diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml deleted file mode 100644 index 5100be5..0000000 --- a/src/ontology/catalog-v001.xml +++ /dev/null @@ -1,7 +0,0 @@ - - - - - - - diff --git a/src/ontology/duo-edit.owl b/src/ontology/duo-edit.owl index 17a3c52..bd4d7aa 100644 --- a/src/ontology/duo-edit.owl +++ b/src/ontology/duo-edit.owl @@ -16,8 +16,10 @@ Stephanie Dyke Giselle Kerry Moran Ncabili + J. Neil Otte Gregory Rushton David An + Cooper Stansbury Dylan Spalding Melanie Courtot @@ -35,6 +37,20 @@ + + + + DUO_preferred_label + + + + + + + + + + @@ -43,12 +59,24 @@ + + + + + + + + + + + + @@ -93,7 +121,10 @@ - An object property linking a consent code to a specific restriction which further constrains it, such as research should be restricted to a specific disease or geographical location. + 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 @@ -132,6 +163,7 @@ + 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 @@ -143,6 +175,7 @@ + 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 @@ -154,6 +187,7 @@ + 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 @@ -165,6 +199,7 @@ + no restriction This consent code primary category indicates there is no restriction on use. DUO:0000004 Note: the NRES alternative term may be confusing as in the UK it also stands for National Research Ethics Service @@ -177,6 +212,7 @@ + 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 general research use and clinical care @@ -188,9 +224,11 @@ + 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 DUO:0000006 - health/medical/biomedical research and clinical care + health or medical or biomedical research and clinical care @@ -205,9 +243,10 @@ + disease-specific research and clinical care This primary category consent code indicates that use is allowed provided it is related to the specified disease. DUO:0000007 - disease-specific research and clinical care + disease specific research and clinical care @@ -216,6 +255,7 @@ + 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 @@ -234,9 +274,10 @@ + research-specific restrictions This secondary category consent code indicates that use is limited to studies of a certain research type. DUO:0000012 - research-specific restrictions + research specific restrictions @@ -245,6 +286,7 @@ + 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 research use only @@ -256,6 +298,7 @@ + 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 @@ -267,6 +310,7 @@ + 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 genetic studies only @@ -278,6 +322,7 @@ + data use requirements Requirements indicate additional conditions set for use. DUO:0000017 data use requirements @@ -289,9 +334,10 @@ + not-for-profit use only This requirement indicates that use is limited to not-for-profit organizations. DUO:0000018 - not-for-profit use only + not for profit use only @@ -300,6 +346,7 @@ + publication required This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community. DUO:0000019 publication required @@ -311,7 +358,8 @@ - This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). + collaboration required + This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). DUO:0000020 collaboration required @@ -322,6 +370,7 @@ + ethics approval required This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. DUO:0000021 ethics approval required @@ -339,6 +388,7 @@ + geographical restriction This requirement indicates that use is limited to within a specific geographic region. DUO:0000022 geographical restriction @@ -350,6 +400,7 @@ + publication moratorium This requirement indicates that requestor agrees not to publish results of studies until a specific date publication embargo DUO:0000024 @@ -362,6 +413,7 @@ + time limit on use This requirement indicates that use is approved for a specific number of months. DUO:0000025 time limit on use @@ -373,9 +425,10 @@ + user-specific restriction This requirement indicates that use is limited to use by approved users. DUO:0000026 - user-specific restriction + user specific restriction @@ -384,9 +437,10 @@ + project-specific restriction This requirement indicates that use is limited to use within an approved project. DUO:0000027 - project-specific restriction + project specific restriction @@ -395,9 +449,10 @@ + institution-specific restriction This requirement indicates that use is limited to use within an approved institution. DUO:0000028 - institution-specific restriction + institution specific restriction @@ -406,10 +461,144 @@ - This requirement indicates that the requestor must return derived/enriched data to the database/resource. - DUO:0000029 - RTN - return to database/resource + 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. + 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. + DUO_0000032 + 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. + 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. + DUO_0000034 + age category research + + + + + + + + + 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. + DUO_0000035 + 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 concerning specific a disease or diseases. + This definition is a placeholder as a result of meetings at ICBO2018. + DUO_0000040 + disease category research @@ -435,6 +624,12 @@ + + + + + + @@ -447,5 +642,5 @@ - +