From 08c2bc5b657b5e9062380868df7916f23e732ab9 Mon Sep 17 00:00:00 2001 From: Melanie Courtot Date: Wed, 5 Jun 2019 13:15:38 +0100 Subject: [PATCH 01/24] created draft basic and csv files --- duo-basic.owl | 527 +++++++- duo.csv | 36 - duo.owl | 2 +- src/ontology/duo-basic.owl | 1156 ++++++++++++++++++ src/ontology/duo.csv | 21 + src/ontology/duo.owl | 2356 ++++++++++++++++++++++++++++++++++++ 6 files changed, 4046 insertions(+), 52 deletions(-) delete mode 100644 duo.csv create mode 100644 src/ontology/duo-basic.owl create mode 100644 src/ontology/duo.csv create mode 100644 src/ontology/duo.owl diff --git a/duo-basic.owl b/duo-basic.owl index b73baba..08ca342 100644 --- a/duo-basic.owl +++ b/duo-basic.owl @@ -7,19 +7,12 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" 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: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 - Melanie Courtot + @@ -35,6 +28,35 @@ + + + + + + + + + + Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. + Really of interest to developers only + BFO OWL specification label + + + + + + + + + Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 + Person:Alan Ruttenberg + Really of interest to developers only + BFO CLIF specification label + + + + + @@ -57,9 +79,42 @@ + + + + example + + 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 + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + example of usage + + + + + + + + in branch + An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. + GROUP:OBI + OBI_0000277 + in branch + + + + - + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + OBI_0000281 + has curation status + @@ -100,13 +155,30 @@ We also have the outstanding issue of how to aim different definitions to differ - + + editor note + + 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> + + editor note + - + + term editor + + Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + term editor + @@ -126,7 +198,28 @@ 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 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition source + + + + + + + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + @@ -143,6 +236,46 @@ 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/ + + 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 + + + + + + + + + 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 + + + + + + + + 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 + + + + @@ -158,6 +291,332 @@ We also have the outstanding issue of how to aim different definitions to differ + + + + expand expression to + ObjectProperty: RO_0002104 +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 + expand expression to + + + + + + + + expand assertion to + ObjectProperty: RO??? +Label: spatially disjoint from +Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. + Chris Mungall + expand assertion to + + + + + + + + first order logic expression + PERSON:Alan Ruttenberg + first order logic expression + + + + + + + + antisymmetric property + part_of antisymmetric property xsd:true + use boolean value xsd:true to indicate that the property is an antisymmetric property + Alan Ruttenberg + antisymmetric property + + + + + + + + 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 . + PERSON:Alan Ruttenberg + PERSON:Bjoern Peters + PERSON:Chris Mungall + PERSON:Melanie Courtot + GROUP:OBO Foundry <http://obofoundry.org/> + OBO foundry unique label + + + + + + + + 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 + has ID digit count + + + + + + + + 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 + has ID range allocated to + + + + + + + + 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 + + + + + + + + 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 + has ID prefix + + + + + + + + elucidation + person:Alan Ruttenberg + Person:Barry Smith + Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms + + elucidation + + + + + + + + has associated axiom(nl) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom associated with a term expressed using natural language + + has associated axiom(nl) + + + + + + + + has associated axiom(fol) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom expressed in first order logic using CLIF syntax + + has associated axiom(fol) + + + + + + + + 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 + is allocated id range + + + + + + + + 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 + retired from use as of + + + + + + + + has axiom id + Person:Alan Ruttenberg + Person:Alan Ruttenberg + A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI + + has axiom label + + + + + + + + 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 + term replaced by + + + + + + + + temporal interpretation + https://github.com/oborel/obo-relations/wiki/ROAndTime + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -166,7 +625,45 @@ We also have the outstanding issue of how to aim different definitions to differ - + + shorthand + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/duo.csv b/duo.csv deleted file mode 100644 index cbf031b..0000000 --- a/duo.csv +++ /dev/null @@ -1,36 +0,0 @@ -id,label,description -DUO:0000021,ethics approval required,This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. -DUO_0000034,age category research,An investigation concerning specific age categories. -DUO:0000006,health or medical or biomedical research,This primary category consent code indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry. -DUO:0000019,publication required,This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community. -DUO:0000026,user specific restriction,This requirement indicates that use is limited to use by approved users. -DUO_0000039,drug development research,Biomedical research concerning drug development. -DUO:0000020,collaboration required,This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). -DUO_0000033,ancestry research,An investigation concerning ancestry or population origins. -DUO:0000005,general research use and clinical care,"This primary category consent code indicates that use is allowed for health/medical/biomedical purposes and other biological research, including the study of population origins or ancestry." -DUO:0000018,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_0000040,disease category research,Biomedical research research concerning specific disease/s -DUO:0000012,research specific restrictions,This secondary category consent code indicates that use is limited to studies of a certain research type. -DUO:0000025,time limit on use,This requirement indicates that use is approved for a specific number of months. -DUO_0000038,genetic research,"Biomedical research concerning genetics (i.e., the study of genes, genetic variations and heredity)." -DUO_0000032,population research,An investigation concerning a specific population group. -DUO:0000004,no restriction,This consent code primary category indicates there is no restriction on use. -DUO:0000017,data use requirements,Requirements indicate additional conditions set for use. -DUO:0000011,population origins or ancestry research,This primary category consent code indicates that use of the data is limited to the study of population origins or ancestry. -DUO:0000024,publication moratorium,This requirement indicates that requestor agrees not to publish results of studies until a specific date -DUO_0000037,biomedical research,"An investigation concerning health, medical, or biomedical research." -DUO_0000031,method development,"An investigation concerning development of methods, algorithms, software or analytical tools." -DUO:0000003,consent code secondary category,A categorical data item indicating the secondary category the consent code belongs to according to Dyke et al. 2016. -DUO:0000016,genetic studies only,"This secondary category consent code indicates that use is limited to genetic studies only (i.e., no phenotype-only research)" -DUO:0000029,return to database or resource,This requirement indicates that the requestor must return derived/enriched data to the database/resource. -DUO_0000036,research control,An investigation concerning use of data as reference or control material. -DUO:0000002,consent code primary category,A categorical data item indicating the primary category the consent code belongs to according to Dyke et al. 2016. -DUO:0000015,no general methods research,"This secondary category consent code indicates that use includes methods development research(e.g., development of software or algorithms) only within the bounds of other use limitations." -DUO:0000028,institution specific restriction,This requirement indicates that use is limited to use within an approved institution. -DUO:0000022,geographical restriction,This requirement indicates that use is limited to within a specific geographic region. -DUO_0000035,gender category research,An investigation concerning specific gender categories. -DUO:0000007,disease specific research,This primary category consent code indicates that use is allowed provided it is related to the specified disease. -DUO:0000001,consent code,"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,general research use,This primary category consent code indicates that use is allowed for general research use for any research purpose. -DUO:0000014,research use only,"This secondary category consent code indicates that use is limited to research purposes (e.g., does not include its use in clinical care)." -DUO:0000027,project specific restriction,This requirement indicates that use is limited to use within an approved project. diff --git a/duo.owl b/duo.owl index ff99579..8f21121 100644 --- a/duo.owl +++ b/duo.owl @@ -12,7 +12,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + Cooper Stansbury David An diff --git a/src/ontology/duo-basic.owl b/src/ontology/duo-basic.owl new file mode 100644 index 0000000..08ca342 --- /dev/null +++ b/src/ontology/duo-basic.owl @@ -0,0 +1,1156 @@ + + + + + + + + + + + + + + + + + + + + + + + Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. + Really of interest to developers only + BFO OWL specification label + + + + + + + + + Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 + Person:Alan Ruttenberg + Really of interest to developers only + BFO CLIF specification label + + + + + + + + + DUO_preferred_label + + + + + + + + editor preferred term + + 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 term + + + + + + + + example + + 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 + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + example of usage + + + + + + + + in branch + An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. + GROUP:OBI + OBI_0000277 + in branch + + + + + + + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + OBI_0000281 + has curation status + + + + + + + + definition + + 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 + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition + definition + + + + + + + + editor note + + 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> + + editor note + + + + + + + + term editor + + Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + term editor + + + + + + + + alternative term + + An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + alternative term + + + + + + + + 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 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition source + + + + + + + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + + + + + + + + curator note + + An administrative note of use for a curator but of no use for a user + PERSON:Alan Ruttenberg + + curator note + + + + + + + + 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. + term tracker item + + + + + + + + + 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 + + + + + + + + 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 + + + + + + + + imported from + + For external terms/classes, the ontology from which the term was imported + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + imported from + + + + + + + + expand expression to + ObjectProperty: RO_0002104 +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 + expand expression to + + + + + + + + expand assertion to + ObjectProperty: RO??? +Label: spatially disjoint from +Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. + Chris Mungall + expand assertion to + + + + + + + + first order logic expression + PERSON:Alan Ruttenberg + first order logic expression + + + + + + + + antisymmetric property + part_of antisymmetric property xsd:true + use boolean value xsd:true to indicate that the property is an antisymmetric property + Alan Ruttenberg + antisymmetric property + + + + + + + + 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 . + PERSON:Alan Ruttenberg + PERSON:Bjoern Peters + PERSON:Chris Mungall + PERSON:Melanie Courtot + GROUP:OBO Foundry <http://obofoundry.org/> + OBO foundry unique label + + + + + + + + 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 + has ID digit count + + + + + + + + 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 + has ID range allocated to + + + + + + + + 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 + + + + + + + + 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 + has ID prefix + + + + + + + + elucidation + person:Alan Ruttenberg + Person:Barry Smith + Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms + + elucidation + + + + + + + + has associated axiom(nl) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom associated with a term expressed using natural language + + has associated axiom(nl) + + + + + + + + has associated axiom(fol) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom expressed in first order logic using CLIF syntax + + has associated axiom(fol) + + + + + + + + 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 + is allocated id range + + + + + + + + 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 + retired from use as of + + + + + + + + has axiom id + Person:Alan Ruttenberg + Person:Alan Ruttenberg + A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI + + has axiom label + + + + + + + + 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 + term replaced by + + + + + + + + temporal interpretation + https://github.com/oborel/obo-relations/wiki/ROAndTime + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + shorthand + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + consent code + 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:0000001 + consent code + + + + + + + + + consent code primary category + A categorical data item indicating the primary category the consent code belongs to according to Dyke et al. 2016. + DUO:0000002 + consent code primary category + + + + + + + + + consent code secondary category + A categorical data item indicating the secondary category the consent code belongs to according to Dyke et al. 2016. + DUO:0000003 + consent code secondary category + + + + + + + + + no restriction + This consent code primary category 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 + + + + + + + + + general research use and clinical care + This primary category consent code 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 + general research use and clinical care + + + + + + + + + health/medical/biomedical research + This primary category consent code 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 + + + + + + + + + disease-specific research + This primary category consent code 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 + + + + + + + + + population origins or ancestry research + This primary category consent code 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 + + + + + + + + + research-specific restrictions + This secondary category consent code indicates that use is limited to studies of a certain research type. + DUO:0000012 + RS + research specific restrictions + + + + + + + + + research use only + This secondary category consent code indicates that use is limited to research purposes (e.g., does not include its use in clinical care). + DUO:0000014 + RU + research use only + + + + + + + + + no general methods research + This secondary category consent code indicates that use includes methods development research(e.g., development of software or algorithms) only within the bounds of other use limitations. + DUO:0000015 + no general methods research + + + + + + + + + genetic studies only + This secondary category consent code indicates that use is limited to genetic studies only (i.e., no phenotype-only research) + DUO:0000016 + GSO + genetic studies only + + + + + + + + data use requirements + Requirements indicate additional conditions set for use. + DUO:0000017 + data use requirements + + + + + + + + + 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 + DUO:0000018 + NPU + not for profit use only + + + + + + + + + publication required + This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community. + DUO:0000019 + PUB + publication required + + + + + + + + + collaboration required + This requirement 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 + + + + + + + + + ethics approval required + This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. + DUO:0000021 + IRB + ethics approval required + + + + + + + + + geographical restriction + This requirement indicates that use is limited to within a specific geographic region. + DUO:0000022 + GS-[XX] + This should be coupled with an ontology term describing the geographical location the restriction applies to. + geographical restriction + + + + + + + + + publication moratorium + This requirement indicates that requestor agrees not to publish results of studies until a specific date + publication embargo + DUO:0000024 + MOR-[XX] + This should be coupled with a date specified as ISO8601 + publication moratorium + + + + + + + + + time limit on use + This requirement indicates that use is approved for a specific number of months. + DUO:0000025 + TS-[XX] + This should be coupled with an integer value indicating the number of months. + time limit on use + + + + + + + + + user-specific restriction + This requirement indicates that use is limited to use by approved users. + DUO:0000026 + US + user specific restriction + + + + + + + + + project-specific restriction + This requirement indicates that use is limited to use within an approved project. + DUO:0000027 + PS + project specific restriction + + + + + + + + + institution-specific restriction + This requirement indicates that use is limited to use within an approved institution. + DUO:0000028 + IS + institution specific restriction + + + + + + + + + return to database/resource + This requirement 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 + + + + + + + + + general research use + This primary category consent code 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 + + + + + + + + investigation + a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). + + investigation + + + + + + + diff --git a/src/ontology/duo.csv b/src/ontology/duo.csv new file mode 100644 index 0000000..30ce0f1 --- /dev/null +++ b/src/ontology/duo.csv @@ -0,0 +1,21 @@ +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 primary category consent code 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 primary category consent code 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 secondary category consent code indicates that use is limited to studies of a certain research type. +DUO:0000025,TS-[XX],time limit on use,This requirement indicates that use is approved for a specific number of months. +DUO:0000004,NRES,no restriction,This consent code primary category indicates there is no restriction on use. +DUO:0000011,POA,population origins or ancestry research,This primary category consent code indicates that use of the data is limited to the study of population origins or ancestry. +DUO:0000024,MOR-[XX],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 secondary category consent code 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-[XX],geographical restriction,This requirement indicates that use is limited to within a specific geographic region. +DUO:0000007,DS,disease specific research,This primary category consent code indicates that use is allowed provided it is related to the specified disease. +DUO:0000042,GRU,general research use,This primary category consent code indicates that use is allowed for general research use for any research purpose. +DUO:0000014,RU,research use only,"This secondary category consent code 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. diff --git a/src/ontology/duo.owl b/src/ontology/duo.owl new file mode 100644 index 0000000..8f21121 --- /dev/null +++ b/src/ontology/duo.owl @@ -0,0 +1,2356 @@ + + + + + + Cooper Stansbury + David An + Dylan Spalding + Giselle Kerry + Gregory Rushton + J. Neil Otte + Moran Ncabili + Stephanie Dyke + Melanie Courtot + + + + + + + + + + + + + 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 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 + + + + + + + + + consent code + 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:0000001 + consent code + + + + + + + + + consent code primary category + A categorical data item indicating the primary category the consent code belongs to according to Dyke et al. 2016. + DUO:0000002 + consent code primary category + + + + + + + + + consent code secondary category + A categorical data item indicating the secondary category the consent code belongs to according to Dyke et al. 2016. + DUO:0000003 + consent code secondary category + + + + + + + + + no restriction + This consent code primary category 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 + + + + + + + + + general research use and clinical care + This primary category consent code 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 + general research use and clinical care + + + + + + + + + health/medical/biomedical research + This primary category consent code 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 + + + + + + + + + + + + + + + disease-specific research + This primary category consent code 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 + + + + + + + + + population origins or ancestry research + This primary category consent code 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 + + + + + + + + + + + + + + + research-specific restrictions + This secondary category consent code indicates that use is limited to studies of a certain research type. + DUO:0000012 + RS + research specific restrictions + + + + + + + + + research use only + This secondary category consent code indicates that use is limited to research purposes (e.g., does not include its use in clinical care). + DUO:0000014 + RU + research use only + + + + + + + + + no general methods research + This secondary category consent code indicates that use includes methods development research(e.g., development of software or algorithms) only within the bounds of other use limitations. + DUO:0000015 + no general methods research + + + + + + + + + genetic studies only + This secondary category consent code indicates that use is limited to genetic studies only (i.e., no phenotype-only research) + DUO:0000016 + GSO + genetic studies only + + + + + + + + + data use requirements + Requirements indicate additional conditions set for use. + DUO:0000017 + data use requirements + + + + + + + + + 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 + DUO:0000018 + NPU + not for profit use only + + + + + + + + + publication required + This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community. + DUO:0000019 + PUB + publication required + + + + + + + + + collaboration required + This requirement 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 + + + + + + + + + ethics approval required + This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. + DUO:0000021 + IRB + ethics approval required + + + + + + + + + + + + + + + geographical restriction + This requirement indicates that use is limited to within a specific geographic region. + DUO:0000022 + GS-[XX] + This should be coupled with an ontology term describing the geographical location the restriction applies to. + geographical restriction + + + + + + + + + publication moratorium + This requirement indicates that requestor agrees not to publish results of studies until a specific date + publication embargo + DUO:0000024 + MOR-[XX] + This should be coupled with a date specified as ISO8601 + publication moratorium + + + + + + + + + time limit on use + This requirement indicates that use is approved for a specific number of months. + DUO:0000025 + TS-[XX] + This should be coupled with an integer value indicating the number of months. + time limit on use + + + + + + + + + user-specific restriction + This requirement indicates that use is limited to use by approved users. + DUO:0000026 + US + user specific restriction + + + + + + + + + project-specific restriction + This requirement indicates that use is limited to use within an approved project. + DUO:0000027 + PS + project specific restriction + + + + + + + + + institution-specific restriction + This requirement indicates that use is limited to use within an approved institution. + DUO:0000028 + IS + institution specific restriction + + + + + + + + + return to database/resource + This requirement 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 + + + + + + + + + general research use + This primary category consent code 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 + + + + + + + + + GAZ:00000448 + geographic location + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From ac61f706dec118e6e5d30997ccd9584f50927000 Mon Sep 17 00:00:00 2001 From: Melanie Courtot Date: Mon, 24 Jun 2019 14:52:42 +0100 Subject: [PATCH 02/24] Update README.md Added DUO users --- README.