diff --git "a/duo/duo.owl" "b/duo/duo.owl" new file mode 100755--- /dev/null +++ "b/duo/duo.owl" @@ -0,0 +1,2748 @@ + + + + + + Contributors to the GA4GH Data Use Ontology workstream are listed at https://github.com/EBISPOT/DUO/blob/master/README.md#contributions + Melanie Courtot + http://creativecommons.org/licenses/by/4.0/ + + + + + + + + + + + DUO_preferred_label + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + is_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. + J. Neil Otte + E.g. A dataset is restricted to an instance of an investigation for a specific disease or at geographical location. + DUO:0000010 + is restricted to + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + consent code + DUO:0000001 + data use permission + + + + + + + + + A categorical data item indicating the primary category the consent code belongs to according to Dyke et al. 2016. + 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. + DUO:0000002 + obsolete consent code primary category + true + + + + + + + + + A categorical data item indicating the secondary category the consent code belongs to according to Dyke et al. 2016. + 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. + DUO:0000003 + obsolete consent code secondary category + true + + + + + + + + + This data use permission indicates there is no restriction on use. + DUO:0000004 + NRES + 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. + Note: the NRES alternative term may be confusing as in the UK it also stands for National Research Ethics Service + no restriction + + + + + + + + + This data use modifier indicates use for purposes of population, origin, or ancestry research is prohibited. + DUO:0000044 + NPOA + population origins or ancestry research prohibited + + + + + + + + + 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. + General Research Use, DUO_0000042 +Clinical Care USe, DUO_0000043 + DUO:0000005 + GRU-CC + 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 + This term was made obsolete as per https://github.com/EBISPOT/DUO/issues/45 + obsolete general research use and clinical care + + + + + + + + + This data use permission indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry. + DUO:0000006 + HMB + health or medical or biomedical research + + + + + + + + + + + + + + + This data use permission indicates that use is allowed provided it is related to the specified disease. + DUO:0000007 + DS + 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. + disease specific research + + + + + + + + + This data use permission indicates that use of the data is limited to the study of population origins or ancestry. + population origins/ancestry research + DUO:0000011 + POA + population origins or ancestry research only + + + + + + + + + + + + + + + This data use modifier indicates that use is limited to studies of a certain research type. + DUO:0000012 + RS + research specific restrictions + + + + + + + + + This data use limitation indicates that use is limited to research purposes (e.g., does not include its use in clinical care). + DUO:0000014 + RU + Deprecated as GRU-CC was split into GRU and CC, so this is not applicable anymore as a qualifier of GRU-CC + obsolete research use only + + + + + + + + + This data use modifier indicates that use does not allow methods development research (e.g., development of software or algorithms). + DUO:0000015 + NMDS + no general methods research + + + + + + + + + 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) + DUO:0000016 + GSO + genetic studies only + + + + + + + + + Data use modifiers indicate additional conditions for use. + DUO:0000017 + data use modifier + + + + + + + + + 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. + DUO:0000018 + NPUNCU + not for profit, non commercial use only + + + + + + + + + This data use modifier indicates that requestor agrees to make results of studies using the data available to the larger scientific community. + DUO:0000019 + PUB + publication required + + + + + + + + + This data use modifier indicates that the requestor must agree to collaboration with the primary study investigator(s). + DUO:0000020 + COL + This could be coupled with a string describing the primary study investigator(s). + collaboration required + + + + + + + + + This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval. + DUO:0000021 + IRB + ethics approval required + + + + + + + + + + + + + + + This data use modifier indicates that use is limited to within a specific geographic region. + DUO:0000022 + GS + This should be coupled with an ontology term describing the geographical location the restriction applies to. + geographical restriction + + + + + + + + + This data use modifier indicates that requestor agrees not to publish results of studies until a specific date. + publication embargo + DUO:0000024 + MOR + This should be coupled with a date specified as ISO8601 + publication moratorium + + + + + + + + + This data use modifier indicates that use is approved for a specific number of months. + DUO:0000025 + TS + This should be coupled with an integer value indicating the number of months. + time limit on use + + + + + + + + + This data use modifier indicates that use is limited to use by approved users. + DUO:0000026 + US + user specific restriction + + + + + + + + + This data use modifier indicates that use is limited to use within an approved project. + DUO:0000027 + PS + project specific restriction + + + + + + + + + This data use modifier indicates that use is limited to use within an approved institution. + DUO:0000028 + IS + institution specific restriction + + + + + + + + + This data use modifier indicates that the requestor must return derived/enriched data to the database/resource. + DUO:0000029 + RTN + return to database or resource + + + + + + + + + method development + An investigation concerning development of methods, algorithms, software or analytical tools. + This definition is a placeholder as a result of meetings at ICBO2018. + DUO:0000031 + method development + + + + + + + + + population research + An investigation concerning a specific population group. + This definition is a placeholder as a result of meetings at ICBO2018. + DUO:0000032 + Should be paired with the an ontology term representing this population (e.g., xxx). + population research + + + + + + + + + ancestry research + An investigation concerning ancestry or population origins. + This definition is a placeholder as a result of meetings at ICBO2018. + DUO:0000033 + ancestry research + + + + + + + + + age category research + An investigation concerning specific age categories. + This definition is a placeholder as a result of meetings at ICBO2018. + DUO:0000034 + Should be paired with the an ontology term representing this population (e.g., xxx). + age category research + + + + + + + + + gender category research + An investigation concerning specific gender categories. + This definition is a placeholder as a result of meetings at ICBO2018. + DUO:0000035 + Should be paired with the an ontology term representing this population (e.g., xxx). + gender category research + + + + + + + + + research control + An investigation concerning use of data as reference or control material. + This definition is a placeholder as a result of meetings at ICBO2018. + DUO:0000036 + research control + + + + + + + + + biomedical research + An investigation concerning health, medical, or biomedical research. + This definition is a placeholder as a result of meetings at ICBO2018. + DUO:0000037 + biomedical research + + + + + + + + + genetic research + Biomedical research concerning genetics (i.e., the study of genes, genetic variations and heredity). + This definition is a placeholder as a result of meetings at ICBO2018. + DUO:0000038 + genetic research + + + + + + + + + drug development research + Biomedical research concerning drug development. + This definition is a placeholder as a result of meetings at ICBO2018. + DUO:0000039 + drug development research + + + + + + + + + disease category research + Biomedical research research concerning specific disease/s + This definition is a placeholder as a result of meetings at ICBO2018. + DUO:0000040 + disease category research + + + + + + + + + This data use permission indicates that use is allowed for general research use for any research purpose. + DUO:0000042 + GRU + 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. + general research use + + + + + + + + + This data use modifier indicates that use is allowed for clinical use and care. + DUO:0000043 + CC + 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. + clinical care use + + + + + + + + + This data use modifier indicates that use of the data is limited to not-for-profit organizations. + DUO:0000045 + NPU + not for profit organisation use only + + + + + + + + + This data use modifier indicates that use of the data is limited to not-for-profit use. + DUO:0000046 + NCU + This indicates that data can be used by commercial organisations for research purposes, but not commercial purposes. + non-commercial use only + + + + + + + + + GAZ:00000448 + geographic location + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. + DOID:4 + EFO:0000408 + ICD10:N18 + ICD9:799.9 + MESH:D004194 + NCIT:C2991 + OGMS:0000031 + Orphanet:377788 + SCTID:64572001 + UMLS:C0012634 + condition + disease + disease or disorder + disease or disorder, non-neoplastic + diseases + diseases and disorders + disorder + disorders + medical condition + other disease + MONDO:0000001 + disease or disorder + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + topic:0003 + Topic + + + + + + + + + + + + + + +