diff --git a/src/ontology/duo-edit.owl b/src/ontology/duo-edit.owl index 99bf64e..bd4d7aa 100644 --- a/src/ontology/duo-edit.owl +++ b/src/ontology/duo-edit.owl @@ -37,6 +37,14 @@ + + + + DUO_preferred_label + + + + @@ -69,14 +77,6 @@ - - - - DUO_preferred_label - - - - @@ -121,10 +121,10 @@ + 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. - is_restricted_to DUO:0000010 is restricted to @@ -163,8 +163,8 @@ + 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. - consent code DUO:0000001 consent code @@ -175,8 +175,8 @@ + consent code primary category A categorical data item indicating the primary category the consent code belongs to according to Dyke et al. 2016. - consent code primary category DUO:0000002 consent code primary category @@ -187,8 +187,8 @@ + consent code secondary category A categorical data item indicating the secondary category the consent code belongs to according to Dyke et al. 2016. - consent code secondary category DUO:0000003 consent code secondary category @@ -199,8 +199,8 @@ + no restriction This consent code primary category indicates there is no restriction on use. - no restriction DUO:0000004 Note: the NRES alternative term may be confusing as in the UK it also stands for National Research Ethics Service no restriction @@ -212,8 +212,8 @@ + 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. - general research use and clinical care DUO:0000005 general research use and clinical care @@ -224,9 +224,9 @@ + health/medical/biomedical research and clinical care 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. health medical biomedical research and clinical care - health/medical/biomedical research and clinical care DUO:0000006 health or medical or biomedical research and clinical care @@ -243,8 +243,8 @@ + disease-specific research and clinical care This primary category consent code indicates that use is allowed provided it is related to the specified disease. - disease-specific research and clinical care DUO:0000007 disease specific research and clinical care @@ -255,9 +255,9 @@ + 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. population origins/ancestry research - population origins or ancestry research DUO:0000011 population origins or ancestry research @@ -274,8 +274,8 @@ + research-specific restrictions This secondary category consent code indicates that use is limited to studies of a certain research type. - research-specific restrictions DUO:0000012 research specific restrictions @@ -286,8 +286,8 @@ + 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). - research use only DUO:0000014 research use only @@ -298,8 +298,8 @@ + 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. - no general methods research DUO:0000015 no general methods research @@ -310,8 +310,8 @@ + genetic studies only This secondary category consent code indicates that use is limited to genetic studies only (i.e., no phenotype-only research) - genetic studies only DUO:0000016 genetic studies only @@ -322,8 +322,8 @@ + data use requirements Requirements indicate additional conditions set for use. - data use requirements DUO:0000017 data use requirements @@ -334,8 +334,8 @@ + not-for-profit use only This requirement indicates that use is limited to not-for-profit organizations. - not-for-profit use only DUO:0000018 not for profit use only @@ -346,8 +346,8 @@ + publication required This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community. - publication required DUO:0000019 publication required @@ -358,8 +358,8 @@ + collaboration required This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). - collaboration required DUO:0000020 collaboration required @@ -370,8 +370,8 @@ + ethics approval required This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. - ethics approval required DUO:0000021 ethics approval required @@ -388,8 +388,8 @@ + geographical restriction This requirement indicates that use is limited to within a specific geographic region. - geographical restriction DUO:0000022 geographical restriction @@ -400,9 +400,9 @@ + publication moratorium This requirement indicates that requestor agrees not to publish results of studies until a specific date publication embargo - publication moratorium DUO:0000024 publication moratorium @@ -413,8 +413,8 @@ + time limit on use This requirement indicates that use is approved for a specific number of months. - time limit on use DUO:0000025 time limit on use @@ -425,8 +425,8 @@ + user-specific restriction This requirement indicates that use is limited to use by approved users. - user-specific restriction DUO:0000026 user specific restriction @@ -437,8 +437,8 @@ + project-specific restriction This requirement indicates that use is limited to use within an approved project. - project-specific restriction DUO:0000027 project specific restriction @@ -449,8 +449,8 @@ + institution-specific restriction This requirement indicates that use is limited to use within an approved institution. - institution-specific restriction DUO:0000028 institution specific restriction @@ -461,8 +461,8 @@ + return to database/resource This requirement indicates that the requestor must return derived/enriched data to the database/resource. - return to database/resource DUO:0000029 RTN return to database or resource @@ -474,9 +474,9 @@ + 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. - method development DUO_0000031 method development @@ -487,10 +487,10 @@ + population research An investigation concerning a specific population group. Should be paired with the an ontology term representing this population (e.g., xxx). This definition is a placeholder as a result of meetings at ICBO2018. - population research DUO_0000032 population research @@ -501,9 +501,9 @@ + ancestry research An investigation concerning ancestry or population origins. This definition is a placeholder as a result of meetings at ICBO2018. - ancestry research DUO_0000033 ancestry research @@ -514,10 +514,10 @@ + age category research An investigation concerning specific age categories. Should be paired with the an ontology term representing this population (e.g., xxx). This definition is a placeholder as a result of meetings at ICBO2018. - age category research DUO_0000034 age category research @@ -528,10 +528,10 @@ + gender category research An investigation concerning specific gender categories. Should be paired with the an ontology term representing this population (e.g., xxx). This definition is a placeholder as a result of meetings at ICBO2018. - gender category research DUO_0000035 gender category research @@ -542,9 +542,9 @@ + 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. - research control DUO_0000036 research control @@ -555,9 +555,9 @@ + biomedical research An investigation concerning health, medical, or biomedical research. This definition is a placeholder as a result of meetings at ICBO2018. - biomedical research DUO_0000037 biomedical research @@ -568,9 +568,9 @@ + 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. - genetic research DUO_0000038 genetic research @@ -581,9 +581,9 @@ + drug development research Biomedical research concerning drug development. This definition is a placeholder as a result of meetings at ICBO2018. - drug development research DUO_0000039 drug development research @@ -594,9 +594,9 @@ + disease category research Biomedical research concerning specific a disease or diseases. This definition is a placeholder as a result of meetings at ICBO2018. - disease category research DUO_0000040 disease category research diff --git a/src/ontology/duo.owl b/src/ontology/duo.owl index 53f3cc7..b44abc4 100644 --- a/src/ontology/duo.owl +++ b/src/ontology/duo.owl @@ -10,8 +10,7 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:obo="http://purl.obolibrary.org/obo/" xmlns:foaf="http://xmlns.com/foaf/0.1/" - xmlns:dc="http://purl.org/dc/elements/1.1/" - xmlns:duo="http://purl.obolibrary.org/obo/duo.owl#"> + xmlns:dc="http://purl.org/dc/elements/1.1/"> @@ -39,6 +38,14 @@ + + + + DUO_preferred_label + + + + @@ -71,14 +78,6 @@ - - - - DUO_preferred_label - - - - @@ -123,10 +122,10 @@ + 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. - is_restricted_to DUO:0000010 is restricted to @@ -439,8 +438,8 @@ + 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. - consent code DUO:0000001 consent code @@ -451,8 +450,8 @@ + consent code primary category A categorical data item indicating the primary category the consent code belongs to according to Dyke et al. 2016. - consent code primary category DUO:0000002 consent code primary category @@ -463,8 +462,8 @@ + consent code secondary category A categorical data item indicating the secondary category the consent code belongs to according to Dyke et al. 2016. - consent code secondary category DUO:0000003 consent code secondary category @@ -475,8 +474,8 @@ + no restriction This consent code primary category indicates there is no restriction on use. - no restriction DUO:0000004 Note: the NRES alternative term may be confusing as in the UK it also stands for National Research Ethics Service no restriction @@ -488,8 +487,8 @@ + 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. - general research use and clinical care DUO:0000005 general research use and clinical care @@ -500,9 +499,9 @@ + health/medical/biomedical research and clinical care 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. health medical biomedical research and clinical care - health/medical/biomedical research and clinical care DUO:0000006 health or medical or biomedical research and clinical care @@ -519,8 +518,8 @@ + disease-specific research and clinical care This primary category consent code indicates that use is allowed provided it is related to the specified disease. - disease-specific research and clinical care DUO:0000007 disease specific research and clinical care @@ -531,9 +530,9 @@ + 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. population origins/ancestry research - population origins or ancestry research DUO:0000011 population origins or ancestry research @@ -550,8 +549,8 @@ + research-specific restrictions This secondary category consent code indicates that use is limited to studies of a certain research type. - research-specific restrictions DUO:0000012 research specific restrictions @@ -562,8 +561,8 @@ + 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). - research use only DUO:0000014 research use only @@ -574,8 +573,8 @@ + 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. - no general methods research DUO:0000015 no general methods research @@ -586,8 +585,8 @@ + genetic studies only This secondary category consent code indicates that use is limited to genetic studies only (i.e., no phenotype-only research) - genetic studies only DUO:0000016 genetic studies only @@ -598,8 +597,8 @@ + data use requirements Requirements indicate additional conditions set for use. - data use requirements DUO:0000017 data use requirements @@ -610,8 +609,8 @@ + not-for-profit use only This requirement indicates that use is limited to not-for-profit organizations. - not-for-profit use only DUO:0000018 not for profit use only @@ -622,8 +621,8 @@ + publication required This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community. - publication required DUO:0000019 publication required @@ -634,8 +633,8 @@ + collaboration required This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). - collaboration required DUO:0000020 collaboration required @@ -646,8 +645,8 @@ + ethics approval required This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. - ethics approval required DUO:0000021 ethics approval required @@ -664,8 +663,8 @@ + geographical restriction This requirement indicates that use is limited to within a specific geographic region. - geographical restriction DUO:0000022 geographical restriction @@ -676,9 +675,9 @@ + publication moratorium This requirement indicates that requestor agrees not to publish results of studies until a specific date publication embargo - publication moratorium DUO:0000024 publication moratorium @@ -689,8 +688,8 @@ + time limit on use This requirement indicates that use is approved for a specific number of months. - time limit on use DUO:0000025 time limit on use @@ -701,8 +700,8 @@ + user-specific restriction This requirement indicates that use is limited to use by approved users. - user-specific restriction DUO:0000026 user specific restriction @@ -713,8 +712,8 @@ + project-specific restriction This requirement indicates that use is limited to use within an approved project. - project-specific restriction DUO:0000027 project specific restriction @@ -725,8 +724,8 @@ + institution-specific restriction This requirement indicates that use is limited to use within an approved institution. - institution-specific restriction DUO:0000028 institution specific restriction @@ -737,8 +736,8 @@ + return to database/resource This requirement indicates that the requestor must return derived/enriched data to the database/resource. - return to database/resource DUO:0000029 RTN return to database or resource @@ -750,9 +749,9 @@ + 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. - method development DUO_0000031 method development @@ -763,10 +762,10 @@ + population research An investigation concerning a specific population group. Should be paired with the an ontology term representing this population (e.g., xxx). This definition is a placeholder as a result of meetings at ICBO2018. - population research DUO_0000032 population research @@ -777,9 +776,9 @@ + ancestry research An investigation concerning ancestry or population origins. This definition is a placeholder as a result of meetings at ICBO2018. - ancestry research DUO_0000033 ancestry research @@ -790,10 +789,10 @@ + age category research An investigation concerning specific age categories. Should be paired with the an ontology term representing this population (e.g., xxx). This definition is a placeholder as a result of meetings at ICBO2018. - age category research DUO_0000034 age category research @@ -804,10 +803,10 @@ + gender category research An investigation concerning specific gender categories. Should be paired with the an ontology term representing this population (e.g., xxx). This definition is a placeholder as a result of meetings at ICBO2018. - gender category research DUO_0000035 gender category research @@ -818,9 +817,9 @@ + 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. - research control DUO_0000036 research control @@ -831,9 +830,9 @@ + biomedical research An investigation concerning health, medical, or biomedical research. This definition is a placeholder as a result of meetings at ICBO2018. - biomedical research DUO_0000037 biomedical research @@ -844,9 +843,9 @@ + 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. - genetic research DUO_0000038 genetic research @@ -857,9 +856,9 @@ + drug development research Biomedical research concerning drug development. This definition is a placeholder as a result of meetings at ICBO2018. - drug development research DUO_0000039 drug development research @@ -870,9 +869,9 @@ + disease category research Biomedical research concerning specific a disease or diseases. This definition is a placeholder as a result of meetings at ICBO2018. - disease category research DUO_0000040 disease category research