WEB: SAS users guide
has super-classes
quantitative confidence value c

standardized mortality ratioc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000150

A data item which is the ratio of observed deaths in the study group to expected deaths in the general population.
Source
http://en.wikipedia.org/wiki/Standardized_mortality_ratio
has super-classes
derived data from inferential statistical analysis c

statistical conclusion validityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000151

An experimental validity that refers to the degree to which conclusions about the relationship among variables based on the data are correct or ‘reasonable’.
Source
http://en.wikipedia.org/wiki/Validity_(statistics)
has super-classes
experimental validity c

statistical errorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000082

A quantitative confidence value that represents unexplained variation in a collection of observations; comopnents of error include random error and lack of fit error
Source
WEB: http://www.itl.nist.gov/div898/handbook/pri/section7/pri7.htm
has super-classes
quantitative confidence value c
has sub-classes
lack of fit error c, type I error c, type II error c

study designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500000

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.
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
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.
has super-classes
plan specification c
has sub-classes
case-control study design c, clinical history design c, clinical study design c, intervention design c, observational design c, population based design c, randomized controlled trial design c, retrospective study design c

study design executionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000471

a planned process that carries out a study design
Is defined by
https://w3id.org/cmeo#
Source
branch derived
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
is equivalent to
planned process c and (realizes op some concretizes op some study design c)
has super-classes
planned process c

study design variable specificationc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#study_design_variable_specification

Is defined by
https://w3id.org/cmeo#
has super-classes
directive information entity c

study group rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000174

a study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Example 
The group of randomized participants that are assigned to a treatment arm of the trial
has super-classes
role c
has sub-classes
cluster study group role c, compound study group role c

study outcome specificationc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#study_outcome_specification

A Study Outcome/Endpoint Specification is a Plan Specification that defines the measurable variables used to assess the effectiveness or impact of an intervention, treatment, or observation within a study. Endpoints are classified into Primary Endpoints (the main variable of interest) and Secondary Endpoints (additional measures that provide supporting information).
Is defined by
https://w3id.org/cmeo#
has super-classes
directive information entity c
has sub-classes
primary outcome specification c, secondary outcome specification c

surgical procedure history exclusion criterionc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#surgical_procedure_history_exclusion_criterion

Is defined by
https://w3id.org/cmeo#
has super-classes
exclusion criterion c

surveillance processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002897

An investigation in which some entity is monitored, and data concerning that entity collected, interpreted, and disseminated, for the purpose of managing, directing, or protecting that entity, or some other entity.
Source
Shane Babcock, OBI
Term status
http://purl.obolibrary.org/obo/IAO_0000120
has super-classes
investigation c

symbolc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000028

An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
Source
based on Oxford English Dictionary
Term status
http://purl.obolibrary.org/obo/IAO_0000125
Example 
a serial number such as "12324X"
a stop sign
a written proper name such as "OBI"
has super-classes
information content entity c
has sub-classes
identifier c

symptomc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#symptom

Is defined by
https://w3id.org/cmeo#
has super-classes
sign or symptom c

temporal instantc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#temporal_instant

(Elucidation) A temporal instant is a zero-dimensional temporal region that has no proper temporal part
has super-classes
zero-dimensional temporal region c

temporal regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000008

has super-classes
occurrent c
has sub-classes
one-dimensional temporal region c, zero-dimensional temporal region c
is in range of
exists at op
is disjoint with
spatiotemporal region c, process c, process boundary c, spatiotemporal region c, process c, process boundary c

test statisticc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000013

A statistic measure that is a function of the samples and considered as a numberical summary of a data-set that reduces the data to one value that can be used to perform a hypothesis test. It can be used to test a finding for statistical signifiance
Source
WEB: http://en.wikipedia.org/wiki/Test_statistic
has super-classes
derived data from inferential statistical analysis c
has sub-classes
kappa statistic c

test validityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000053

A validity that refers to the degree to which evidence and theory support the interpretations of test scores (as entailed by proposed uses of tests).
Source
http://en.wikipedia.org/wiki/Validity_(statistics)
has super-classes
validity c

tetrachoric correlation coefficientc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/STATO_0000212

a tetrachoric correlation coefficient is a polychoric correlation coefficient for 2 dichotomous variables used as proxy for correlation between 2 continuous latent variables.
has super-classes
polychoric correlation coefficient c

textual entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000300

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.
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Example 
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
has super-classes
information content entity c
has sub-classes
email address c

three-dimensional spatial regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000028