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/README.md b/README.md index c3277ab..24505fa 100644 --- a/README.md +++ b/README.md @@ -10,6 +10,7 @@ Table of Contents * [Stable release versions](#stable-release-versions) * [Editors' version](#editors-version) * [Contact](#contact) + * [DUO users](#duo-users) * [DUO - Full documentation](#duo---full-documentation) * [What is DUO?](#what-is-duo-1) * [How did DUO come about?](#how-did-duo-come-about) @@ -64,6 +65,12 @@ Editors of this ontology should use the edit version, [src/ontology/duo-edit.owl ## Contact Please use this GitHub repository's [Issue tracker](https://github.com/EBISPOT/duo/issues) to request new terms/classes or report errors or specific concerns related to the ontology. +## DUO - users +Several projects have now implemented DUO in production pipelines: +- the Broad Institute’s Data Use Oversight System, [DUOS](https://duos.broadinstitute.org/#/home) +- the European Genome-phenome Archive (EGA). See [here](https://ega-archive.org/datasets/EGAD00001000002)for example. +- the Data Information System, [DAISY](https://elixir-luxembourg.org/data-information-system-daisy) + # DUO - Full documentation ## What is DUO? From fc539460a3320a5aacc8e540192662dd3840fa39 Mon Sep 17 00:00:00 2001 From: Melanie Courtot Date: Mon, 24 Jun 2019 14:53:51 +0100 Subject: [PATCH 03/24] Update README.md added use cases --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 24505fa..1e0f792 100644 --- a/README.md +++ b/README.md @@ -68,8 +68,10 @@ Please use this GitHub repository's [Issue tracker](https://github.com/EBISPOT/d ## DUO - users Several projects have now implemented DUO in production pipelines: - the Broad Institute’s Data Use Oversight System, [DUOS](https://duos.broadinstitute.org/#/home) -- the European Genome-phenome Archive (EGA). See [here](https://ega-archive.org/datasets/EGAD00001000002)for example. +- the European Genome-phenome Archive (EGA). See [here](https://ega-archive.org/datasets/EGAD00001000002) for example. - the Data Information System, [DAISY](https://elixir-luxembourg.org/data-information-system-daisy) + +[Contact](#contact) us to tell us about your implementation! # DUO - Full documentation From 4294f47359a3ab7c784f6e1f663b4cd822bee07c Mon Sep 17 00:00:00 2001 From: Melanie Courtot Date: Mon, 24 Jun 2019 14:56:11 +0100 Subject: [PATCH 04/24] Update README.md repaired users link --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 1e0f792..508eb82 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ Table of Contents * [Stable release versions](#stable-release-versions) * [Editors' version](#editors-version) * [Contact](#contact) - * [DUO users](#duo-users) + * [DUO users](#duo---users) * [DUO - Full documentation](#duo---full-documentation) * [What is DUO?](#what-is-duo-1) * [How did DUO come about?](#how-did-duo-come-about) From ac91dda149c5c8e4d2778b9e86c2601436648f1f Mon Sep 17 00:00:00 2001 From: Audald Lloret-Villas Date: Thu, 27 Jun 2019 14:57:13 +0200 Subject: [PATCH 05/24] Add Jordi Rambla to contributor list --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 508eb82..963f5fb 100644 --- a/README.md +++ b/README.md @@ -229,7 +229,8 @@ J. Patrick Woolley, Emily Kirby, Josh Leslie, Francis Jeanson, Moran N. Cabili, - Greeshma Neglur (NCI Commons/U chicago) - Laura Paglione (Spherical Cow) - Ravi Pandya (Microsoft Research) -- Anthony Philippakis (Broad Institute of MIT and Harvard) +- Anthony Philippakis (Broad Institute of MIT and Harvard) +- Jordi Rambla (Centre for Genomic Regulation, EGA) - Greg Rushton (Broad Institute of MIT and Harvard) - Kathy Reinold (Broad Institute of MIT and Harvard) - Laura Rodriguez (NHGRI) From c0ef995ff1bae309f1836d73d729abbc08d2cf3c Mon Sep 17 00:00:00 2001 From: Melanie Courtot Date: Thu, 27 Jun 2019 14:04:30 +0100 Subject: [PATCH 06/24] Update .travis.yml removed oraclejdk replaced by openjdk --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 1f2e582..140ec95 100644 --- a/.travis.yml +++ b/.travis.yml @@ -2,7 +2,7 @@ ## Go to: https://travis-ci.org/EBISPOT for details language: java jdk: - - oraclejdk8 + - openjdk8 before_script: - mkdir -p bin From f8c229cc151f9dd018968bc30a3fb1b019026033 Mon Sep 17 00:00:00 2001 From: Melanie Courtot Date: Tue, 30 Jul 2019 11:35:57 +0100 Subject: [PATCH 07/24] Update README.md added Heidi and Melissa --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 963f5fb..c0f5864 100644 --- a/README.md +++ b/README.md @@ -221,6 +221,7 @@ J. Patrick Woolley, Emily Kirby, Josh Leslie, Francis Jeanson, Moran N. Cabili, - Melanie Courtot (EMBL-EBI) - Stacey Donnelly (GA4GH/Broad) - Stephanie Dyke (Mc Gill) +- Melissa Haendel (OHSU) - Francis Jeanson (IAMOPEN) - Giselle Kerry (EMBL-EBI, EGA) - Melissa Konopko (Wellcome Sanger Institute) @@ -235,6 +236,7 @@ J. Patrick Woolley, Emily Kirby, Josh Leslie, Francis Jeanson, Moran N. Cabili, - Kathy Reinold (Broad Institute of MIT and Harvard) - Laura Rodriguez (NHGRI) - Andrea Saltzman (Broad) +- Heidi Sofia (NIH) - Dylan Spalding (EMBL-EBI, EGA) - Anne-Marie Tasse (McGill University) - Adrian Thorogood (McGill University) From 4cbb7f77e39edf762e4ec00dad389362b79c0896 Mon Sep 17 00:00:00 2001 From: Melanie Courtot Date: Fri, 29 Nov 2019 15:33:15 +0000 Subject: [PATCH 08/24] Removed unused [xx] descriptions in shorthand forms (closes #28), fixed IDs annotation properties with underscoe, closes #32 --- src/ontology/duo-edit.owl | 67 +++++++++++++++++++++------------------ 1 file changed, 37 insertions(+), 30 deletions(-) diff --git a/src/ontology/duo-edit.owl b/src/ontology/duo-edit.owl index 1502c80..99cfe07 100644 --- a/src/ontology/duo-edit.owl +++ b/src/ontology/duo-edit.owl @@ -1,26 +1,27 @@ + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:dcterms="dcterms:" + xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - Stephanie Dyke - Giselle Kerry - Moran Ncabili - J. Neil Otte - Gregory Rushton - David An Cooper Stansbury + David An Dylan Spalding + Giselle Kerry + Gregory Rushton + J. Neil Otte + Moran Ncabili + Stephanie Dyke Melanie Courtot @@ -43,12 +44,19 @@ DUO_preferred_label - - + + + + + + + + + - @@ -156,7 +163,7 @@ This primary category consent code 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 - general research use and clinical care + general research use and clinical care @@ -344,7 +351,7 @@ geographical restriction This requirement indicates that use is limited to within a specific geographic region. DUO:0000022 - GS-[XX] + GS This should be coupled with an ontology term describing the geographical location the restriction applies to. geographical restriction @@ -359,7 +366,7 @@ This requirement indicates that requestor agrees not to publish results of studies until a specific date publication embargo DUO:0000024 - MOR-[XX] + MOR This should be coupled with a date specified as ISO8601 publication moratorium @@ -373,7 +380,7 @@ time limit on use This requirement indicates that use is approved for a specific number of months. DUO:0000025 - TS-[XX] + TS This should be coupled with an integer value indicating the number of months. time limit on use @@ -439,7 +446,7 @@ 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 + DUO:0000031 method development @@ -452,7 +459,7 @@ population research An investigation concerning a specific population group. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000032 + DUO:0000032 Should be paired with the an ontology term representing this population (e.g., xxx). population research @@ -466,7 +473,7 @@ ancestry research An investigation concerning ancestry or population origins. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000033 + DUO:0000033 ancestry research @@ -479,7 +486,7 @@ age category research An investigation concerning specific age categories. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000034 + DUO:0000034 Should be paired with the an ontology term representing this population (e.g., xxx). age category research @@ -493,7 +500,7 @@ gender category research An investigation concerning specific gender categories. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000035 + DUO:0000035 Should be paired with the an ontology term representing this population (e.g., xxx). gender category research @@ -507,7 +514,7 @@ 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 + DUO:0000036 research control @@ -520,7 +527,7 @@ biomedical research An investigation concerning health, medical, or biomedical research. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000037 + DUO:0000037 biomedical research @@ -533,7 +540,7 @@ 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 + DUO:0000038 genetic research @@ -546,7 +553,7 @@ drug development research Biomedical research concerning drug development. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000039 + DUO:0000039 drug development research @@ -559,7 +566,7 @@ disease category research Biomedical research research concerning specific disease/s This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000040 + DUO:0000040 disease category research @@ -618,5 +625,5 @@ - + From d3554e304c1e96bc52f2b26b6511abb976084569 Mon Sep 17 00:00:00 2001 From: haoyuanli Date: Wed, 4 Dec 2019 10:17:37 -0800 Subject: [PATCH 09/24] Add string definition for shorthand labels The shorthand labels don't have string definition, this PR adds declares type string for them --- src/ontology/duo-edit.owl | 38 +++++++++++++++++++------------------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/src/ontology/duo-edit.owl b/src/ontology/duo-edit.owl index 99cfe07..ce2db5e 100644 --- a/src/ontology/duo-edit.owl +++ b/src/ontology/duo-edit.owl @@ -147,7 +147,7 @@ no restriction This consent code primary category indicates there is no restriction on use. DUO:0000004 - NRES + 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 @@ -162,7 +162,7 @@ general research use and clinical care This primary category consent code 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 + GRU-CC general research use and clinical care @@ -175,7 +175,7 @@ health/medical/biomedical research This primary category consent code indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry. DUO:0000006 - HMB + HMB health or medical or biomedical research @@ -194,7 +194,7 @@ disease-specific research This primary category consent code indicates that use is allowed provided it is related to the specified disease. DUO:0000007 - DS + 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 @@ -209,7 +209,7 @@ This primary category consent code indicates that use of the data is limited to the study of population origins or ancestry. population origins/ancestry research DUO:0000011 - POA + POA population origins or ancestry research @@ -228,7 +228,7 @@ research-specific restrictions This secondary category consent code indicates that use is limited to studies of a certain research type. DUO:0000012 - RS + RS research specific restrictions @@ -241,7 +241,7 @@ research use only This secondary category consent code indicates that use is limited to research purposes (e.g., does not include its use in clinical care). DUO:0000014 - RU + RU research use only @@ -266,7 +266,7 @@ genetic studies only This secondary category consent code indicates that use is limited to genetic studies only (i.e., no phenotype-only research) DUO:0000016 - GSO + GSO genetic studies only @@ -292,7 +292,7 @@ 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 DUO:0000018 - NPU + NPU not for profit use only @@ -305,7 +305,7 @@ publication required This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community. DUO:0000019 - PUB + PUB publication required @@ -318,7 +318,7 @@ collaboration required This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). DUO:0000020 - COL + COL This could be coupled with a string describing the primary study investigator(s). collaboration required @@ -332,7 +332,7 @@ ethics approval required This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. DUO:0000021 - IRB + IRB ethics approval required @@ -351,7 +351,7 @@ geographical restriction This requirement indicates that use is limited to within a specific geographic region. DUO:0000022 - GS + GS This should be coupled with an ontology term describing the geographical location the restriction applies to. geographical restriction @@ -366,7 +366,7 @@ This requirement indicates that requestor agrees not to publish results of studies until a specific date publication embargo