duo.owl
type: Ontology
version IRI: duo.owl
imports: iao.owl
contributor: Contributors to the GA4GH Data Use Ontology workstream are listed at https://github.com/EBISPOT/DUO/blob/master/README.md#contributions
creator: Melanie Courtot
license: http://creativecommons.org/licenses/by/4.0/

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

data use permission
type: Class
subclass of: IAO_0000027
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 permission
IAO_0000115: This data use permission 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

population origins or ancestry research prohibited
type: Class
subclass of: data use modifier
IAO_0000115: This data use modifier indicates use for purposes of population, origin, or ancestry research is prohibited.
id: DUO:0000044
shorthand: NPOA

obsolete general research use and clinical care
type: Class
subclass of: ObsoleteClass
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.
IAO_0100001: General Research Use, DUO_0000042 Clinical Care USe, DUO_0000043
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
comment: This term was made obsolete as per https://github.com/EBISPOT/DUO/issues/45

health or medical or biomedical research
type: Class
subclass of: general research use
IAO_0000115: This data use permission 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 or disorder
IAO_0000115: This data use permission 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 to specify the disease the restriction applies to. DUO recommends MONDO be used, to provide the basis for automated evaluation. For more information see https://github.com/EBISPOT/DUO/blob/master/MONDO_Overview.md Other resources, such as the Disease Ontology, HPO, SNOMED-CT or others, can also be used. When those other resources are being used, this may require an extra mapping step to leverage automated matching algorithms.

population origins or ancestry research only
type: Class
subclass of: data use permission
IAO_0000115: This data use permission 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 modifier
subclass of: Restriction
  on property: is restricted to
  some values from: Topic
IAO_0000115: This data use modifier indicates that use is limited to studies of a certain research type.
id: DUO:0000012
shorthand: RS

obsolete research use only
type: Class
subclass of: ObsoleteClass
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
comment: Deprecated as GRU-CC was split into GRU and CC, so this is not applicable anymore as a qualifier of GRU-CC

no general methods research
type: Class
subclass of: data use modifier
IAO_0000115: This data use modifier indicates that use does not allow methods development research (e.g., development of software or algorithms).
id: DUO:0000015
shorthand: NMDS

genetic studies only
type: Class
subclass of: data use modifier
IAO_0000115: This data use modifier indicates that use is limited to genetic studies only (i.e., studies that include genotype research alone or both genotype and phenotype research, but not phenotype research exclusively)
id: DUO:0000016
shorthand: GSO

data use modifier
type: Class
subclass of: IAO_0000027
IAO_0000115: Data use modifiers indicate additional conditions for use.
id: DUO:0000017

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

publication required
type: Class
subclass of: data use modifier
IAO_0000115: This data use modifier 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 modifier
IAO_0000115: This data use modifier 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 modifier
IAO_0000115: This data use modifier 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 modifier
subclass of: Restriction
  on property: is restricted to
  some values from: geographic location
IAO_0000115: This data use modifier 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 modifier
IAO_0000115: This data use modifier 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 modifier
IAO_0000115: This data use modifier 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 modifier
IAO_0000115: This data use modifier indicates that use is limited to use by approved users.
id: DUO:0000026
shorthand: US

project specific restriction
type: Class
subclass of: data use modifier
IAO_0000115: This data use modifier 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 modifier
IAO_0000115: This data use modifier 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 modifier
IAO_0000115: This data use modifier 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 permission
IAO_0000115: This data use permission 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.

clinical care use
type: Class
subclass of: data use modifier
IAO_0000115: This data use modifier indicates that use is allowed for clinical use and care.
id: DUO:0000043
shorthand: CC
comment: Clinical Care is defined as Health care or services provided at home, in a healthcare facility or hospital. Data may be used for clinical decision making.

not for profit organisation use only
type: Class
subclass of: not for profit, non commercial use only
IAO_0000115: This data use modifier indicates that use of the data is limited to not-for-profit organizations.
id: DUO:0000045
shorthand: NPU

non-commercial use only
type: Class
subclass of: not for profit, non commercial use only
IAO_0000115: This data use modifier indicates that use of the data is limited to not-for-profit use.
id: DUO:0000046
shorthand: NCU
comment: This indicates that data can be used by commercial organisations for research purposes, but not commercial purposes.

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

disease or disorder
type: Class
subclass of: BFO_0000016
IAO_0000115: A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
has db xref: DOID:4
has db xref: EFO:0000408
has db xref: ICD10:N18
has db xref: ICD9:799.9
has db xref: MESH:D004194
has db xref: NCIT:C2991
has db xref: OGMS:0000031
has db xref: Orphanet:377788
has db xref: SCTID:64572001
has db xref: UMLS:C0012634
has exact synonym: condition
has exact synonym: disease
has exact synonym: disease or disorder
has exact synonym: disease or disorder, non-neoplastic
has exact synonym: diseases
has exact synonym: diseases and disorders
has exact synonym: disorder
has exact synonym: disorders
has exact synonym: medical condition
has exact synonym: other disease
id: MONDO:0000001

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