diff --git a/duo-basic.owl b/duo-basic.owl index 334c267..59b06f3 100644 --- a/duo-basic.owl +++ b/duo-basic.owl @@ -9,10 +9,12 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:skos="http://www.w3.org/2004/02/skos/core#" + xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -68,21 +70,13 @@ - editor preferred label - editor preferred label - editor preferred term editor preferred term - editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - editor preferred label - editor preferred label - editor preferred term editor preferred term - editor preferred term~editor preferred label @@ -90,7 +84,7 @@ - example + example of usage A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober @@ -120,7 +114,6 @@ PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot - OBI_0000281 has curation status @@ -130,10 +123,7 @@ definition - definition - textual definition - The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith @@ -159,8 +149,6 @@ We also have the outstanding issue of how to aim different definitions to differ GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition - definition - textual definition @@ -172,7 +160,7 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober - GROUP:OBI:<http://purl.obfoundry.org/obo/obi> + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note @@ -213,9 +201,9 @@ We also have the outstanding issue of how to aim different definitions to differ definition source - formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 + Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source @@ -251,13 +239,13 @@ We also have the outstanding issue of how to aim different definitions to differ - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - An IRI or similar locator for a request or discussion of an ontology term. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'tracker item' can associate a tracker with a specific ontology term. + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'tracker item' can associate a tracker with a specific ontology term. term tracker item @@ -266,10 +254,11 @@ We also have the outstanding issue of how to aim different definitions to differ + ontology term requester - The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester @@ -280,10 +269,10 @@ We also have the outstanding issue of how to aim different definitions to differ is denotator type - relates an class defined in an ontology, to the type of it's denotator - In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') - Alan Ruttenberg - is denotator type + Relates an class defined in an ontology, to the type of it's denotator + In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') + Alan Ruttenberg + is denotator type @@ -312,7 +301,7 @@ Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall + Chris Mungall expand expression to @@ -348,7 +337,7 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. antisymmetric property part_of antisymmetric property xsd:true - use boolean value xsd:true to indicate that the property is an antisymmetric property + Use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property @@ -361,7 +350,7 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. - The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . + The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall @@ -375,14 +364,15 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + has ID digit count + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" - Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) - Person:Alan Ruttenberg + Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) + Person:Alan Ruttenberg has ID digit count @@ -391,12 +381,13 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. - Datatype: idrange:1 + has ID range allocated + Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] - Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms - Person:Alan Ruttenberg + Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms + Person:Alan Ruttenberg has ID range allocated to @@ -405,15 +396,16 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + has ID policy for + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" - Relating an ontology used to record id policy to the ontology namespace whose policy it manages - Person:Alan Ruttenberg - has ID policy for + Relating an ontology used to record id policy to the ontology namespace whose policy it manages + Person:Alan Ruttenberg + has ID policy for @@ -421,14 +413,15 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + has ID prefix + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" - Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. - Person:Alan Ruttenberg + Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. + Person:Alan Ruttenberg has ID prefix @@ -477,9 +470,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] is allocated id range - Add as annotation triples in the granting ontology Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" PERSON:Alan Ruttenberg + Add as annotation triples in the granting ontology is allocated id range @@ -490,22 +483,33 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] retired from use as of relates a class of CRID to the date after which further instances should not be made, according to the central authority - In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp - Alan Ruttenberg + In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp + Alan Ruttenberg retired from use as of + + + + has ontology root term + Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. + Nicolas Matentzoglu + has ontology root term + + + + - A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. - David Osumi-Sutherland - #40 - VFB - 2018-09-21T16:43:39Z - Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + may be identical to + A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. + David Osumi-Sutherland + #40 + VFB + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. may be identical to @@ -514,6 +518,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + scheduled for obsoletion on or after Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. Chris Mungall, Jie Zheng https://github.com/geneontology/go-ontology/issues/15532 @@ -543,10 +548,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] term replaced by - Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg + Add as annotation triples in the granting ontology term replaced by @@ -657,6 +662,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + @@ -669,21 +680,27 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + - + - + - + - + + + + - + + + + @@ -701,10 +718,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - label - label - + @@ -714,12 +728,24 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + @@ -740,11 +766,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - data use limitation - 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. + 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 limitation + data use permission @@ -753,27 +778,24 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - no restriction - This data use limitation indicates there is no restriction on use. + 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 + no restriction - + - - - general research use and clinical care - 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. - 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 - general research use and clinical care + + + 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 @@ -782,11 +804,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - health/medical/biomedical research - This data use limitation indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry. + 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 + health or medical or biomedical research @@ -795,12 +816,15 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - disease-specific research - This data use limitation indicates that use is allowed provided it is related to the specified disease. + 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, such as the Disease Ontology, HPO, MonDO to specify the disease the restriction applies to. - disease specific research + 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 @@ -808,13 +832,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - population origins or ancestry research - This data use limitation indicates that use of the data is limited to the study of population origins or ancestry. + + 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 + population origins or ancestry research only @@ -822,25 +845,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - research-specific restrictions - This data use limitation indicates that use is limited to studies of a certain research type. + + This data use modifier indicates that use is limited to studies of a certain research type. DUO:0000012 RS - research specific restrictions - - - - - - - - - research use only - 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 - research use only + research specific restrictions @@ -848,11 +857,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - no general methods research - 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. + + This data use modifier indicates that use does not allow methods development research (e.g., development of software or algorithms). DUO:0000015 - no general methods research + NMDS + no general methods research @@ -860,12 +869,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - genetic studies only - This data use limitation indicates that use is limited to genetic studies only (i.e., no phenotype-only 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 + genetic studies only @@ -873,10 +881,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - data use requirements - Requirements indicate additional conditions set for use. + Data use modifiers indicate additional conditions for use. DUO:0000017 - data use requirements + data use modifier @@ -885,12 +892,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - not-for-profit use only - This requirement indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use. - non-commercial use + 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 - NPU - not for profit use only + NPUNCU + not for profit, non commercial use only @@ -899,11 +904,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - publication required - This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community. + 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 + publication required @@ -912,12 +916,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - collaboration required - This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). + 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 + collaboration required @@ -926,11 +929,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - ethics approval required - This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. + This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval. DUO:0000021 IRB - ethics approval required + ethics approval required @@ -939,12 +941,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - geographical restriction - This requirement indicates that use is limited to within a specific geographic region. + 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 + geographical restriction @@ -953,13 +954,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - publication moratorium - This requirement indicates that requestor agrees not to publish results of studies until a specific date - publication embargo + 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 + publication moratorium @@ -968,12 +968,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - time limit on use - This requirement indicates that use is approved for a specific number of months. + 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 + time limit on use @@ -982,11 +981,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - user-specific restriction - This requirement indicates that use is limited to use by approved users. + This data use modifier indicates that use is limited to use by approved users. DUO:0000026 US - user specific restriction + user specific restriction @@ -995,11 +993,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - project-specific restriction - This requirement indicates that use is limited to use within an approved project. + This data use modifier indicates that use is limited