Example 
a cube-shaped region of space
a sphere-shaped region of space,
has super-classes
spatial region c
is disjoint with
two-dimensional spatial region c, zero-dimensional spatial region c, one-dimensional spatial region c, two-dimensional spatial region c, zero-dimensional spatial region c, one-dimensional spatial region c

time to event measurementc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#time_to_event_measurement

Is defined by
https://w3id.org/cmeo#
has super-classes
measurement c

timeline specificationc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#timeline_specification

Is defined by
https://w3id.org/cmeo#
has super-classes
directive information entity c

transfer functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000383

A transfer function is a function to displace a material from one location to another.
Term status
http://purl.obolibrary.org/obo/IAO_0000122
has super-classes
function c

two-dimensional continuant fiat boundaryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000146

has super-classes
continuant fiat boundary c
is disjoint with
one-dimensional continuant fiat boundary c, one-dimensional continuant fiat boundary c, zero-dimensional continuant fiat boundary c

two-dimensional spatial regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000009

Example 
an infinitely thin plane in space.
the surface of a sphere-shaped part of space
has super-classes
spatial region c
is disjoint with
three-dimensional spatial region c, zero-dimensional spatial region c, one-dimensional spatial region c, three-dimensional spatial region c

type 1 error ratec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000078

A quantitative confidence value that refers to the probability of incorrectly concluding that there is a statistically significant difference in a dataset. Alpha is the number after a p-value. Thus, a statistically significant difference reported as p<0.05 means that there is less than a 5 percent chance that the difference could have occurred by chance.
Source
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
has super-classes
quantitative confidence value c

type 2 error ratec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000079

A quantitative confidence value that refers to the probability of incorrectly concluding that there was no statistically significant difference in a dataset. This error often reflects insufficient power of the study.
Source
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
has super-classes
quantitative confidence value c

type I errorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000100

A statistical error that the null hypothesis is true but has been rejected; a test result that indicates a given condition has been fulfilled, when it actually has not been fulfilled
Source
WEB: http://en.wikipedia.org/wiki/Type_I_and_type_II_errors
has super-classes
statistical error c

type II errorc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000101

A statistical error that the null hypothesis is false but has been accepted; a test result indicates that a condition failed, while it actually was successful.
Source
WEB: http://en.wikipedia.org/wiki/Type_I_and_type_II_errors
has super-classes
statistical error c

uncertaintyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000251

A disposition that inheres in some objects, which prevents accurate prediction or determination of the quality of a material entity. It is realized in objective process or subjective process.
has super-classes
disposition c

use of medication inclusion criterionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002558

An inclusion criterion that defines and states a a set of medications, which, if used by an entity, makes that entity suitable for a given task or participation in a given process.
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Example 
"received at least 2 days of vancomycin"
has super-classes
inclusion criterion c

validityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000060

A data item that refers to the extent to which a concept conclusion or measurement is well-founded and corresponds accurately to the real world.
Here is another definition: Validity is the extend to which an observation reflects the "truth" of the phenomenon being measured. Reference: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
Source
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
http://en.wikipedia.org/wiki/Validity_(statistics)
has super-classes
derived data from inferential statistical analysis c
has sub-classes
diagnostic validity c, experimental validity c, test validity c

value specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001933

An information content entity that specifies a value within a classification scheme or on a quantitative scale.
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
has super-classes
information content entity c
has sub-classes
categorical value specification c, missing value specification c, scalar value specification c
is in domain of
specifies value of op
is in range of
has value specification op

variablec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/STATO_0000258

A directive information entity that specifies a data item that can be measured or counted and is used in a statistical analysis.
Source
WEB: http://en.wikipedia.org/wiki/Variable_%28mathematics%29
WEB: http://www.abs.gov.au/websitedbs/a3121120.nsf/home/statistical+language+-+what+are+variables
has super-classes
data item c
has sub-classes
categorical variable c, continuous variable c, random variable c

