From aef12a39b42c0b8a2871c92156cb93e8025dd3c6 Mon Sep 17 00:00:00 2001 From: Melanie Courtot Date: Mon, 9 Apr 2018 11:19:22 +0100 Subject: [PATCH 01/12] Update README.md added EGA link --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ccd152a..2eebe3c 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ An ontology based on the consent codes decsription from the Dyke et al. paper at It allows to semantically tag datasets with restriction about their usage, making them discoverable automatically based on the authorization level of users, or intended usage. -This resource is based on the OBO Foundry principles, and its use is under review by the European Genome-phenome Archive (EGA) at EMBL-EBI as well as the Broad Institute for the [Data Use Oversight System](https://duos.broadinstitute.org/#/home) (DUOS). +This resource is based on the OBO Foundry principles, and its use is under review by the [European Genome-phenome Archive](https://ega-archive.org) (EGA) at EMBL-EBI as well as the Broad Institute for the [Data Use Oversight System](https://duos.broadinstitute.org/#/home) (DUOS). Here is a hierarchical view of the DUO: From 6d18c7f4d49ba7b1835af2a329b0453f826c5f61 Mon Sep 17 00:00:00 2001 From: CooperStansbury Date: Fri, 10 Aug 2018 13:43:58 -0400 Subject: [PATCH 02/12] add new classes and definitions of processes per discussions at ICBO2018 --- src/ontology/duo-edit.owl | 109 +++++++++++++++++++++++++++++++++++++- 1 file changed, 107 insertions(+), 2 deletions(-) diff --git a/src/ontology/duo-edit.owl b/src/ontology/duo-edit.owl index 17a3c52..3ac0056 100644 --- a/src/ontology/duo-edit.owl +++ b/src/ontology/duo-edit.owl @@ -93,7 +93,7 @@ - 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. + A is restricted to B iff A is a continuant and B is an investigation and A may only participate in instances of a class C, of which B is an instance. DUO:0000010 is restricted to @@ -111,6 +111,12 @@ + + + + + + @@ -414,6 +420,105 @@ + + + + + general research + + + + + + + + + method development + + + + + + + + + population research + + + + + + + + + ancestry research + + + + + + + + + age category research + + + + + + + + + gender category research + + + + + + + + + research control + + + + + + + + + biomedical research + + + + + + + + + genetic research + + + + + + + + + drug development research + + + + + + + + + disease category research + + + + @@ -447,5 +552,5 @@ - + From 12764e0531556d08d7125e7e2b121f521a109eaa Mon Sep 17 00:00:00 2001 From: CooperStansbury Date: Fri, 10 Aug 2018 16:51:44 -0400 Subject: [PATCH 03/12] refined definitions for research processes based on Toronto DUO meeting proceedings --- src/ontology/duo-edit.owl | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/ontology/duo-edit.owl b/src/ontology/duo-edit.owl index 3ac0056..fe344ad 100644 --- a/src/ontology/duo-edit.owl +++ b/src/ontology/duo-edit.owl @@ -433,6 +433,7 @@ + Development of methods, algorithms, software and analytical tools. method development @@ -442,6 +443,7 @@ + Research concerning a specific population group; Should be paired with the an ontology term representing this population (e.g., xxx). population research @@ -451,6 +453,7 @@ + Research concerning ancestry or population origins. ancestry research @@ -460,6 +463,7 @@ + Research concerning specific age categories; Should be paired with the an ontology term representing this population (e.g., xxx). age category research @@ -469,6 +473,7 @@ + Research concerning specific gender categories; Should be paired with the an ontology term representing this population (e.g., xxx). gender category research @@ -478,6 +483,7 @@ + Use of data as reference or control material. research control @@ -487,6 +493,7 @@ + Health/medical/biomedical research. biomedical research @@ -496,6 +503,7 @@ + Research concerning genetics (i.e., the study of genes, genetic variations and heredity). genetic research @@ -505,6 +513,7 @@ + Research concerning drug development. drug development research @@ -514,6 +523,7 @@ + Research concerning specific disease/s. disease category research From 65977fd8c8b0029c8895c0bbb915d28b294ab002 Mon Sep 17 00:00:00 2001 From: CooperStansbury Date: Fri, 10 Aug 2018 16:56:49 -0400 Subject: [PATCH 04/12] IAO:denotes to reflect design patterns results of ICBO2018 discussions --- src/ontology/duo-edit.owl | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/src/ontology/duo-edit.owl b/src/ontology/duo-edit.owl index fe344ad..f102889 100644 --- a/src/ontology/duo-edit.owl +++ b/src/ontology/duo-edit.owl @@ -43,12 +43,24 @@ + + + + + + + + + + + + @@ -94,12 +106,20 @@ A is restricted to B iff A is a continuant 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 + + + + + + + + + + + @@ -444,6 +450,11 @@ + 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. + A process of using data in research for a specific purpose. + Suggeest using OBI 'investigation' (http://purl.obolibrary.org/obo/OBI_0000066) + This definition is a placeholder as a result of meetings at ICBO2018. + DUO_0000030 general research @@ -453,7 +464,9 @@ - Development of methods, algorithms, software and analytical tools. + General research 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 @@ -463,7 +476,10 @@ - Research concerning a specific population group; Should be paired with the an ontology term representing this population (e.g., xxx). + General research 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 @@ -473,7 +489,9 @@ - Research concerning ancestry or population origins. + General research concerning ancestry or population origins. + This definition is a placeholder as a result of meetings at ICBO2018. + DUO_0000033 ancestry research @@ -483,7 +501,10 @@ - Research concerning specific age categories; Should be paired with the an ontology term representing this population (e.g., xxx). + General research 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 @@ -493,7 +514,10 @@ - Research concerning specific gender categories; Should be paired with the an ontology term representing this population (e.g., xxx). + General research 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 @@ -504,6 +528,8 @@ Use of data as reference or control material. + This definition is a placeholder as a result of meetings at ICBO2018. + DUO_0000036 research control @@ -513,7 +539,9 @@ - Health/medical/biomedical research. + General research concerning health, medical, or biomedical research. + This definition is a placeholder as a result of meetings at ICBO2018. + DUO_0000037 biomedical research @@ -523,7 +551,9 @@ - Research concerning genetics (i.e., the study of genes, genetic variations and heredity). + General 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 @@ -533,7 +563,9 @@ - Research concerning drug development. + General research concerning drug development. + This definition is a placeholder as a result of meetings at ICBO2018. + DUO_0000039 drug development research @@ -543,7 +575,9 @@ - Research concerning specific disease/s. + General research concerning specific a disease or diseases. + This definition is a placeholder as a result of meetings at ICBO2018. + DUO_0000040 disease category research From eb8a509de7006feb251b899939aa66fe296f6977 Mon Sep 17 00:00:00 2001 From: CooperStansbury Date: Wed, 15 Aug 2018 09:20:27 -0400 Subject: [PATCH 06/12] add Cooper and Neil to contributor list --- src/ontology/duo-edit.owl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/ontology/duo-edit.owl b/src/ontology/duo-edit.owl index be1a2a7..4d8f0f8 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 From 3fc2687e92f9e9170aec44567b72a185b574980e Mon Sep 17 00:00:00 2001 From: CooperStansbury Date: Wed, 15 Aug 2018 10:38:15 -0400 Subject: [PATCH 07/12] fix xsd:string types on all annotations --- src/ontology/duo-edit.owl | 86 +++++++++++++++++++-------------------- 1 file changed, 43 insertions(+), 43 deletions(-) diff --git a/src/ontology/duo-edit.owl b/src/ontology/duo-edit.owl index 4d8f0f8..40281e7 100644 --- a/src/ontology/duo-edit.owl +++ b/src/ontology/duo-edit.owl @@ -113,7 +113,7 @@ - A is restricted to B iff A is a continuant and B is an investigation and A may only participate in instances of a class C, of which B is an instance. + 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 @@ -345,7 +345,7 @@ - This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). + This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). DUO:0000020 collaboration required @@ -440,9 +440,9 @@ - This requirement indicates that the requestor must return derived/enriched data to the database/resource. - DUO:0000029 - RTN + This requirement indicates that the