to use within an approved project. DUO:0000027 PS - project specific restriction + project specific restriction @@ -1008,11 +1005,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - institution-specific restriction - This requirement indicates that use is limited to use within an approved institution. + This data use modifier indicates that use is limited to use within an approved institution. DUO:0000028 IS - institution specific restriction + institution specific restriction @@ -1021,8 +1017,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - return to database/resource - This requirement indicates that the requestor must return derived/enriched data to the database/resource. + 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 @@ -1167,12 +1162,49 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - general research use - This data use limitation indicates that use is allowed for general research use for any research purpose. + 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 + 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 diff --git a/duo.csv b/duo.csv index e46a0bd..1ef1a0c 100644 --- a/duo.csv +++ b/duo.csv @@ -1,21 +1,26 @@ id,shorthand,label,description -DUO:0000021,IRB,ethics approval required,This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. -DUO:0000006,HMB,health or medical or biomedical research,This data use limitation indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry. -DUO:0000019,PUB,publication required,This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community. -DUO:0000026,US,user specific restriction,This requirement indicates that use is limited to use by approved users. -DUO:0000020,COL,collaboration required,This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). -DUO:0000005,GRU-CC,general research use and clinical care,"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." -DUO:0000018,NPU,not for profit use only,"This requirement indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use." -DUO:0000012,RS,research specific restrictions,This data use limitation indicates that use is limited to studies of a certain research type. -DUO:0000025,TS,time limit on use,This requirement indicates that use is approved for a specific number of months. -DUO:0000004,NRES,no restriction,This data use limitation indicates there is no restriction on use. -DUO:0000011,POA,population origins or ancestry research,This data use limitation indicates that use of the data is limited to the study of population origins or ancestry. -DUO:0000024,MOR,publication moratorium,This requirement indicates that requestor agrees not to publish results of studies until a specific date -DUO:0000016,GSO,genetic studies only,"This data use limitation indicates that use is limited to genetic studies only (i.e., no phenotype-only research)" -DUO:0000029,RTN,return to database or resource,This requirement indicates that the requestor must return derived/enriched data to the database/resource. -DUO:0000028,IS,institution specific restriction,This requirement indicates that use is limited to use within an approved institution. -DUO:0000022,GS,geographical restriction,This requirement indicates that use is limited to within a specific geographic region. -DUO:0000007,DS,disease specific research,This data use limitation indicates that use is allowed provided it is related to the specified disease. -DUO:0000042,GRU,general research use,This data use limitation indicates that use is allowed for general research use for any research purpose. -DUO:0000014,RU,research use only,"This data use limitation indicates that use is limited to research purposes (e.g., does not include its use in clinical care)." -DUO:0000027,PS,project specific restriction,This requirement indicates that use is limited to use within an approved project. +DUO:0000021,IRB,ethics approval required,This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval. +DUO:0000006,HMB,health or medical or biomedical research,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:0000019,PUB,publication required,This data use modifier indicates that requestor agrees to make results of studies using the data available to the larger scientific community. +DUO:0000026,US,user specific restriction,This data use modifier indicates that use is limited to use by approved users. +DUO:0000044,NPOA,population origins or ancestry research prohibited,"This data use modifier indicates use for purposes of population, origin, or ancestry research is prohibited." +DUO:0000020,COL,collaboration required,This data use modifier indicates that the requestor must agree to collaboration with the primary study investigator(s). +DUO:0000046,NCU,non-commercial use only,This data use modifier indicates that use of the data is limited to not-for-profit use. +DUO:0000018,NPUNCU,"not for profit, non commercial use only","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:0000012,RS,research specific restrictions,This data use modifier indicates that use is limited to studies of a certain research type. +DUO:0000025,TS,time limit on use,This data use modifier indicates that use is approved for a specific number of months. +DUO:0000004,NRES,no restriction,This data use permission indicates there is no restriction on use. +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 organizations. +DUO:0000017,,data use modifier,Data use modifiers indicate additional conditions for use. +DUO:0000011,POA,population origins or ancestry research only,This data use permission indicates that use of the data is limited to the study of population origins or ancestry. +DUO:0000024,MOR,publication moratorium,This data use modifier indicates that requestor agrees not to publish results of studies until a specific date. +DUO:0000016,GSO,genetic studies only,"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:0000029,RTN,return to database or resource,This data use modifier indicates that the requestor must return derived/enriched data to the database/resource. +DUO:0000043,CC,clinical care use,This data use modifier indicates that use is allowed for clinical use and care. +DUO:0000015,NMDS,no general methods research,"This data use modifier indicates