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