Venn diagramc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000181

A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets.
Source
WEB: http://en.wikipedia.org/wiki/Venn_diagram
Term status
http://purl.obolibrary.org/obo/IAO_0000122
has super-classes
graph c

vital signc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#vital_sign

Is defined by
https://w3id.org/cmeo#
has super-classes
sign or symptom c

wearable devicec back to ToC or Class ToC

IRI: https://w3id.org/cmeo#wearable_device

Wearable devices such as activity trackers are an example of the Internet of things, since "things" such as electronics, software, sensors, and connectivity are effectors that enable objects to exchange data (including data quality[5]) through the internet with a manufacturer, operator, and/or other connected devices, without requiring human intervention.
has super-classes
device c
has sub-classes
sensor c

weightc back to ToC or Class ToC

IRI: https://w3id.org/cmeo#weight

has super-classes
morphology c

weighted datac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000014

A derived data from inferential statistical analysis that is obtained by applying a weighting process to adjust the impact of cases for representing the population from which the data sample is drawn.
Source
WEB: https://www.fedview.opm.gov/2010/reports/weighteddef.htm
has super-classes
derived data from inferential statistical analysis c
has sub-classes
weighted kappa c

weighted kappac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBCS_0000113

A weighted data that measures the agreement for categorical data; a generalization of the Kappa statistics to situations in which the categories are not equal in some respect so weighted by an objective or subjective function
Source
WEB: http://www.statistics.com
has super-classes
weighted data c

zero-dimensional continuant fiat boundaryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000147

Example 
the geographic North Pole
the point of origin of some spatial coordinate system.
the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
has super-classes
continuant fiat boundary c
is disjoint with
one-dimensional continuant fiat boundary c, one-dimensional continuant fiat boundary c, two-dimensional continuant fiat boundary c

zero-dimensional spatial regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000018

has super-classes
spatial region c
is disjoint with
three-dimensional spatial region c, two-dimensional spatial region c, one-dimensional spatial region c, three-dimensional spatial region c

zero-dimensional temporal regionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000148

Example 
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
has super-classes
temporal region c
has sub-classes
temporal instant c
is disjoint with
one-dimensional temporal region c

Object Properties

capable ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002215

A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
has domain
independent continuant c
has range
process c

concretizesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000059

A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
Example 
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
has domain
process c or specifically dependent continuant c
has range
generically dependent continuant c
is inverse of
is concretized as op

contains processop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000067

[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
is inverse of
occurs in op

denoted byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000235

inverse of the relation 'denotes'
has domain
entity c
has range
information content entity c
is inverse of
denotes op

denotesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000219

A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
Source
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
Example 
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
has super-properties
is about op
has domain
information content entity c
has range
entity c
is inverse of
denoted by op

DEPRECATED bearer ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0004097

Is deprecated
true

DEPRECATED inheres inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0004096

DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information.
Is deprecated
true

describesop back to ToC or Object Property ToC

IRI: https://w3id.org/cmeo#describes

disposition ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000092

This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
has super-properties
inheres in op
is inverse of
has disposition op

exists atop back to ToC or Object Property ToC

IRI: https://w3id.org/cmeo#exists_at

(Elucidation) exists at is a relation between a particular and some temporal region at which the particular exists
Example 
First World War exists at 1914-1916; Mexico exists at January 1, 2000
has domain
entity c
has range
temporal region c

function ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000079

a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
Example 
this catalysis function is a function of this enzyme
has super-properties
inheres in op
has domain
function c
is inverse of
has function op

has characteristicop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000053

Inverse of characteristic_of
Example 
this apple is bearer of this red color
this vase is bearer of this fragility

has characteristics: inverse functional

has sub-properties
has disposition op, has function op, has quality op, has role op
has range
specifically dependent continuant c
is inverse of
inheres in op

has direct partop back to ToC or Object Property ToC

IRI: https://w3id.org/cmeo#has_direct_part

has super-properties
has part op

has dispositionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000091

a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has super-properties
has characteristic op
has domain
independent continuant c
has range
disposition c
is inverse of
disposition of op

has functionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000085

a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
Example 
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
has super-properties
has characteristic op
has domain
independent continuant c
has range
function c
is inverse of
function of op

has grainop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000643

the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
Source
PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
Term status
http://purl.obolibrary.org/obo/IAO_0000120
has super-properties
has part op

has measurement unit labelop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000039

has characteristics: functional

has super-properties
has part op
has range
measurement unit label c

has memberop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002351

has member is a mereological relation between a collection and an item.
Source
SIO

has characteristics: irreflexive

has super-properties
has part op
is inverse of
member of op

has outputop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000299

The inverse property of is_specified_output_of
Term status
http://purl.obolibrary.org/obo/IAO_0000122
has super-properties
has participant op
has domain
planned process c
is inverse of
is output of op

has partop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000051

a core relation that holds between a whole and its part
Example 
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)

has characteristics: transitive

has sub-properties
has direct part op, has grain op, has measurement unit label op, has member op, has time stamp op, has value specification op
is inverse of
part of op

has participantop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000057

a relation between a process and a continuant, in which the continuant is somehow involved in the process
Source
http://www.obofoundry.org/ro/#OBO_REL:has_participant
Example 
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
has sub-properties
has output op, has_input op
has domain
occurrent c
has range
continuant c
is inverse of
participates in op

has qualityop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000086

a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
Example 
this apple has quality this red color
has super-properties
has characteristic op
has range
quality c
is inverse of
quality of op

has roleop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000087

a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
Example 
this person has role this investigator role (more colloquially: this person has this role of investigator)
has super-properties
has characteristic op
has domain
independent continuant c
has range
role c
is inverse of
role of op

has time stampop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000581

relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
Term status
http://purl.obolibrary.org/obo/IAO_0000123

has characteristics: functional

has super-properties
has part op

has value specificationop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001938

A relation between an information content entity and a value specification that specifies its value.
Source
OBI
Term status
http://purl.obolibrary.org/obo/IAO_0000120
has super-properties
has part op
has domain
information content entity c
has range
value specification c

has_inputop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000293

The inverse property of is_specified_input_of
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
see is_input_of example_of_usage
has super-properties
has participant op
has domain
planned process c
is inverse of
is input of op

immediately precedesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002090

X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
has super-properties
precedes op

inheres inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000052

a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
Example 
this fragility is a characteristic of this vase
this red color is a characteristic of this apple

has characteristics: functional

has sub-properties
disposition of op, function of op, quality of op, role of op
is inverse of
has characteristic op

is aboutop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000136

A (currently) primitive relation that relates an information artifact to an entity.
Source
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
Term status
http://purl.obolibrary.org/obo/IAO_0000125
Example 
This document is about information artifacts and their representations
has sub-properties
denotes op, specifies value of op
has domain
information content entity c

is concretized asop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000058

A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
Example 
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
has domain
generically dependent continuant c
has range
specifically dependent continuant c
is inverse of
concretizes op

is described byop back to ToC or Object Property ToC

IRI: https://w3id.org/cmeo#is_described_by

is grain ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000645

A relation between granular parts and the whole of which they are a part. Granular parts have indeterminate number such that removing one granular part does not necessarily damage or diminish the whole.
Source
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
Term status
http://purl.obolibrary.org/obo/IAO_0000120
has super-properties
part of op

is input ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000295

A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Example 
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
has super-properties
participates in op
has range
planned process c
is inverse of
has_input op

is output ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000312

A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
Term status
http://purl.obolibrary.org/obo/IAO_0000122
has super-properties
participates in op
has range
planned process c
is inverse of
has output op

is restricted toop back to ToC or Object Property ToC

IRI: https://w3id.org/cmeo#restricted_to

A is restricted to B iff A is a consent code and B is an investigation and A may only participate in instances of a class C, of which B is an instance.

located inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0001025

a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Source
http://www.obofoundry.org/ro/#OBO_REL:located_in
Example 
my brain is located in my head
this rat is located in this cage

has characteristics: transitive

has domain
independent continuant c
independent continuant c and (not (spatial region c))
has range
independent continuant c
independent continuant c and (not (spatial region c))
is inverse of
location of op

location ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0001015

a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Example 
my head is the location of my brain
this cage is the location of this rat

has characteristics: transitive

is inverse of
located in op

member ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002350

is member of is a mereological relation between a item and a collection.
Source
SIO
Example 
An organism that is a member of a population of organisms
has super-properties
part of op
is inverse of
has member op

obsolete_describesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000222

Is deprecated
true

obsolete_has_functionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000306

Relation between an independent continuant and a function.
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Is deprecated
true
Example 
heart has_function to-pump-blood

obsolete_has_qualityop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000298

A relation between an entity and a quality. For types: E has_quality Q iff: for any eEt, exists qQt such that q inheres_in e at t. For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality [GOC:cjm]
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Is deprecated
true

obsolete_has_roleop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000316

A relation between a continuant C and a role R. The reciprocal relation of role_of.
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Is deprecated
true

obsolete_is_concretization_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000294

Is a relationship between a generically dependent continuant and a specifically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter.
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true

obsolete_is_concretized_asop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000297

Is a relationship between a specifically dependent continuant and a generically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter.
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true

obsolete_is_described_byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_1110112

Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true

obsolete_is_realized_byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000300

Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Is deprecated
true

obsolete_materially denotesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000220

Is deprecated
true

obsolete_realizesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000308

Relation between a process and a function, where the unfolding of the process requires the execution of the function. Class level: P realizes F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation [GOC:cjm]
Term status
http://purl.obolibrary.org/obo/IAO_0000122
Is deprecated
true
Example 
example of usage: The process of 'histidine catabolism' (GO:0006548) realizes the 
function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity' 
denotes a function and not a process). We leave open the possibility of defining 
in future the sub-relations directly_realizes (as bewteen a function and it's 
functioning) and indirectly_realizes.

obsolete_representsop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000223

Is deprecated
true

obsolete_results_fromop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000365

Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true

obsolete_specifically denotesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000135

c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.
Source
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
Term status
http://purl.obolibrary.org/obo/IAO_0000125
Is deprecated
true
Example 
The process of creation is, for example,  writing down on paper the name of a friend by deliberately creating a certain pattern using ink.

Here the ink + paper is the independent continuant and the carrier is the pattern in the ink.

c = pattern in the ink
b = paper + ink
r = friend

obsoleted_has_specified_input_informationop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000315

A relation between a process and a participant in that process, that consumes a data set . The process is the realization of a concretization of a directive information entity (objective specification or plan specification). In general, not all data present at the beginning of the process are specified_data.
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true

obsoleted_has_specified_output_informationop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000301

A relation between a participant in a process, that produces a data set . The process is the realization of a concretization of a realizable information entity (objective specification or plan specification). In general, not all data present at the end of the process are specified_data.
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true

obsoleted_is_device_forop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000311

Relationship between a device and a protocol application in which it participates
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true
Example 
some LKB 1272 Clinigamma counter is_device_for instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay

obsoleted_is_reagent_inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000307

Relationship between a substance and a protocol application in which it participates, where the substance has a ReagentRole
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true
Example 
some Triton X-100 (Sigma-Aldrich) is_reagent_in instance of Chromium Release Assay described at  https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay

obsoleted_is_specified_information_intput_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000644

Is the inverse relation of has_specfied_input_information
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true

obsoleted_is_specified_information_output_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000459

A relation between a data set and the process in which it participates and was produced. Inverse of outputs_specified_data relation.
Source
Editor
Term status
http://purl.obolibrary.org/obo/IAO_0000120
Is deprecated
true

obsoleted_utilizes_deviceop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000313