that use does not allow methods development research (e.g., development of software or algorithms)." +DUO:0000028,IS,institution specific restriction,This data use modifier indicates that use is limited to use within an approved institution. +DUO:0000022,GS,geographical restriction,This data use modifier indicates that use is limited to within a specific geographic region. +DUO:0000007,DS,disease specific research,This data use permission indicates that use is allowed provided it is related to the specified disease. +DUO:0000001,,data use permission,"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." +DUO:0000042,GRU,general research use,This data use permission indicates that use is allowed for general research use for any research purpose. +DUO:0000027,PS,project specific restriction,This data use modifier indicates that use is limited to use within an approved project. diff --git a/duo.owl b/duo.owl index 015981a..9a12602 100644 --- a/duo.owl +++ b/duo.owl @@ -9,21 +9,16 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:dcterms="dcterms:" + xmlns:skos="http://www.w3.org/2004/02/skos/core#" + xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + - Cooper Stansbury - David An - Dylan Spalding - Giselle Kerry - Gregory Rushton - J. Neil Otte - Moran Ncabili - Stephanie Dyke + 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/ @@ -47,6 +42,18 @@ + + + + + + + + + + + + @@ -59,6 +66,12 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -382,26 +443,14 @@ - - - - - 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 ] - DOID:4 - disease - - - - - data use limitation - 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. + 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 limitation + data use permission @@ -438,13 +487,24 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - no restriction - This data use limitation indicates there is no restriction on use. + 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 + 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 @@ -452,13 +512,15 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - - general research use and clinical care - 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. + + 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 - general research use and clinical care + This term was made obsolete as per https://github.com/EBISPOT/DUO/issues/45 + obsolete general research use and clinical care @@ -467,11 +529,10 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - health/medical/biomedical research - This data use limitation indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry. + 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 + health or medical or biomedical research @@ -483,15 +544,18 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - + - disease-specific research - This data use limitation indicates that use is allowed provided it is related to the specified disease. + 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, such as the Disease Ontology, HPO, MonDO to specify the disease the restriction applies to. - disease specific research + 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 @@ -499,13 +563,12 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - - population origins or ancestry research - This data use limitation indicates that use of the data is limited to the study of population origins or ancestry. + + 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 + population origins or ancestry research only @@ -513,18 +576,17 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - + - research-specific restrictions - This data use limitation indicates that use is limited to studies of a certain research type. + This data use modifier indicates that use is limited to studies of a certain research type. DUO:0000012 RS - research specific restrictions + research specific restrictions @@ -532,12 +594,12 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - - research use only - This data use limitation indicates that use is limited to research purposes (e.g., does not include its use in clinical care). + + 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 - research use only + 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 @@ -545,11 +607,11 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - - no general methods research - 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. + + This data use modifier indicates that use does not allow methods development research (e.g., development of software or algorithms). DUO:0000015 - no general methods research + NMDS + no general methods research @@ -557,12 +619,11 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - - genetic studies only - This data use limitation indicates that use is limited to genetic studies only (i.e., no phenotype-only 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 + genetic studies only @@ -571,10 +632,9 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - data use requirements - Requirements indicate additional conditions set for use. + Data use modifiers indicate additional conditions for use. DUO:0000017 - data use requirements + data use modifier @@ -583,12 +643,10 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - not-for-profit use only - This requirement indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use. - non-commercial use + 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 - NPU - not for profit use only + NPUNCU + not for profit, non commercial use only @@ -597,11 +655,10 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - publication required - This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community. + 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 + publication required @@ -610,12 +667,11 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - collaboration required - This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). + 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 + collaboration required @@ -624,11 +680,10 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - ethics approval required - This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. + This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval. DUO:0000021 