DUO:0000024 - MOR + MOR This should be coupled with a date specified as ISO8601 publication moratorium @@ -380,7 +380,7 @@ time limit on use This requirement indicates that use is approved for a specific number of months. DUO:0000025 - TS + TS This should be coupled with an integer value indicating the number of months. time limit on use @@ -394,7 +394,7 @@ user-specific restriction This requirement indicates that use is limited to use by approved users. DUO:0000026 - US + US user specific restriction @@ -407,7 +407,7 @@ project-specific restriction This requirement indicates that use is limited to use within an approved project. DUO:0000027 - PS + PS project specific restriction @@ -420,7 +420,7 @@ institution-specific restriction This requirement indicates that use is limited to use within an approved institution. DUO:0000028 - IS + IS institution specific restriction @@ -579,7 +579,7 @@ general research use This primary category consent code indicates that use is allowed for general research use for any research purpose. DUO:0000042 - GRU + 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 From 9af15822d0514aa9831c581a668d652a75910069 Mon Sep 17 00:00:00 2001 From: Melanie Courtot Date: Mon, 3 Feb 2020 11:50:24 +0000 Subject: [PATCH 10/24] closes #29 --- src/ontology/duo-edit.owl | 76 +++++++++++++++++++++------------------ 1 file changed, 41 insertions(+), 35 deletions(-) diff --git a/src/ontology/duo-edit.owl b/src/ontology/duo-edit.owl index ce2db5e..8b28abe 100644 --- a/src/ontology/duo-edit.owl +++ b/src/ontology/duo-edit.owl @@ -108,10 +108,11 @@ - consent code + 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. + consent code DUO:0000001 - consent code + data use limitation @@ -119,11 +120,13 @@ - - consent code primary category + 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 - consent code primary category + obsolete consent code primary category + true @@ -131,11 +134,13 @@ - - consent code secondary category + 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 - consent code secondary category + obsolete consent code secondary category + true @@ -143,9 +148,9 @@ - + no restriction - This consent code primary category indicates there is no restriction on use. + This data use limitation 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. @@ -160,9 +165,10 @@ general research use and clinical care - This primary category consent code 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. 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 @@ -171,9 +177,9 @@ - + health/medical/biomedical research - This primary category consent code indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry. + 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:0000006 HMB health or medical or biomedical research @@ -192,7 +198,7 @@ disease-specific research - This primary category consent code indicates that use is allowed provided it is related to the specified disease. + This data use limitation 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. @@ -204,9 +210,9 @@ - + population origins or ancestry research - This primary category consent code indicates that use of the data is limited to the study of population origins or ancestry. + This data use limitation indicates that use of the data is limited to the study of population origins or ancestry. population origins/ancestry research DUO:0000011 POA @@ -218,7 +224,7 @@ - + @@ -226,7 +232,7 @@ research-specific restrictions - This secondary category consent code indicates that use is limited to studies of a certain research type. + This data use limitation indicates that use is limited to studies of a certain research type. DUO:0000012 RS research specific restrictions @@ -237,9 +243,9 @@ - + research use only - This secondary category consent code 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 @@ -250,9 +256,9 @@ - + no general methods research - This secondary category consent code 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 limitation indicates that use includes methods development research(e.g., development of software or algorithms) only within the bounds of other use limitations. DUO:0000015 no general methods research @@ -262,9 +268,9 @@ - + genetic studies only - This secondary category consent code indicates that use is limited to genetic studies only (i.e., no phenotype-only research) + This data use limitation indicates that use is limited to genetic studies only (i.e., no phenotype-only research) DUO:0000016 GSO genetic studies only @@ -292,7 +298,7 @@ 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 DUO:0000018 - NPU + NPU not for profit use only @@ -305,7 +311,7 @@ publication required This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community. DUO:0000019 - PUB + PUB publication required @@ -318,7 +324,7 @@ collaboration required This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). DUO:0000020 - COL + COL This could be coupled with a string describing the primary study investigator(s). collaboration required @@ -332,7 +338,7 @@ ethics approval required This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. DUO:0000021 - IRB + IRB ethics approval required @@ -351,7 +357,7 @@ geographical restriction This requirement indicates that use is limited to within a specific geographic region. DUO:0000022 - GS + GS This should be coupled with an ontology term describing the geographical location the restriction applies to. geographical restriction @@ -366,7 +372,7 @@ This requirement indicates that requestor agrees not to publish results of studies until a specific date publication embargo DUO:0000024 - MOR + MOR This should be coupled with a date specified as ISO8601 publication moratorium @@ -380,7 +386,7 @@ time limit on use This requirement indicates that use is approved for a specific number of months. DUO:0000025 - TS + TS This should be coupled with an integer value indicating the number of months. time limit on use @@ -394,7 +400,7 @@ user-specific restriction This requirement indicates that use is limited to use by approved users. DUO:0000026 - US + US user specific restriction @@ -407,7 +413,7 @@ project-specific restriction This requirement indicates that use is limited to use within an approved project. DUO:0000027 - PS + PS project specific restriction @@ -420,7 +426,7 @@ institution-specific restriction This requirement indicates that use is limited to use within an approved institution. DUO:0000028 - IS + IS institution specific restriction @@ -575,7 +581,7 @@ - + general research use This primary category consent code indicates that use is allowed for general research use for any research purpose. DUO:0000042 From 37e1e8e6233c8c3d9ad7c3ba66031d0f9fefee5f Mon Sep 17 00:00:00 2001 From: Melanie Courtot Date: Mon, 3 Feb 2020 11:58:53 +0000 Subject: [PATCH 11/24] updated definition of general research use to reflect label data use limitation --- src/ontology/duo-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/duo-edit.owl b/src/ontology/duo-edit.owl index 8b28abe..e93205e 100644 --- a/src/ontology/duo-edit.owl +++ b/src/ontology/duo-edit.owl @@ -583,7 +583,7 @@ This is better done by Schemablocks and constraining the pattern of usage of DUO general research use - This primary category consent code indicates that use is allowed for general research use for any research purpose. + This data use limitation 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. From 331be887f74d72e50404237cf51d0c3dcc015cb4 Mon Sep 17 00:00:00 2001 From: Melanie Courtot Date: Mon, 3 Feb 2020 12:01:47 +0000 Subject: [PATCH 12/24] new release --- src/ontology/duo-basic.owl | 195 +++++++++++++--------- src/ontology/duo.csv | 24 +-- src/ontology/duo.owl | 329 ++++++++++++++++++++++++++++++------- 3 files changed, 400 insertions(+), 148 deletions(-) diff --git a/src/ontology/duo-basic.owl b/src/ontology/duo-basic.owl index 08ca342..334c267 100644 --- a/src/ontology/duo-basic.owl +++ b/src/ontology/duo-basic.owl @@ -12,7 +12,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -68,13 +68,21 @@ + 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 @@ -122,7 +130,10 @@ 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 @@ -149,6 +160,7 @@ We also have the outstanding issue of how to aim different definitions to differ definition definition + textual definition @@ -485,6 +497,34 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + 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 + + + + + + + + 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 + https://github.com/information-artifact-ontology/ontology-metadata/issues/32 + GO ontology + scheduled for obsoletion on or after + + + + + @@ -515,8 +555,8 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation - https://github.com/oborel/obo-relations/wiki/ROAndTime @@ -617,6 +657,18 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + @@ -625,9 +677,13 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - shorthand - + + + + + + + @@ -645,7 +701,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + + label + label + @@ -681,34 +740,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - consent code + 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. + consent code DUO:0000001 - consent code - - - - - - - - - consent code primary category - A categorical data item indicating the primary category the consent code belongs to according to Dyke et al. 2016. - DUO:0000002 - consent code primary category - - - - - - - - - consent code secondary category - A categorical data item indicating the secondary category the consent code belongs to according to Dyke et al. 2016. - DUO:0000003 - consent code secondary category + data use limitation @@ -716,11 +752,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + no restriction - This consent code primary category indicates there is no restriction on use. + This data use limitation indicates there is no restriction on use. DUO:0000004 - NRES + 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 @@ -733,9 +769,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] general research use and clinical care - This primary category consent code 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. DUO:0000005 - GRU-CC + 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 @@ -744,11 +781,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + health/medical/biomedical research - This primary category consent code indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry. + 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:0000006 - HMB + HMB health or medical or biomedical research @@ -759,9 +796,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] disease-specific research - This primary category consent code indicates that use is allowed provided it is related to the specified disease. + This data use limitation indicates that use is allowed provided it is related to the specified disease. DUO:0000007 - DS + 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 @@ -771,12 +808,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + population origins or ancestry research - This primary category consent code indicates that use of the data is limited to the study of population origins or ancestry. + This data use limitation indicates that use of the data is limited to the study of population origins or ancestry. population origins/ancestry research DUO:0000011 - POA + POA population origins or ancestry research @@ -785,11 +822,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + research-specific restrictions - This secondary category consent code indicates that use is limited to studies of a certain research type. + This data use limitation indicates that use is limited to studies of a certain research type. DUO:0000012 - RS + RS research specific restrictions @@ -798,11 +835,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + research use only - This secondary category consent code 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 + RU research use only @@ -811,9 +848,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + no general methods research - This secondary category consent code 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 limitation indicates that use includes methods development research(e.g., development of software or algorithms) only within the bounds of other use limitations. DUO:0000015 no general methods research @@ -823,11 +860,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + genetic studies only - This secondary category consent code indicates that use is limited to genetic studies only (i.e., no phenotype-only research) + This data use limitation indicates that use is limited to genetic studies only (i.e., no phenotype-only research) DUO:0000016 - GSO + GSO