requestor must return derived/enriched data to the database/resource. + DUO:0000029 + RTN return to database/resource @@ -452,12 +452,12 @@ - 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. - A process of using data in research for a specific purpose. - Suggeest using OBI 'investigation' (http://purl.obolibrary.org/obo/OBI_0000066) - This definition is a placeholder as a result of meetings at ICBO2018. + 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. + A process of using data in research for a specific purpose. + Suggeest using OBI 'investigation' (http://purl.obolibrary.org/obo/OBI_0000066) + This definition is a placeholder as a result of meetings at ICBO2018. DUO_0000030 - general research + general research @@ -466,10 +466,10 @@ - General research concerning development of methods, algorithms, software or analytical tools. - This definition is a placeholder as a result of meetings at ICBO2018. + General research 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 + method development @@ -478,11 +478,11 @@ - General research 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. + General research 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 + population research @@ -491,10 +491,10 @@ - General research concerning ancestry or population origins. - This definition is a placeholder as a result of meetings at ICBO2018. + General research concerning ancestry or population origins. + This definition is a placeholder as a result of meetings at ICBO2018. DUO_0000033 - ancestry research + ancestry research @@ -503,11 +503,11 @@ - General research 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. + General research 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 + age category research @@ -516,11 +516,11 @@ - General research 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. + General research 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 + gender category research @@ -529,10 +529,10 @@ - Use of data as reference or control material. - This definition is a placeholder as a result of meetings at ICBO2018. + Use of data as reference or control material. + This definition is a placeholder as a result of meetings at ICBO2018. DUO_0000036 - research control + research control @@ -541,10 +541,10 @@ - General research concerning health, medical, or biomedical research. - This definition is a placeholder as a result of meetings at ICBO2018. + General research concerning health, medical, or biomedical research. + This definition is a placeholder as a result of meetings at ICBO2018. DUO_0000037 - biomedical research + biomedical research @@ -553,10 +553,10 @@ - General 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. + General 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 + genetic research @@ -565,10 +565,10 @@ - General research concerning drug development. - This definition is a placeholder as a result of meetings at ICBO2018. + General research concerning drug development. + This definition is a placeholder as a result of meetings at ICBO2018. DUO_0000039 - drug development research + drug development research @@ -577,10 +577,10 @@ - General research concerning specific a disease or diseases. - This definition is a placeholder as a result of meetings at ICBO2018. + General research concerning specific a disease or diseases. + This definition is a placeholder as a result of meetings at ICBO2018. DUO_0000040 - disease category research + disease category research From 8fa194468eda5e044314df813cfb02cf664e3de8 Mon Sep 17 00:00:00 2001 From: CooperStansbury Date: Wed, 15 Aug 2018 10:44:11 -0400 Subject: [PATCH 08/12] add OBI investigation per discussions with Neil and Melanie 8.21.2018 --- src/ontology/duo-edit.owl | 66 ++++++++++++++------------------------- 1 file changed, 23 insertions(+), 43 deletions(-) diff --git a/src/ontology/duo-edit.owl b/src/ontology/duo-edit.owl index 40281e7..5df724f 100644 --- a/src/ontology/duo-edit.owl +++ b/src/ontology/duo-edit.owl @@ -122,12 +122,6 @@ - - - - - - - - - - - @@ -448,25 +436,11 @@ - - - - - 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. - A process of using data in research for a specific purpose. - Suggeest using OBI 'investigation' (http://purl.obolibrary.org/obo/OBI_0000066) - This definition is a placeholder as a result of meetings at