IRB - ethics approval required + ethics approval required @@ -643,12 +698,11 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - geographical restriction - This requirement indicates that use is limited to within a specific geographic region. + 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 + geographical restriction @@ -657,13 +711,12 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - publication moratorium - This requirement indicates that requestor agrees not to publish results of studies until a specific date - publication embargo + 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 + publication moratorium @@ -672,12 +725,11 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - time limit on use - This requirement indicates that use is approved for a specific number of months. + 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 + time limit on use @@ -686,11 +738,10 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - user-specific restriction - This requirement indicates that use is limited to use by approved users. + This data use modifier indicates that use is limited to use by approved users. DUO:0000026 US - user specific restriction + user specific restriction @@ -699,11 +750,10 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - project-specific restriction - This requirement indicates that use is limited to use within an approved project. + This data use modifier indicates that use is limited to use within an approved project. DUO:0000027 PS - project specific restriction + project specific restriction @@ -712,11 +762,10 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - institution-specific restriction - This requirement indicates that use is limited to use within an approved institution. + This data use modifier indicates that use is limited to use within an approved institution. DUO:0000028 IS - institution specific restriction + institution specific restriction @@ -725,8 +774,7 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - return to database/resource - This requirement indicates that the requestor must return derived/enriched data to the database/resource. + 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 @@ -871,12 +919,49 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - general research use - This data use limitation indicates that use is allowed for general research use for any research purpose. + 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 + 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 @@ -967,6 +1052,7 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO + @@ -1755,6 +1841,22 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO + + + + + + + + + + + + + + + + @@ -1806,7 +1908,7 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - + @@ -2219,6 +2321,30 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO + + + + + + + + + + + + + + + + + + + + + + + + @@ -2227,6 +2353,70 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2395,6 +2585,43 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO + + + + + 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 + + + + + + + + + + @@ -2419,6 +2646,14 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO + + + + + + + + @@ -2435,18 +2670,10 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - - - - - - - - - + @@ -2475,14 +2702,6 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - - - - - - - - @@ -2518,51 +2737,11 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 2582008..da7de15 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -13,8 +13,8 @@ all: $(ONT).owl $(ONT)-basic.owl $(ONT).csv test:all prepare_release: - $(ROBOT) reason -i $(SRC) -r ELK relax reduce -r ELK annotate -V $(BASE)/releases/`date +%Y-%m-%d`/$(ONT).owl -o $(ONT).owl - cp $(ONT).owl $(RELEASEDIR) &&\ + $(ROBOT) reason -i $(SRC) -r ELK relax reduce -r ELK annotate -V $(BASE)/releases/`date +%Y-%m-%d`/$(ONT).owl -o $(ONT).owl + cp $(ONT).owl $(ONT)-basic.owl $(ONT).csv $(RELEASEDIR) &&\ git add $(RELEASEDIR)/*.owl echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release on github" @@ -22,32 +22,9 @@ prepare_release: $(ONT).owl: $(SRC) $(ROBOT) reason -i $< -r ELK relax reduce -r ELK annotate -V $(BASE)/releases/`date +%Y-%m-%d`/$(ONT).owl -o $@ -# remove OBO which doesn't work with IAO and is not needed -#$(ONT).obo: $(ONT).owl -# $(ROBOT) convert -i $< -f obo -o $(ONT).obo.tmp && mv $(ONT).obo.tmp $@ - - -# IMPORTS = iao bfo -# IMPORTS_OWL = $(patsubst %, imports/%_import.owl,$(IMPORTS)) - -# # Make this target to regenerate ALL -# all_imports: $(IMPORTS_OWL) - -# # Use ROBOT, driven entirely by terms lists NOT from source ontology -# imports/%_import.owl: mirror/%.owl imports/%_terms.txt -# $(ROBOT) extract -i $< -T imports/$*_terms.txt --method BOT -O $(BASE)/$@ -o $@ -# .PRECIOUS: imports/%_import.owl - -# remove OBO which doesn't work with IAO and is not needed -# imports/%_import.obo: imports/%_import.owl -# $(OWLTOOLS) $(USECAT) $< -o -f obo $@ - -# clone remote ontology locally, performing some excision of relations and annotations - - - $(ONT)-basic.owl: $(ONT).owl root-terms.txt $(ROBOT) merge -i $(ONT).owl filter --term-file root-terms.txt --select "annotations self descendants ontology" annotate --ontology-iri $(BASE)-basic.owl -V $(BASE)/releases/`date +%Y-%m-%d`/$(ONT)-basic.owl -o $@ + $(ONT).csv: $(ONT)-basic.owl make-csv.sparql $(ROBOT) query -i $(ONT)-basic.owl --query make-csv.sparql $(ONT).csv @@ -57,5 +34,5 @@ mirror/%.owl: $(SRC) $(OWLTOOLS) $(OBO)/$*.owl --remove-annotation-assertions -l -s -d --remove-dangling-annotations -o $@ .PRECIOUS: mirror/%.owl -release: $(ONT).owl #$(ONT).obo +release: $(ONT).owl $(ONT)-basic.owl $(ONT).csv cp $^ $RELEASEDIR diff --git a/src/ontology/README-editors.md b/src/ontology/README-editors.md index 895da13..35eb872 100644 --- a/src/ontology/README-editors.md +++ b/src/ontology/README-editors.md @@ -50,9 +50,9 @@ to release: If this looks good type: - make prepare-release + make prepare_release -This generates derived files such as duo.owl and duo.obo and places +This generates derived files such as duo.owl and duo.csv and places them in the top level (../..). The versionIRI will be added. Commit and push these files.