genetic studies only @@ -852,7 +889,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 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 DUO:0000018 - NPU + NPU not for profit use only @@ -865,7 +902,7 @@ 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. DUO:0000019 - PUB + PUB publication required @@ -878,7 +915,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] collaboration required This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). DUO:0000020 - COL + COL This could be coupled with a string describing the primary study investigator(s). collaboration required @@ -892,7 +929,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] ethics approval required This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. DUO:0000021 - IRB + IRB ethics approval required @@ -905,7 +942,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] geographical restriction This requirement indicates that use is limited to within a specific geographic region. DUO:0000022 - GS-[XX] + GS This should be coupled with an ontology term describing the geographical location the restriction applies to. geographical restriction @@ -920,7 +957,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] This requirement indicates that requestor agrees not to publish results of studies until a specific date publication embargo DUO:0000024 - MOR-[XX] + MOR This should be coupled with a date specified as ISO8601 publication moratorium @@ -934,7 +971,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] time limit on use This requirement indicates that use is approved for a specific number of months. DUO:0000025 - TS-[XX] + TS This should be coupled with an integer value indicating the number of months. time limit on use @@ -948,7 +985,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] user-specific restriction This requirement indicates that use is limited to use by approved users. DUO:0000026 - US + US user specific restriction @@ -961,7 +998,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] project-specific restriction This requirement indicates that use is limited to use within an approved project. DUO:0000027 - PS + PS project specific restriction @@ -974,7 +1011,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] institution-specific restriction This requirement indicates that use is limited to use within an approved institution. DUO:0000028 - IS + IS institution specific restriction @@ -1000,7 +1037,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 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 + DUO:0000031 method development @@ -1013,7 +1050,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] population research An investigation concerning a specific population group. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000032 + DUO:0000032 Should be paired with the an ontology term representing this population (e.g., xxx). population research @@ -1027,7 +1064,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] ancestry research An investigation concerning ancestry or population origins. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000033 + DUO:0000033 ancestry research @@ -1040,7 +1077,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] age category research An investigation concerning specific age categories. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000034 + DUO:0000034 Should be paired with the an ontology term representing this population (e.g., xxx). age category research @@ -1054,7 +1091,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] gender category research An investigation concerning specific gender categories. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000035 + DUO:0000035 Should be paired with the an ontology term representing this population (e.g., xxx). gender category research @@ -1068,7 +1105,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 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 + DUO:0000036 research control @@ -1081,7 +1118,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] biomedical research An investigation concerning health, medical, or biomedical research. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000037 + DUO:0000037 biomedical research @@ -1094,7 +1131,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 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 + DUO:0000038 genetic research @@ -1107,7 +1144,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] drug development research Biomedical research concerning drug development. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000039 + DUO:0000039 drug development research @@ -1120,7 +1157,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] disease category research Biomedical research research concerning specific disease/s This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000040 + DUO:0000040 disease category research @@ -1129,11 +1166,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + general research use - This primary category consent code indicates that use is allowed for general research use for any research purpose. + This data use limitation indicates that use is allowed for general research use for any research purpose. DUO:0000042 - GRU + 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 diff --git a/src/ontology/duo.csv b/src/ontology/duo.csv index 30ce0f1..e46a0bd 100644 --- a/src/ontology/duo.csv +++ b/src/ontology/duo.csv @@ -1,21 +1,21 @@ 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 primary category consent code 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 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 primary category consent code 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,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 secondary category consent code indicates that use is limited to studies of a certain research type. -DUO:0000025,TS-[XX],time limit on use,This requirement indicates that use is approved for a specific number of months. -DUO:0000004,NRES,no restriction,This consent code primary category indicates there is no restriction on use. -DUO:0000011,POA,population origins or ancestry research,This primary category consent code indicates that use of the data is limited to the study of population origins or ancestry. -DUO:0000024,MOR-[XX],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 secondary category consent code indicates that use is limited to genetic studies only (i.e., no phenotype-only research)" +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-[XX],geographical restriction,This requirement indicates that use is limited to within a specific geographic region. -DUO:0000007,DS,disease specific research,This primary category consent code indicates that use is allowed provided it is related to the specified disease. -DUO:0000042,GRU,general research use,This primary category consent code indicates that use is allowed for general research use for any research purpose. -DUO:0000014,RU,research use only,"This secondary category consent code indicates that use is limited to research purposes (e.g., does not include its use in clinical care)." +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. diff --git a/src/ontology/duo.owl b/src/ontology/duo.owl index 8f21121..015981a 100644 --- a/src/ontology/duo.owl +++ b/src/ontology/duo.owl @@ -9,10 +9,11 @@ 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:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + Cooper Stansbury David An @@ -396,10 +397,11 @@ - consent code + 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. + consent code DUO:0000001 - consent code + data use limitation @@ -407,11 +409,13 @@ - - consent code primary category + 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 - consent code primary category + obsolete consent code primary category + true @@ -419,11 +423,13 @@ - - consent code secondary category + 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 - consent code secondary category + obsolete consent code secondary category + true @@ -431,11 +437,11 @@ - + no restriction - This consent code primary category indicates there is no restriction on use. + This data use limitation indicates there is no restriction on use. DUO:0000004 - NRES + 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 @@ -448,9 +454,10 @@ general research use and clinical care - This primary category consent code 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. DUO:0000005 - GRU-CC + 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 @@ -459,11 +466,11 @@ - + health/medical/biomedical research - This primary category consent code indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry. + 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:0000006 - HMB + HMB health or medical or biomedical research @@ -480,9 +487,9 @@ disease-specific research - This primary category consent code indicates that use is allowed provided it is related to the specified disease. + This data use limitation indicates that use is allowed provided it is related to the specified disease. DUO:0000007 - DS + 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 @@ -492,12 +499,12 @@ - + population origins or ancestry research - This primary category consent code indicates that use of the data is limited to the study of population origins or ancestry. + This data use limitation indicates that use of the data is limited to the study of population origins or ancestry. population origins/ancestry research DUO:0000011 - POA + POA population origins or ancestry research @@ -506,7 +513,7 @@ - + @@ -514,9 +521,9 @@ research-specific restrictions - This secondary category consent code indicates that use is limited to studies of a certain research type. + This data use limitation indicates that use is limited to studies of a certain research type. DUO:0000012 - RS + RS research specific restrictions @@ -525,11 +532,11 @@ - + research use only - This secondary category consent code 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 + RU research use only @@ -538,9 +545,9 @@ - + no general methods research - This secondary category consent code 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 limitation indicates that use includes methods development research(e.g., development of software or algorithms) only within the bounds of other use limitations. DUO:0000015 no general methods research @@ -550,11 +557,11 @@ - + genetic studies only - This secondary category consent code indicates that use is limited to genetic studies only (i.e., no phenotype-only research) + This data use limitation indicates that use is limited to genetic studies only (i.e., no phenotype-only research) DUO:0000016 - GSO + GSO genetic studies only @@ -580,7 +587,7 @@ 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 DUO:0000018 - NPU + NPU not for profit use only @@ -593,7 +600,7 @@ publication required This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community. DUO:0000019 - PUB + PUB publication required @@ -606,7 +613,7 @@ collaboration required This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). DUO:0000020 - COL + COL This could be coupled with a string describing the primary study investigator(s). collaboration required @@ -620,7 +627,7 @@ ethics approval required This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. DUO:0000021 - IRB + IRB ethics approval required @@ -639,7 +646,7 @@ geographical restriction This requirement indicates that use is limited to within a specific geographic region. DUO:0000022 - GS-[XX] + GS This should be coupled with an ontology term describing the geographical location the restriction applies to. geographical restriction @@ -654,7 +661,7 @@ This requirement indicates that requestor agrees not to publish results of studies until a specific date publication embargo DUO:0000024 - MOR-[XX] + MOR This should be coupled with a date specified as ISO8601 publication moratorium @@ -668,7 +675,7 @@ time limit on use This requirement indicates that use is approved for a specific number of months. DUO:0000025 - TS-[XX] + TS This should be coupled with an integer value indicating the number of months. time limit on use @@ -682,7 +689,7 @@ user-specific restriction This requirement indicates that use is limited to use by approved users. DUO:0000026 - US + US user specific restriction @@ -695,7 +702,7 @@ project-specific restriction This requirement indicates that use is limited to use within an approved project. DUO:0000027 - PS + PS project specific restriction @@ -708,7 +715,7 @@ institution-specific restriction This requirement indicates that use is limited to use within an approved institution. DUO:0000028 - IS + IS institution specific restriction @@ -734,7 +741,7 @@ 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 + DUO:0000031 method development @@ -747,7 +754,7 @@ population research An investigation concerning a specific population group. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000032 + DUO:0000032 Should be paired with the an ontology term representing this population (e.g., xxx). population research @@ -761,7 +768,7 @@ ancestry research An investigation concerning ancestry or population origins. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000033 + DUO:0000033 ancestry research @@ -774,7 +781,7 @@ age category research An investigation concerning specific age categories. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000034 + DUO:0000034 Should be paired with the an ontology term representing this population (e.g., xxx). age category research @@ -788,7 +795,7 @@ gender category research An investigation concerning specific gender categories. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000035 + DUO:0000035 Should be paired with the an ontology term representing this population (e.g., xxx). gender category research @@ -802,7 +809,7 @@ 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 + DUO:0000036 research control @@ -815,7 +822,7 @@ biomedical research An investigation concerning health, medical, or biomedical research. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000037 + DUO:0000037 biomedical research @@ -828,7 +835,7 @@ 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 + DUO:0000038 genetic research @@ -841,7 +848,7 @@ drug development research Biomedical research concerning drug development. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000039 + DUO:0000039 drug development research @@ -854,7 +861,7 @@ disease category research Biomedical research research concerning specific disease/s This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000040 + DUO:0000040 disease category research @@ -863,11 +870,11 @@ - + general research use - This primary category consent code indicates that use is allowed for general research use for any research purpose. + This data use limitation indicates that use is allowed for general research use for any research purpose. DUO:0000042 - GRU + 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 @@ -2220,6 +2227,174 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2252,10 +2427,26 @@ + + + + + + + + + + + + + + + + - + @@ -2263,11 +2454,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + From ecaf2d9a8d730bc82642b009e0e9445d33428461 Mon Sep 17 00:00:00 2001 From: Melanie Courtot Date: Mon, 3 Feb 2020 12:06:15 +0000 Subject: [PATCH 13/24] added top-level files --- duo-basic.owl | 195 ++++++++++++++++++------------ duo.owl | 329 +++++++++++++++++++++++++++++++++++++++++--------- 2 files changed, 388 insertions(+), 136 deletions(-) diff --git a/duo-basic.owl b/duo-basic.owl index 08ca342..334c267 100644 --- a/duo-basic.owl +++ b/duo-basic.owl @@ -12,7 +12,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -68,13 +68,21 @@ + 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 @@ -122,7 +130,10 @@ 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 @@ -149,6 +160,7 @@ We also have the outstanding issue of how to aim different definitions to differ definition definition + textual definition @@ -485,6 +497,34 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + 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 + + + + + + + + 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 + https://github.com/information-artifact-ontology/ontology-metadata/issues/32 + GO ontology + scheduled for obsoletion on or after + + + + + @@ -515,8 +555,8 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation - https://github.com/oborel/obo-relations/wiki/ROAndTime @@ -617,6 +657,18 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + @@ -625,9 +677,13 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - - shorthand - + + + + + + + @@ -645,7 +701,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + + label + label + @@ -681,34 +740,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - consent code + 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. + consent code DUO:0000001 - consent code - - - - - - - - - consent code primary category - A categorical data item indicating the primary category the consent code belongs to according to Dyke et al. 2016. - DUO:0000002 - consent code primary category - - - - - - - - - consent code secondary category - A categorical data item indicating the secondary category the consent code belongs to according to Dyke et al. 2016. - DUO:0000003 - consent code secondary category + data use limitation @@ -716,11 +752,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + no restriction - This consent code primary category indicates there is no restriction on use. + This data use limitation indicates there is no restriction on use. DUO:0000004 - NRES + 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 @@ -733,9 +769,10 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] general research use and clinical care - This primary category consent code 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. DUO:0000005 - GRU-CC + 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 @@ -744,11 +781,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + health/medical/biomedical research - This primary category consent code indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry. + 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:0000006 - HMB + HMB health or medical or biomedical research @@ -759,9 +796,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] disease-specific research - This primary category consent code indicates that use is allowed provided it is related to the specified disease. + This data use limitation indicates that use is allowed provided it is related to the specified disease. DUO:0000007 - DS + 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 @@ -771,12 +808,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + population origins or ancestry research - This primary category consent code indicates that use of the data is limited to the study of population origins or ancestry. + This data use limitation indicates that use of the data is limited to the study of population origins or ancestry. population origins/ancestry research DUO:0000011 - POA + POA population origins or ancestry research @@ -785,11 +822,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + research-specific restrictions - This secondary category consent code indicates that use is limited to studies of a certain research type. + This data use limitation indicates that use is limited to studies of a certain research type. DUO:0000012 - RS + RS research specific restrictions @@ -798,11 +835,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + research use only - This secondary category consent code 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 + RU research use only @@ -811,9 +848,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + no general methods research - This secondary category consent code 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 limitation indicates that use includes methods development research(e.g., development of software or algorithms) only within the bounds of other use limitations. DUO:0000015 no general methods research @@ -823,11 +860,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + genetic studies only - This secondary category consent code indicates that use is limited to genetic studies only (i.e., no phenotype-only research) + This data use limitation indicates that use is limited to genetic studies only (i.e., no phenotype-only research) DUO:0000016 - GSO + GSO genetic studies only @@ -852,7 +889,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 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 DUO:0000018 - NPU + NPU not for profit use only @@ -865,7 +902,7 @@ 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. DUO:0000019 - PUB + PUB publication required @@ -878,7 +915,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] collaboration required This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). DUO:0000020 - COL + COL This could be coupled with a string describing the primary study investigator(s). collaboration required @@ -892,7 +929,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] ethics approval required This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. DUO:0000021 - IRB + IRB ethics approval required @@ -905,7 +942,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] geographical restriction This requirement indicates that use is limited to within a specific geographic region. DUO:0000022 - GS-[XX] + GS This should be coupled with an ontology term describing the geographical location the restriction applies to. geographical restriction @@ -920,7 +957,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] This requirement indicates that requestor agrees not to publish results of studies until a specific date publication embargo DUO:0000024 - MOR-[XX] + MOR This should be coupled with a date specified as ISO8601 publication moratorium @@ -934,7 +971,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] time limit on use This requirement indicates that use is approved for a specific number of months. DUO:0000025 - TS-[XX] + TS This should be coupled with an integer value indicating the number of months. time limit on use @@ -948,7 +985,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] user-specific restriction This requirement indicates that use is limited to use by approved users. DUO:0000026 - US + US user specific restriction @@ -961,7 +998,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] project-specific restriction This requirement indicates that use is limited to use within an approved project. DUO:0000027 - PS + PS project specific restriction @@ -974,7 +1011,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] institution-specific restriction This requirement indicates that use is limited to use within an approved institution. DUO:0000028 - IS + IS institution specific restriction @@ -1000,7 +1037,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 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 + DUO:0000031 method development @@ -1013,7 +1050,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] population research An investigation concerning a specific population group. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000032 + DUO:0000032 Should be paired with the an ontology term representing this population (e.g., xxx). population research @@ -1027,7 +1064,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] ancestry research An investigation concerning ancestry or population origins. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000033 + DUO:0000033 ancestry research @@ -1040,7 +1077,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] age category research An investigation concerning specific age categories. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000034 + DUO:0000034 Should be paired with the an ontology term representing this population (e.g., xxx). age category research @@ -1054,7 +1091,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] gender category research An investigation concerning specific gender categories. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000035 + DUO:0000035 Should be paired with the an ontology term representing this population (e.g., xxx). gender category research @@ -1068,7 +1105,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 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 + DUO:0000036 research control @@ -1081,7 +1118,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] biomedical research An investigation concerning health, medical, or biomedical research. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000037 + DUO:0000037 biomedical research @@ -1094,7 +1131,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 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 + DUO:0000038 genetic research @@ -1107,7 +1144,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] drug development research Biomedical research concerning drug development. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000039 + DUO:0000039 drug development research @@ -1120,7 +1157,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] disease category research Biomedical research research concerning specific disease/s This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000040 + DUO:0000040 disease category research @@ -1129,11 +1166,11 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + general research use - This primary category consent code indicates that use is allowed for general research use for any research purpose. + This data use limitation indicates that use is allowed for general research use for any research purpose. DUO:0000042 - GRU + 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 diff --git a/duo.owl b/duo.owl index 8f21121..015981a 100644 --- a/duo.owl +++ b/duo.owl @@ -9,10 +9,11 @@ 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:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + Cooper Stansbury David An @@ -396,10 +397,11 @@ - consent code + 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. + consent code DUO:0000001 - consent code + data use limitation @@ -407,11 +409,13 @@ - - consent code primary category + 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 - consent code primary category + obsolete consent code primary category + true @@ -419,11 +423,13 @@ - - consent code secondary category + 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 - consent code secondary category + obsolete consent code secondary category + true @@ -431,11 +437,11 @@ - + no restriction - This consent code primary category indicates there is no restriction on use. + This data use limitation indicates there is no restriction on use. DUO:0000004 - NRES + 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 @@ -448,9 +454,10 @@ general research use and clinical care - This primary category consent code 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. DUO:0000005 - GRU-CC + 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 @@ -459,11 +466,11 @@ - + health/medical/biomedical research - This primary category consent code indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry. + 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:0000006 - HMB + HMB health or medical or biomedical research @@ -480,9 +487,9 @@ disease-specific research - This primary category consent code indicates that use is allowed provided it is related to the specified disease. + This data use limitation indicates that use is allowed provided it is related to the specified disease. DUO:0000007 - DS + 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 @@ -492,12 +499,12 @@ - + population origins or ancestry research - This primary category consent code indicates that use of the data is limited to the study of population origins or ancestry. + This data use limitation indicates that use of the data is limited to the study of population origins or ancestry. population origins/ancestry research DUO:0000011 - POA + POA population origins or ancestry research @@ -506,7 +513,7 @@ - + @@ -514,9 +521,9 @@ research-specific restrictions - This secondary category consent code indicates that use is limited to studies of a certain research type. + This data use limitation indicates that use is limited to studies of a certain research type. DUO:0000012 - RS + RS research specific restrictions @@ -525,11 +532,11 @@ - + research use only - This secondary category consent code 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 + RU research use only @@ -538,9 +545,9 @@ - + no general methods research - This secondary category consent code 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 limitation indicates that use includes methods development research(e.g., development of software or algorithms) only within the bounds of other use limitations. DUO:0000015 no general methods research @@ -550,11 +557,11 @@ - + genetic studies only - This secondary category consent code indicates that use is limited to genetic studies only (i.e., no phenotype-only research) + This data use limitation indicates that use is limited to genetic studies only (i.e., no phenotype-only research) DUO:0000016 - GSO + GSO genetic studies only @@ -580,7 +587,7 @@ 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 DUO:0000018 - NPU + NPU not for profit use only @@ -593,7 +600,7 @@ publication required This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community. DUO:0000019 - PUB + PUB publication required @@ -606,7 +613,7 @@ collaboration required This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). DUO:0000020 - COL + COL This could be coupled with a string describing the primary study investigator(s). collaboration required @@ -620,7 +627,7 @@ ethics approval required This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. DUO:0000021 - IRB + IRB ethics approval required @@ -639,7 +646,7 @@ geographical restriction This requirement indicates that use is limited to within a specific geographic region. DUO:0000022 - GS-[XX] + GS This should be coupled with an ontology term describing the geographical location the restriction applies to. geographical restriction @@ -654,7 +661,7 @@ This requirement indicates that requestor agrees not to publish results of studies until a specific date publication embargo DUO:0000024 - MOR-[XX] + MOR This should be coupled with a date specified as ISO8601 publication moratorium @@ -668,7 +675,7 @@ time limit on use This requirement indicates that use is approved for a specific number of months. DUO:0000025 - TS-[XX] + TS This should be coupled with an integer value indicating the number of months. time limit on use @@ -682,7 +689,7 @@ user-specific restriction This requirement indicates that use is limited to use by approved users. DUO:0000026 - US + US user specific restriction @@ -695,7 +702,7 @@ project-specific restriction This requirement indicates that use is limited to use within an approved project. DUO:0000027 - PS + PS project specific restriction @@ -708,7 +715,7 @@ institution-specific restriction This requirement indicates that use is limited to use within an approved institution. DUO:0000028 - IS + IS institution specific restriction @@ -734,7 +741,7 @@ 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 + DUO:0000031 method development @@ -747,7 +754,7 @@ population research An investigation concerning a specific population group. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000032 + DUO:0000032 Should be paired with the an ontology term representing this population (e.g., xxx). population research @@ -761,7 +768,7 @@ ancestry research An investigation concerning ancestry or population origins. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000033 + DUO:0000033 ancestry research @@ -774,7 +781,7 @@ age category research An investigation concerning specific age categories. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000034 + DUO:0000034 Should be paired with the an ontology term representing this population (e.g., xxx). age category research @@ -788,7 +795,7 @@ gender category research An investigation concerning specific gender categories. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000035 + DUO:0000035 Should be paired with the an ontology term representing this population (e.g., xxx). gender category research @@ -802,7 +809,7 @@ 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 + DUO:0000036 research control @@ -815,7 +822,7 @@ biomedical research An investigation concerning health, medical, or biomedical research. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000037 + DUO:0000037 biomedical research @@ -828,7 +835,7 @@ 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 + DUO:0000038 genetic research @@ -841,7 +848,7 @@ drug development research Biomedical research concerning drug development. This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000039 + DUO:0000039 drug development research @@ -854,7 +861,7 @@ disease category research Biomedical research research concerning specific disease/s This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000040 + DUO:0000040 disease category research @@ -863,11 +870,11 @@ - + general research use - This primary category consent code indicates that use is allowed for general research use for any research purpose. + This data use limitation indicates that use is allowed for general research use for any research purpose. DUO:0000042 - GRU + 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 @@ -2220,6 +2227,174 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2252,10 +2427,26 @@ + + + + + + + + + + + + + + + + - + @@ -2263,11 +2454,35 @@ + + + + + + + + + + + + + + + + + + + + + + + + From 305fbe41e323fc4e79cfa15ef4166ec5d446b524 Mon Sep 17 00:00:00 2001 From: Melanie Courtot Date: Mon, 3 Feb 2020 12:09:59 +0000 Subject: [PATCH 14/24] created csv file --- duo.csv | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 duo.csv diff --git a/duo.csv b/duo.csv new file mode 100644 index 0000000..e46a0bd --- /dev/null +++ b/duo.csv @@ -0,0 +1,21 @@ +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. From 8a92bb3f19d914f7c48ddb9c15831e8a8c7e5d97 Mon Sep 17 00:00:00 2001 From: Melanie Courtot Date: Thu, 6 Feb 2020 11:59:56 +0000 Subject: [PATCH 15/24] Create release_notes.md added release notes --- doc/release_notes.md | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 doc/release_notes.md diff --git a/doc/release_notes.md b/doc/release_notes.md new file mode 100644 index 0000000..f7ceb6c --- /dev/null +++ b/doc/release_notes.md @@ -0,0 +1,19 @@ + +# DUO - Release notes + +## v2020-02-03 + +This release addresses several outstanding tickets: + +- A flat file (CSV) version of DUO is now being created at release time. This file is available from http://purl.obolibrary.org/obo/duo/duo.csv Despite being versioned this file does not include the version explicitely: a ticket has been created to do this in the next release, https://github.com/EBISPOT/DUO/issues/40 +- HMB has been moved to be a child of GRU and sibling of GRU-CC : HMB definition doesn't include clinical care and the hierarchy was therefore updated to reflect this. +- The term 'consent code' has been relabeled as 'data use limitation'. To optimise search the term 'consent code' has been retained as an alternative term. +- The term 'consent code primary category' and 'secondary category' have been deprecated: they were not used to tag datasets but instead as patterns for DUO codes capture. Those patterns are institue specific and would be better reflected by Schemablocks constraints specific to a repository. + + +Minnor fixes +- Addition of xsd:dtaatype to text field, as per https://github.com/EBISPOT/DUO/issues/33. Reported and fixed by @haoyuanli +- Consistency of ID annotation properties, as per https://github.com/EBISPOT/DUO/issues/32. Reported by @haoyuanli +- typo has been ported back to IAO, https://github.com/EBISPOT/DUO/issues/24 + +## no release notes for older versions From 9dc7ff7c07aa9f6b8192b7ab528652a5dd1f9842 Mon Sep 17 00:00:00 2001 From: Melanie Courtot Date: Thu, 6 Feb 2020 15:10:30 +0000 Subject: [PATCH 16/24] Update doc/release_notes.md Co-Authored-By: Greg Rushton --- doc/release_notes.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/release_notes.md b/doc/release_notes.md index f7ceb6c..c772403 100644 --- a/doc/release_notes.md +++ b/doc/release_notes.md @@ -12,7 +12,7 @@ This release addresses several outstanding tickets: Minnor fixes -- Addition of xsd:dtaatype to text field, as per https://github.com/EBISPOT/DUO/issues/33. Reported and fixed by @haoyuanli +- Addition of xsd:datatype to text field, as per https://github.com/EBISPOT/DUO/issues/33. Reported and fixed by @haoyuanli - Consistency of ID annotation properties, as per https://github.com/EBISPOT/DUO/issues/32. Reported by @haoyuanli - typo has been ported back to IAO, https://github.com/EBISPOT/DUO/issues/24 From 2065db7464c78554dbcf6daa9a1bbdae0ec4d980 Mon Sep 17 00:00:00 2001 From: Melanie Courtot Date: Thu, 6 Feb 2020 15:10:41 +0000 Subject: [PATCH 17/24] Update doc/release_notes.md Co-Authored-By: solideoglori <52168754+solideoglori@users.noreply.github.com> --- doc/release_notes.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/release_notes.md b/doc/release_notes.md index c772403..70ece65 100644 --- a/doc/release_notes.md +++ b/doc/release_notes.md @@ -5,7 +5,7 @@ This release addresses several outstanding tickets: -- A flat file (CSV) version of DUO is now being created at release time. This file is available from http://purl.obolibrary.org/obo/duo/duo.csv Despite being versioned this file does not include the version explicitely: a ticket has been created to do this in the next release, https://github.com/EBISPOT/DUO/issues/40 +- A flat file (CSV) version of DUO is now being created at release time. This file is available from http://purl.obolibrary.org/obo/duo/duo.csv Despite being versioned this file does not include the version explicitly: a ticket has been created to do this in the next release, https://github.com/EBISPOT/DUO/issues/40 - HMB has been moved to be a child of GRU and sibling of GRU-CC : HMB definition doesn't include clinical care and the hierarchy was therefore updated to reflect this. - The term 'consent code' has been relabeled as 'data use limitation'. To optimise search the term 'consent code' has been retained as an alternative term. - The term 'consent code primary category' and 'secondary category' have been deprecated: they were not used to tag datasets but instead as patterns for DUO codes capture. Those patterns are institue specific and would be better reflected by Schemablocks constraints specific to a repository. From fc3264751eb27881af8890105e6d35e047b2bbc9 Mon Sep 17 00:00:00 2001 From: Melanie Courtot Date: Mon, 17 Feb 2020 09:20:53 +0000 Subject: [PATCH 18/24] Fixes csv export, closes #48 --- src/ontology/duo-basic.owl | 2 +- src/ontology/duo.csv | 13 +++++++++++++ src/ontology/make-csv.sparql | 3 ++- 3 files changed, 16 insertions(+), 2 deletions(-) diff --git a/src/ontology/duo-basic.owl b/src/ontology/duo-basic.owl index 334c267..93d89b3 100644 --- a/src/ontology/duo-basic.owl +++ b/src/ontology/duo-basic.owl @@ -12,7 +12,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + diff --git a/src/ontology/duo.csv b/src/ontology/duo.csv index e46a0bd..7894922 100644 --- a/src/ontology/duo.csv +++ b/src/ontology/duo.csv @@ -1,21 +1,34 @@ 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:0000034,,age category research,An investigation concerning specific age categories. 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:0000039,,drug development research,Biomedical research concerning drug development. DUO:0000020,COL,collaboration required,This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). +DUO:0000033,,ancestry research,An investigation concerning ancestry or population origins. 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:0000040,,disease category research,Biomedical research research concerning specific disease/s 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:0000038,,genetic research,"Biomedical research concerning genetics (i.e., the study of genes, genetic variations and heredity)." +DUO:0000032,,population research,An investigation concerning a specific population group. DUO:0000004,NRES,no restriction,This data use limitation indicates there is no restriction on use. +DUO:0000017,,data use requirements,Requirements indicate additional conditions set for 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:0000037,,biomedical research,"An investigation concerning health, medical, or biomedical research." +DUO:0000031,,method development,"An investigation concerning development of methods, algorithms, software or analytical tools." 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:0000036,,research control,An investigation concerning use of data as reference or control material. +DUO:0000015,,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." 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:0000035,,gender category research,An investigation concerning specific gender categories. DUO:0000007,DS,disease specific research,This data use limitation indicates that use is allowed provided it is related to the specified disease. +DUO:0000001,,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." 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. diff --git a/src/ontology/make-csv.sparql b/src/ontology/make-csv.sparql index 50a70b8..b6dcc29 100644 --- a/src/ontology/make-csv.sparql +++ b/src/ontology/make-csv.sparql @@ -1,8 +1,9 @@ PREFIX rdfs: + SELECT ?id ?shorthand ?label ?description WHERE { ?term rdfs:label ?label ; ?description ; ?id; - ?shorthand + OPTIONAL {?term ?shorthand} } From 38b8e9439819ee16a58bdf683d63aa8f305b35da Mon Sep 17 00:00:00 2001 From: Pinar Date: Wed, 6 May 2020 16:11:26 +0200 Subject: [PATCH 19/24] Fixed DAISY link on DUO readme The link was broken, changed to DAISY GitHub page. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index c0f5864..f1a46be 100644 --- a/README.md +++ b/README.md @@ -69,7 +69,7 @@ Please use this GitHub repository's [Issue tracker](https://github.com/EBISPOT/d Several projects have now implemented DUO in production pipelines: - the Broad Institute’s Data Use Oversight System, [DUOS](https://duos.broadinstitute.org/#/home) - the European Genome-phenome Archive (EGA). See [here](https://ega-archive.org/datasets/EGAD00001000002) for example. -- the Data Information System, [DAISY](https://elixir-luxembourg.org/data-information-system-daisy) +- the Data Information System, [DAISY](https://github.com/elixir-luxembourg/daisy) [Contact](#contact) us to tell us about your implementation! From f3c2cb5557fc1aff73448c83532399d6228dd1ce Mon Sep 17 00:00:00 2001 From: Melanie Courtot Date: Fri, 17 Jul 2020 10:38:54 +0100 Subject: [PATCH 20/24] Update .travis.yml removed unnecessary jars --- .travis.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.travis.yml b/.travis.yml index 140ec95..3322381 100644 --- a/.travis.yml +++ b/.travis.yml @@ -7,13 +7,13 @@ jdk: before_script: - mkdir -p bin - export PATH=$PATH:$PWD/bin - - wget http://build.berkeleybop.org/userContent/owltools/owltools -O bin/owltools - - wget http://build.berkeleybop.org/userContent/owltools/ontology-release-runner -O bin/ontology-release-runner - - wget http://build.berkeleybop.org/userContent/owltools/owltools-runner-all.jar -O bin/owltools-runner-all.jar - - wget http://build.berkeleybop.org/userContent/owltools/owltools-oort-all.jar -O bin/owltools-oort-all.jar - - wget https://raw.githubusercontent.com/ontodev/robot/master/bin/robot -O bin/robot + # - wget http://build.berkeleybop.org/userContent/owltools/owltools -O bin/owltools +# - wget http://build.berkeleybop.org/userContent/owltools/ontology-release-runner -O bin/ontology-release-runner +# - wget http://build.berkeleybop.org/userContent/owltools/owltools-runner-all.jar -O bin/owltools-runner-all.jar +# - wget http://build.berkeleybop.org/userContent/owltools/owltools-oort-all.jar -O bin/owltools-oort-all.jar + # - wget https://raw.githubusercontent.com/ontodev/robot/master/bin/robot -O bin/robot - wget https://github.com/ontodev/robot/releases/download/v1.2.0/robot.jar -O bin/robot.jar - - wget --no-check-certificate https://raw.githubusercontent.com/cmungall/pattern2owl/master/apply-pattern.py -O bin/apply-pattern.py + # - wget --no-check-certificate https://raw.githubusercontent.com/cmungall/pattern2owl/master/apply-pattern.py -O bin/apply-pattern.py - chmod +x bin/* # command to run tests From f1b6e321509e903672d98571f208be2cda0bcf0f Mon Sep 17 00:00:00 2001 From: Melanie Courtot Date: Fri, 17 Jul 2020 10:42:24 +0100 Subject: [PATCH 21/24] Update .travis.yml reverting - owltools is needed --- .travis.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.travis.yml b/.travis.yml index 3322381..140ec95 100644 --- a/.travis.yml +++ b/.travis.yml @@ -7,13 +7,13 @@ jdk: before_script: - mkdir -p bin - export PATH=$PATH:$PWD/bin - # - wget http://build.berkeleybop.org/userContent/owltools/owltools -O bin/owltools -# - wget http://build.berkeleybop.org/userContent/owltools/ontology-release-runner -O bin/ontology-release-runner -# - wget http://build.berkeleybop.org/userContent/owltools/owltools-runner-all.jar -O bin/owltools-runner-all.jar -# - wget http://build.berkeleybop.org/userContent/owltools/owltools-oort-all.jar -O bin/owltools-oort-all.jar - # - wget https://raw.githubusercontent.com/ontodev/robot/master/bin/robot -O bin/robot + - wget http://build.berkeleybop.org/userContent/owltools/owltools -O bin/owltools + - wget http://build.berkeleybop.org/userContent/owltools/ontology-release-runner -O bin/ontology-release-runner + - wget http://build.berkeleybop.org/userContent/owltools/owltools-runner-all.jar -O bin/owltools-runner-all.jar + - wget http://build.berkeleybop.org/userContent/owltools/owltools-oort-all.jar -O bin/owltools-oort-all.jar + - wget https://raw.githubusercontent.com/ontodev/robot/master/bin/robot -O bin/robot - wget https://github.com/ontodev/robot/releases/download/v1.2.0/robot.jar -O bin/robot.jar - # - wget --no-check-certificate https://raw.githubusercontent.com/cmungall/pattern2owl/master/apply-pattern.py -O bin/apply-pattern.py + - wget --no-check-certificate https://raw.githubusercontent.com/cmungall/pattern2owl/master/apply-pattern.py -O bin/apply-pattern.py - chmod +x bin/* # command to run tests From 246b9f5027118bbe459328929999ab6006dc039c Mon Sep 17 00:00:00 2001 From: "James A. Overton" Date: Fri, 17 Jul 2020 09:17:48 -0400 Subject: [PATCH 22/24] Update URLs for owltools Based on this change to ODK: https://github.com/INCATools/ontology-development-kit/commit/707c817db29ca3af01233589b42df723bba695bb --- .travis.yml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index 140ec95..4acf998 100644 --- a/.travis.yml +++ b/.travis.yml @@ -7,10 +7,11 @@ jdk: before_script: - mkdir -p bin - export PATH=$PATH:$PWD/bin - - wget http://build.berkeleybop.org/userContent/owltools/owltools -O bin/owltools - - wget http://build.berkeleybop.org/userContent/owltools/ontology-release-runner -O bin/ontology-release-runner - - wget http://build.berkeleybop.org/userContent/owltools/owltools-runner-all.jar -O bin/owltools-runner-all.jar - - wget http://build.berkeleybop.org/userContent/owltools/owltools-oort-all.jar -O bin/owltools-oort-all.jar + - export OWLTOOLS=2020-04-06 + - wget https://github.com/owlcollab/owltools/releases/download/${OWLTOOLS}/owltools -O bin/owltools + - wget https://github.com/owlcollab/owltools/releases/download/${OWLTOOLS}/ontology-release-runner -O bin/ontology-release-runner + - wget https://github.com/owlcollab/owltools/releases/download/${OWLTOOLS}/owltools-runner-all.jar -O bin/owltools-runner-all.jar + - wget https://github.com/owlcollab/owltools/releases/download/${OWLTOOLS}/owltools-oort-all.jar -O bin/owltools-oort-all.jar - wget https://raw.githubusercontent.com/ontodev/robot/master/bin/robot -O bin/robot - wget https://github.com/ontodev/robot/releases/download/v1.2.0/robot.jar -O bin/robot.jar - wget --no-check-certificate https://raw.githubusercontent.com/cmungall/pattern2owl/master/apply-pattern.py -O bin/apply-pattern.py From 8e66fd6362cf57f70e5e6d9dfaba92c608a042f0 Mon Sep 17 00:00:00 2001 From: "James A. Overton" Date: Fri, 17 Jul 2020 09:21:05 -0400 Subject: [PATCH 23/24] Try omitting release-runner-all.jar --- .travis.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 4acf998..be3fa98 100644 --- a/.travis.yml +++ b/.travis.yml @@ -10,7 +10,6 @@ before_script: - export OWLTOOLS=2020-04-06 - wget https://github.com/owlcollab/owltools/releases/download/${OWLTOOLS}/owltools -O bin/owltools - wget https://github.com/owlcollab/owltools/releases/download/${OWLTOOLS}/ontology-release-runner -O bin/ontology-release-runner - - wget https://github.com/owlcollab/owltools/releases/download/${OWLTOOLS}/owltools-runner-all.jar -O bin/owltools-runner-all.jar - wget https://github.com/owlcollab/owltools/releases/download/${OWLTOOLS}/owltools-oort-all.jar -O bin/owltools-oort-all.jar - wget https://raw.githubusercontent.com/ontodev/robot/master/bin/robot -O bin/robot - wget https://github.com/ontodev/robot/releases/download/v1.2.0/robot.jar -O bin/robot.jar From 7f8b74273a1798d6298b0be7e008d47040335bf3 Mon Sep 17 00:00:00 2001 From: MKonopko Date: Tue, 21 Jul 2020 15:07:03 +0100 Subject: [PATCH 24/24] Adding the 2019 DUO Webinar --- README.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/README.md b/README.md index f1a46be..9ac0020 100644 --- a/README.md +++ b/README.md @@ -18,6 +18,7 @@ Table of Contents * [Examples of use](#examples-of-use) * [Tagging with ‘data use restrictions/conditions’](#tagging-with-data-use-restrictionsconditions) * [Powering dataset access screening queries](#powering-dataset-access-screening-queries) + * [DUO Webinar](#duo-webinar) * [Automated data access requests](#automated-data-access-requests) * [How does querying work when using DUO?](#how-does-querying-work-when-using-duo) * [Research Purpose : Data Use Limitation Matching](#research-purpose--data-use-limitation-matching) @@ -126,6 +127,11 @@ The following figure illustrates how DUO terms can be used to represent data use ![alt tag](https://github.com/EBISPOT/DUO/blob/master/doc/figs/DUO_matching.png "DUO matching") +### DUO Webinar +[Watch a webinar here](https://www.youtube.com/watch?v=8ZyU34xpi4M&t=1s) with an explanation of the DUO as well as several global users describing how they integrate it into their systems. + +[![](http://img.youtube.com/vi/8ZyU34xpi4M/0.jpg)](http://www.youtube.com/watch?v=8ZyU34xpi4M "") + ## Automated data access requests In the long term, we envision DUO coupled with matching algorithms such as DUOS to empower services that automatically determine if a user’s research purpose is compatible with data use restrictions on datasets and in turn determine whether to give a researcher access to the data.