ICBO2018. - DUO_0000030 - general research - - - - - - General research concerning development of methods, algorithms, software or analytical tools. + + 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 @@ -477,8 +451,8 @@ - - General research concerning a specific population group. + + 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 @@ -490,8 +464,8 @@ - - General research concerning ancestry or population origins. + + An investigation concerning ancestry or population origins. This definition is a placeholder as a result of meetings at ICBO2018. DUO_0000033 ancestry research @@ -502,8 +476,8 @@ - - General research concerning specific age categories. + + 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 @@ -515,8 +489,8 @@ - - General research concerning specific gender categories. + + 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 @@ -528,8 +502,8 @@ - - Use of data as reference or control material. + + 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 @@ -540,8 +514,8 @@ - - General research concerning health, medical, or 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 @@ -553,7 +527,7 @@ - General research concerning genetics (i.e., the study of genes, genetic variations and heredity). + 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 @@ -565,7 +539,7 @@ - General research concerning drug development. + Biomedical research concerning drug development. This definition is a placeholder as a result of meetings at ICBO2018. DUO_0000039 drug development research @@ -577,7 +551,7 @@ - General research concerning specific a disease or diseases. + 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 @@ -606,6 +580,12 @@ + + + + + + From 37299bcd5954903eb1b83fcdfdef33d7691289d1 Mon Sep 17 00:00:00 2001 From: CooperStansbury Date: Wed, 5 Sep 2018 09:09:45 -0400 Subject: [PATCH 09/12] add DUO preferred label to retain labels Per discussion 8/21 with Melanie and Neil --- src/ontology/Makefile | 43 +++++++++++++------------- src/ontology/duo-edit.owl | 64 +++++++++++++++++++++++++++++++++------ 2 files changed, 75 insertions(+), 32 deletions(-) diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 04c5fa2..08beb2e 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -8,43 +8,42 @@ OWLTOOLS= owltools USECAT= --use-catalog all: $(ONT).owl - + test:all -prepare_release: +prepare_release: $(ROBOT) reason -i $(SRC) -r ELK relax reduce -r ELK annotate -V $(BASE)/releases/`date +%Y-%m-%d`/$(ONT).owl -o $(ONT).owl cp $(ONT).owl $(RELEASEDIR) &&\ - git add $(RELEASEDIR)/*.owl + git add $(RELEASEDIR)/*.owl echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release on github" - + $(ONT).owl: $(SRC) $(ROBOT) reason -i $< -r ELK relax reduce -r ELK annotate -V $(BASE)/releases/`date +%Y-%m-%d`/$(ONT).owl -o $@ -# remove OBO which doesn't work with IAO and is not needed -#$(ONT).obo: $(ONT).owl -# $(ROBOT) convert -i $< -f obo -o $(ONT).obo.tmp && mv $(ONT).obo.tmp $@ - - +# # remove OBO which doesn't work with IAO and is not needed +# $(ONT).obo: $(ONT).owl +# $(ROBOT) convert -i $< -f obo -o $(ONT).obo.tmp && mv $(ONT).obo.tmp $@ +# # IMPORTS = iao bfo # IMPORTS_OWL = $(patsubst %, imports/%_import.owl,$(IMPORTS)) - +# # # Make this target to regenerate ALL # all_imports: $(IMPORTS_OWL) - +# # # Use ROBOT, driven entirely by terms lists NOT from source ontology # imports/%_import.owl: mirror/%.owl imports/%_terms.txt # $(ROBOT) extract -i $< -T imports/$*_terms.txt --method BOT -O $(BASE)/$@ -o $@ # .PRECIOUS: imports/%_import.owl - -# remove OBO which doesn't work with IAO and is not needed +# +# # remove OBO which doesn't work with IAO and is not needed # imports/%_import.obo: imports/%_import.owl -# $(OWLTOOLS) $(USECAT) $< -o -f obo $@ - -# clone remote ontology locally, performing some excision of relations and annotations -mirror/%.owl: $(SRC) - $(OWLTOOLS) $(OBO)/$*.owl --remove-annotation-assertions -l -s -d --remove-dangling-annotations -o $@ -.PRECIOUS: mirror/%.owl - -release: $(ONT).owl #$(ONT).obo - cp $^ $RELEASEDIR +# $(OWLTOOLS) $(USECAT) $< -o -f obo $@ +# +# # clone remote ontology locally, performing some excision of relations and annotations +# mirror/%.owl: $(SRC) +# $(OWLTOOLS) $(OBO)/$*.owl --remove-annotation-assertions -l -s -d --remove-dangling-annotations -o $@ +# .PRECIOUS: mirror/%.owl +# +# release: $(ONT).owl #$(ONT).obo +# cp $^ $RELEASEDIR diff --git a/src/ontology/duo-edit.owl b/src/ontology/duo-edit.owl index 5df724f..99bf64e 100644 --- a/src/ontology/duo-edit.owl +++ b/src/ontology/duo-edit.owl @@ -69,6 +69,14 @@ + + + + DUO_preferred_label + + + + @@ -114,8 +122,9 @@ 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. + 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 @@ -155,6 +164,7 @@ 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 @@ -166,6 +176,7 @@ 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 @@ -177,6 +188,7 @@ 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 @@ -188,6 +200,7 @@ 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 @@ -200,6 +213,7 @@ 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. + general research use and clinical care DUO:0000005 general research use and clinical care @@ -211,8 +225,10 @@ 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/medical/biomedical research and clinical care + health or medical or biomedical research and clinical care @@ -228,8 +244,9 @@ 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 + disease specific research and clinical care @@ -240,6 +257,7 @@ 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 + population origins or ancestry research DUO:0000011 population origins or ancestry research @@ -257,8 +275,9 @@ 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 + research specific restrictions @@ -268,6 +287,7 @@ 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 @@ -279,6 +299,7 @@ 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 @@ -290,6 +311,7 @@ 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 @@ -301,6 +323,7 @@ Requirements indicate additional conditions set for use. + data use requirements DUO:0000017 data use requirements @@ -312,8 +335,9 @@ This requirement indicates that use is limited to not-for-profit organizations. + not-for-profit use only DUO:0000018 - not-for-profit use only + not for profit use only @@ -323,6 +347,7 @@ 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 @@ -334,6 +359,7 @@ This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). + collaboration required DUO:0000020 collaboration required @@ -345,6 +371,7 @@ This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. + ethics approval required DUO:0000021 ethics approval required @@ -362,6 +389,7 @@ This requirement indicates that use is limited to within a specific geographic region. + geographical restriction DUO:0000022 geographical restriction @@ -374,6 +402,7 @@ This requirement indicates that requestor agrees not to publish results of studies until a specific date publication embargo + publication moratorium DUO:0000024 publication moratorium @@ -385,6 +414,7 @@ This requirement indicates that use is approved for a specific number of months. + time limit on use DUO:0000025 time limit on use @@ -396,8 +426,9 @@ This requirement indicates that use is limited to use by approved users. + user-specific restriction DUO:0000026 - user-specific restriction + user specific restriction @@ -407,8 +438,9 @@ This requirement indicates that use is limited to use within an approved project. + project-specific restriction DUO:0000027 - project-specific restriction + project specific restriction @@ -418,8 +450,9 @@ This requirement indicates that use is limited to use within an approved institution. + institution-specific restriction DUO:0000028 - institution-specific restriction + institution specific restriction @@ -429,9 +462,10 @@ 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/resource + return to database or resource @@ -442,6 +476,7 @@ 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 @@ -455,6 +490,7 @@ 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 @@ -467,6 +503,7 @@ 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 @@ -480,6 +517,7 @@ 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 @@ -493,6 +531,7 @@ 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 @@ -505,6 +544,7 @@ 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 @@ -517,6 +557,7 @@ 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 @@ -529,6 +570,7 @@ 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 @@ -541,6 +583,7 @@ 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 @@ -553,6 +596,7 @@ 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 