Relationship between protocol application and an intrument in which it participates
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true
Example 
see example_of_usage for is_device_for

obsoleted_utilizes_reagentop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000309

Relationship between a protocol application and a substance that has role reagent that participates in the protocol application
Term status
http://purl.obolibrary.org/obo/IAO_0000123
Is deprecated
true
Example 
see example_of_usage for is_reagent_in

occurs inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000066

b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
has domain
occurrent c
has range
independent continuant c
is inverse of
contains process op
has sub-property chains
part of op o occurs in op
occurs in op o part of op

part ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000050

a core relation that holds between a part and its whole
Example 
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)

has characteristics: transitive

has sub-properties
is grain of op, member of op
is inverse of
has part op

participates inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000056

a relation between a continuant and a process, in which the continuant is somehow involved in the process
Example 
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
has sub-properties
is input of op, is output of op
has domain
continuant c
has range
occurrent c
is inverse of
has participant op

precedesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000063

x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.

has characteristics: transitive

has sub-properties
immediately precedes op
has domain
occurrent c
has range
occurrent c
has sub-property chains
part of op o precedes op

provisionsop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000646

A relation between an organisation or person and a material entity, where the organization or person provides or supplies the material entity for others to use
Term status
http://purl.obolibrary.org/obo/IAO_0000123

quality ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000080

a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
Example 
this red color is a quality of this apple
has super-properties
inheres in op
is inverse of
has quality op

realized inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000054

Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
Example 
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
has domain
realizable entity c
has range
process c
is inverse of
realizes op

realizesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000055

Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
Example 
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
has domain
process c
has range
realizable entity c
is inverse of
realized in op

role ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000081

a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
Example 
this investigator role is a role of this person
has super-properties
inheres in op
is inverse of
has role op

specifies value ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001927

A relation between a value specification and an entity which the specification is about.
Term status
http://purl.obolibrary.org/obo/IAO_0000123
has super-properties
is about op
has domain
value specification c

Data Properties

has valuedp back to ToC or Data Property ToC

IRI: https://w3id.org/cmeo#has_value

Named Individuals

ambidexterousni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000979

Term status
http://purl.obolibrary.org/obo/IAO_0000123
belongs to
categorical label c
has facts
editor preferred label ap "ambidexterous"
has curation status ap metadata incomplete ni

left handedni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000998

Term status
http://purl.obolibrary.org/obo/IAO_0000123
belongs to
categorical label c
has facts
editor preferred label ap "left handed"
has curation status ap metadata incomplete ni

right handedni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000958

Term status
http://purl.obolibrary.org/obo/IAO_0000123
belongs to
categorical label c
has facts
editor preferred label ap "right handed"
has curation status ap metadata incomplete ni

Thermo Fisher Scientificni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002193

An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific.
Source
https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific
Term status
http://purl.obolibrary.org/obo/IAO_0000120
belongs to
organization c
has facts
editor preferred label ap "Thermo Fisher Scientific"
has curation status ap metadata complete ni
textual definition ap "An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific."@en
term editor ap "Chris Stoeckert, Helena Ellis"
definition source ap "https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific"

SWRL rules

Rule #1back to ToC or SWRL ToC

has characteristic op(?e,?d) , disposition c(?d) -> has disposition op(?e,?d)

Rule #2back to ToC or SWRL ToC

has characteristic op(?e,?d) , quality c(?d) -> has quality op(?e,?d)

Rule #3back to ToC or SWRL ToC

has characteristic op(?e,?d) , role c(?d) -> has role op(?e,?d)

Rule #4back to ToC or SWRL ToC

has characteristic op(?e,?d) , function c(?d) -> has function op(?e,?d)

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties
ni: Named Individuals

References back to ToC

Add your references here. It is recommended to have them as a list.

Acknowledgments back to ToC

The authors would like to thank Silvio Peroni for developing LODE, a Live OWL Documentation Environment, which is used for representing the Cross Referencing Section of this document and Daniel Garijo for developing Widoco, the program used to create the template used in this documentation.