duo.owl
type: Ontology
version IRI: duo.owl
imports: iao.owl
contributor: Cooper Stansbury
contributor: David An
contributor: Dylan Spalding
contributor: Giselle Kerry
contributor: Gregory Rushton
contributor: J. Neil Otte
contributor: Moran Ncabili
contributor: Stephanie Dyke
creator: Melanie Courtot

DUO_preferred_label
type: AnnotationProperty

is restricted to
type: ObjectProperty
DUO_preferred_label: is_restricted_to
IAO_0000115: 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.
IAO_0000117: J. Neil Otte
IAO_0000232: E.g. A dataset is restricted to an instance of an investigation for a specific disease or at geographical location.
id: DUO:0000010

disease
type: Class
subclass of: BFO_0000016
IAO_0000115: A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. [url:http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf ]
id: DOID:4

data use limitation
type: Class
subclass of: IAO_0000027
DUO_preferred_label: data use limitation
IAO_0000115: 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.
IAO_0000118: consent code
id: DUO:0000001

obsolete consent code primary category
type: Class
subclass of: ObsoleteClass
IAO_0000115: A categorical data item indicating the primary category the consent code belongs to according to Dyke et al. 2016.
IAO_0000231: This term was depreacted as it is not used to tag datasets but instead as patterns for DUO codes capture. This is an archive specific requirement, e.g. "one code from a primary category and one or more from a second category' This is better done by Schemablocks and constraining the pattern of usage of DUO terms at each archive level.
id: DUO:0000002
deprecated: true

obsolete consent code secondary category
type: Class
subclass of: ObsoleteClass
IAO_0000115: A categorical data item indicating the secondary category the consent code belongs to according to Dyke et al. 2016.
IAO_0000231: This term was depreacted as it is not used to tag datasets but instead as patterns for DUO codes capture. This is an archive specific requirement, e.g. "one code from a primary category and one or more from a second category' This is better done by Schemablocks and constraining the pattern of usage of DUO terms at each archive level.
id: DUO:0000003
deprecated: true

no restriction
type: Class
subclass of: data use limitation
DUO_preferred_label: no restriction
IAO_0000115: This data use limitation indicates there is no restriction on use.
id: DUO:0000004
shorthand: NRES
comment: 20180907, Meeting Moran Melanie: This is to be thought about more carefully - what is the intent when using 'no restriction' as usually users still need to be researchers.
comment: Note: the NRES alternative term may be confusing as in the UK it also stands for National Research Ethics Service

general research use and clinical care
type: Class
subclass of: general research use
DUO_preferred_label: general research use and clinical care
IAO_0000115: This data use limitation indicates that use is allowed for health/medical/biomedical purposes and other biological research, including the study of population origins or ancestry.
id: DUO:0000005
shorthand: GRU-CC
comment: This term includes clinical care, which was not defined in the original consent codes paper. This term does not have a usage in our current use cases and we recommend using DUO:0000042, General Research Use, instead

health or medical or biomedical research
type: Class
subclass of: general research use
DUO_preferred_label: health/medical/biomedical research
IAO_0000115: This data use limitation indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry.
id: DUO:0000006
shorthand: HMB

disease specific research
type: Class
subclass of: health or medical or biomedical research
subclass of: Restriction
  on property: is restricted to
  some values from: disease
DUO_preferred_label: disease-specific research
IAO_0000115: This data use limitation indicates that use is allowed provided it is related to the specified disease.
id: DUO:0000007
shorthand: DS
comment: This term should be coupled with a term describing a disease from an ontology, such as the Disease Ontology, HPO, MonDO to specify the disease the restriction applies to.

population origins or ancestry research
type: Class
subclass of: general research use
DUO_preferred_label: population origins or ancestry research
IAO_0000115: This data use limitation indicates that use of the data is limited to the study of population origins or ancestry.
IAO_0000118: population origins/ancestry research
id: DUO:0000011
shorthand: POA

research specific restrictions
type: Class
subclass of: data use limitation
subclass of: Restriction
  on property: is restricted to
  some values from: Topic
DUO_preferred_label: research-specific restrictions
IAO_0000115: This data use limitation indicates that use is limited to studies of a certain research type.
id: DUO:0000012
shorthand: RS

research use only
type: Class
subclass of: data use limitation
DUO_preferred_label: research use only
IAO_0000115: This data use limitation indicates that use is limited to research purposes (e.g., does not include its use in clinical care).
id: DUO:0000014
shorthand: RU

no general methods research
type: Class
subclass of: data use limitation
DUO_preferred_label: no general methods research
IAO_0000115: This data use limitation indicates that use includes methods development research(e.g., development of software or algorithms) only within the bounds of other use limitations.
id: DUO:0000015

genetic studies only
type: Class
subclass of: data use limitation
DUO_preferred_label: genetic studies only
IAO_0000115: This data use limitation indicates that use is limited to genetic studies only (i.e., no phenotype-only research)
id: DUO:0000016
shorthand: GSO

data use requirements
type: Class
subclass of: IAO_0000027
DUO_preferred_label: data use requirements
IAO_0000115: Requirements indicate additional conditions set for use.
id: DUO:0000017

not for profit use only
type: Class
subclass of: data use requirements
DUO_preferred_label: not-for-profit use only
IAO_0000115: This requirement indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use.
IAO_0000118: non-commercial use
id: DUO:0000018
shorthand: NPU

publication required
type: Class
subclass of: data use requirements
DUO_preferred_label: publication required
IAO_0000115: This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community.
id: DUO:0000019
shorthand: PUB

collaboration required
type: Class
subclass of: data use requirements
DUO_preferred_label: collaboration required
IAO_0000115: This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s).
id: DUO:0000020
shorthand: COL
comment: This could be coupled with a string describing the primary study investigator(s).

ethics approval required
type: Class
subclass of: data use requirements
DUO_preferred_label: ethics approval required
IAO_0000115: This requirement indicates that the requestor must provide documentation of local IRB/ERB approval.
id: DUO:0000021
shorthand: IRB

geographical restriction
type: Class
subclass of: data use requirements
subclass of: Restriction
  on property: is restricted to
  some values from: geographic location
DUO_preferred_label: geographical restriction
IAO_0000115: This requirement indicates that use is limited to within a specific geographic region.
id: DUO:0000022
shorthand: GS
comment: This should be coupled with an ontology term describing the geographical location the restriction applies to.

publication moratorium
type: Class
subclass of: data use requirements
DUO_preferred_label: publication moratorium
IAO_0000115: This requirement indicates that requestor agrees not to publish results of studies until a specific date
IAO_0000118: publication embargo
id: DUO:0000024
shorthand: MOR
comment: This should be coupled with a date specified as ISO8601

time limit on use
type: Class
subclass of: data use requirements
DUO_preferred_label: time limit on use
IAO_0000115: This requirement indicates that use is approved for a specific number of months.
id: DUO:0000025
shorthand: TS
comment: This should be coupled with an integer value indicating the number of months.

user specific restriction
type: Class
subclass of: data use requirements
DUO_preferred_label: user-specific restriction
IAO_0000115: This requirement indicates that use is limited to use by approved users.
id: DUO:0000026
shorthand: US

project specific restriction
type: Class
subclass of: data use requirements
DUO_preferred_label: project-specific restriction
IAO_0000115: This requirement indicates that use is limited to use within an approved project.
id: DUO:0000027
shorthand: PS

institution specific restriction
type: Class
subclass of: data use requirements
DUO_preferred_label: institution-specific restriction
IAO_0000115: This requirement indicates that use is limited to use within an approved institution.
id: DUO:0000028
shorthand: IS

return to database or resource
type: Class
subclass of: data use requirements
DUO_preferred_label: return to database/resource
IAO_0000115: This requirement indicates that the requestor must return derived/enriched data to the database/resource.
id: DUO:0000029
shorthand: RTN

method development
type: Class
subclass of: OBI_0000066
DUO_preferred_label: method development
IAO_0000115: An investigation concerning development of methods, algorithms, software or analytical tools.
IAO_0000232: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000031

population research
type: Class
subclass of: OBI_0000066
DUO_preferred_label: population research
IAO_0000115: An investigation concerning a specific population group.
IAO_0000232: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000032
comment: Should be paired with the an ontology term representing this population (e.g., xxx).

ancestry research
type: Class
subclass of: OBI_0000066
DUO_preferred_label: ancestry research
IAO_0000115: An investigation concerning ancestry or population origins.
IAO_0000232: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000033

age category research
type: Class
subclass of: OBI_0000066
DUO_preferred_label: age category research
IAO_0000115: An investigation concerning specific age categories.
IAO_0000232: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000034
comment: Should be paired with the an ontology term representing this population (e.g., xxx).

gender category research
type: Class
subclass of: OBI_0000066
DUO_preferred_label: gender category research
IAO_0000115: An investigation concerning specific gender categories.
IAO_0000232: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000035
comment: Should be paired with the an ontology term representing this population (e.g., xxx).

research control
type: Class
subclass of: OBI_0000066
DUO_preferred_label: research control
IAO_0000115: An investigation concerning use of data as reference or control material.
IAO_0000232: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000036

biomedical research
type: Class
subclass of: OBI_0000066
DUO_preferred_label: biomedical research
IAO_0000115: An investigation concerning health, medical, or biomedical research.
IAO_0000232: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000037

genetic research
type: Class
subclass of: biomedical research
DUO_preferred_label: genetic research
IAO_0000115: Biomedical research concerning genetics (i.e., the study of genes, genetic variations and heredity).
IAO_0000232: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000038

drug development research
type: Class
subclass of: biomedical research
DUO_preferred_label: drug development research
IAO_0000115: Biomedical research concerning drug development.
IAO_0000232: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000039

disease category research
type: Class
subclass of: biomedical research
DUO_preferred_label: disease category research
IAO_0000115: Biomedical research research concerning specific disease/s
IAO_0000232: This definition is a placeholder as a result of meetings at ICBO2018.
id: DUO:0000040

general research use
type: Class
subclass of: data use limitation
DUO_preferred_label: general research use
IAO_0000115: This data use limitation indicates that use is allowed for general research use for any research purpose.
id: DUO:0000042
shorthand: GRU
comment: This includes but is not limited to: health/medical/biomedical purposes, fundamental biology research, the study of population origins or ancestry, statistical methods and algorithms development, and social-sciences research.

geographic location
type: Class
subclass of: BFO_0000029
id: GAZ:00000448

Topic
type: Class
subclass of: IAO_0000030
IAO_0000115: A category denoting a rather broad domain or field of interest, study, application, work, data, or technology. Topics have no clearly defined borders between each other.
id: topic:0003