From cc07c0e31780e28a77aa17af7251b776b13f6e85 Mon Sep 17 00:00:00 2001 From: CooperStansbury Date: Wed, 5 Sep 2018 11:18:00 -0400 Subject: [PATCH 10/12] roll-back to original Makefile run 'make' on updated duo-edit.owl to finalize first PR to DUO --- src/ontology/Makefile | 43 +- src/ontology/catalog-v001.xml | 7 - src/ontology/duo.owl | 2049 +++++++++++++++++++++++++++++++++ 3 files changed, 2071 insertions(+), 28 deletions(-) delete mode 100644 src/ontology/catalog-v001.xml create mode 100644 src/ontology/duo.owl diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 08beb2e..04c5fa2 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -8,42 +8,43 @@ OWLTOOLS= owltools USECAT= --use-catalog all: $(ONT).owl - + test:all -prepare_release: +prepare_release: $(ROBOT) reason -i $(SRC) -r ELK relax reduce -r ELK annotate -V $(BASE)/releases/`date +%Y-%m-%d`/$(ONT).owl -o $(ONT).owl cp $(ONT).owl $(RELEASEDIR) &&\ - git add $(RELEASEDIR)/*.owl + git add $(RELEASEDIR)/*.owl echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release on github" - + $(ONT).owl: $(SRC) $(ROBOT) reason -i $< -r ELK relax reduce -r ELK annotate -V $(BASE)/releases/`date +%Y-%m-%d`/$(ONT).owl -o $@ -# # remove OBO which doesn't work with IAO and is not needed -# $(ONT).obo: $(ONT).owl -# $(ROBOT) convert -i $< -f obo -o $(ONT).obo.tmp && mv $(ONT).obo.tmp $@ -# +# remove OBO which doesn't work with IAO and is not needed +#$(ONT).obo: $(ONT).owl +# $(ROBOT) convert -i $< -f obo -o $(ONT).obo.tmp && mv $(ONT).obo.tmp $@ + + # IMPORTS = iao bfo # IMPORTS_OWL = $(patsubst %, imports/%_import.owl,$(IMPORTS)) -# + # # Make this target to regenerate ALL # all_imports: $(IMPORTS_OWL) -# + # # Use ROBOT, driven entirely by terms lists NOT from source ontology # imports/%_import.owl: mirror/%.owl imports/%_terms.txt # $(ROBOT) extract -i $< -T imports/$*_terms.txt --method BOT -O $(BASE)/$@ -o $@ # .PRECIOUS: imports/%_import.owl -# -# # remove OBO which doesn't work with IAO and is not needed + +# remove OBO which doesn't work with IAO and is not needed # imports/%_import.obo: imports/%_import.owl -# $(OWLTOOLS) $(USECAT) $< -o -f obo $@ -# -# # clone remote ontology locally, performing some excision of relations and annotations -# mirror/%.owl: $(SRC) -# $(OWLTOOLS) $(OBO)/$*.owl --remove-annotation-assertions -l -s -d --remove-dangling-annotations -o $@ -# .PRECIOUS: mirror/%.owl -# -# release: $(ONT).owl #$(ONT).obo -# cp $^ $RELEASEDIR +# $(OWLTOOLS) $(USECAT) $< -o -f obo $@ + +# clone remote ontology locally, performing some excision of relations and annotations +mirror/%.owl: $(SRC) + $(OWLTOOLS) $(OBO)/$*.owl --remove-annotation-assertions -l -s -d --remove-dangling-annotations -o $@ +.PRECIOUS: mirror/%.owl + +release: $(ONT).owl #$(ONT).obo + cp $^ $RELEASEDIR 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.owl b/src/ontology/duo.owl new file mode 100644 index 0000000..53f3cc7 --- /dev/null +++ b/src/ontology/duo.owl @@ -0,0 +1,2049 @@ + + + + + + Stephanie Dyke + Giselle Kerry + Moran Ncabili + J. Neil Otte + Gregory Rushton + David An + Cooper Stansbury + Dylan Spalding + Melanie Courtot + + + + + + + + + + + + + + + + + + + definition + + + + + + + + + + + + + + + + + + + + + + + + + + DUO_preferred_label + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + Requirements indicate additional conditions set for use. + data use requirements + DUO:0000017 + data use requirements + + + + + + + + + This requirement indicates that use is limited to not-for-profit organizations. + not-for-profit use only + DUO:0000018 + not for profit use only + + + + + + + + + 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 + + + + + + + + + This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). + collaboration required + DUO:0000020 + collaboration required + + + + + + + + + This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. + ethics approval required + DUO:0000021 + ethics approval required + + + + + + + + + + + + + + + This requirement indicates that use is limited to within a specific geographic region. + geographical restriction + DUO:0000022 + geographical restriction + + + + + + + + + This requirement indicates that requestor agrees not to publish results of studies until a specific date + publication embargo + publication moratorium + DUO:0000024 + publication moratorium + + + + + + + + + This requirement indicates that use is approved for a specific number of months. + time limit on use + DUO:0000025 + time limit on use + + + + + + + + + This requirement indicates that use is limited to use by approved users. + user-specific restriction + DUO:0000026 + user specific restriction + + + + + + + + + This requirement indicates that use is limited to use within an approved project. + project-specific restriction + DUO:0000027 + project specific restriction + + + + + + + + + This requirement indicates that use is limited to use within an approved institution. + institution-specific restriction + DUO:0000028 + institution specific restriction + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 11d3780c60b050b98db4a61a56fc8fdff6ac3823 Mon Sep 17 00:00:00 2001 From: CooperStansbury Date: Wed, 5 Sep 2018 11:44:27 -0400 Subject: [PATCH 11/12] fix DUO_preferred_label PURL --- src/ontology/duo-edit.owl | 86 ++++++++++++++++++------------------- src/ontology/duo.owl | 89 +++++++++++++++++++-------------------- 2 files changed, 87 insertions(+), 88 deletions(-) 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 From aa06f32bc35b24673d6cc2eddfd0c8a320e643a6 Mon Sep 17 00:00:00 2001 From: Melanie Courtot Date: Fri, 7 Sep 2018 11:39:31 +0100 Subject: [PATCH 12/12] Delete duo.owl Removing the main duo.owl file as this should be generated by the makefile --- src/ontology/duo.owl | 2048 ------------------------------------------ 1 file changed, 2048 deletions(-) delete mode 100644 src/ontology/duo.owl diff --git a/src/ontology/duo.owl b/src/ontology/duo.owl deleted file mode 100644 index b44abc4..0000000 --- a/src/ontology/duo.owl +++ /dev/null @@ -1,2048 +0,0 @@ - - - - - - Stephanie Dyke - Giselle Kerry - Moran Ncabili - J. Neil Otte - Gregory Rushton - David An - Cooper Stansbury - Dylan Spalding - Melanie Courtot - - - - - - - - - - - - - DUO_preferred_label - - - - - - - - - - - - - - definition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - 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 - general research use and clinical care - - - - - - - - - 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 or medical or biomedical research and clinical care - - - - - - - - - - - - - - - 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 - - - - - - - - - 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 - 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 - 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 - 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 - 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 is limited to not-for-profit organizations. - DUO:0000018 - 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 - publication required - - - - - - - - - collaboration required - This requirement indicates that the requestor must agree to collaboration with the primary study investigator(s). - DUO:0000020 - collaboration required - - - - - - - - - ethics approval required - This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. - DUO:0000021 - ethics approval required - - - - - - - - - - - - - - - geographical restriction - This requirement indicates that use is limited to within a specific geographic region. - DUO:0000022 - geographical restriction - - - - - - - - - publication moratorium - This requirement indicates that requestor agrees not to publish results of studies until a specific date - publication embargo - DUO:0000024 - publication moratorium - - - - - - - - - time limit on use - This requirement indicates that use is approved for a specific number of months. - DUO:0000025 - time limit on use - - - - - - - - - user-specific restriction - This requirement indicates that use is limited to use by approved users. - DUO:0000026 - user specific restriction - - - - - - - - - project-specific restriction - This requirement indicates that use is limited to use within an approved project. - DUO:0000027 - project specific restriction - - - - - - - - - institution-specific restriction - This requirement indicates that use is limited to use within an approved institution. - DUO:0000028 - 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. - 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 - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -