Custom ontologies for HMD submissions

fair-genomes.yml

@@ -577,7 +577,7 @@ modules:
             values: String
     - name: HMD Submission
       description: Items specific to use in the 1+MG GDI project for metadata submission.
-      ontology: AFRL:0000449 [http://purl.allotrope.org/ontologies/role#AFRL_0000449]
+      ontology: FG:0000750 [https://w3id.org/fair-genomes/resource/FG_0000750]
       elements:
           - name: Submitter Role
             description: Role of the Submitter (e.g. Oncologist in charge of the patient, Research Project PI).
@@ -604,8 +604,8 @@ modules:
             ontology: MS:1001922 [http://purl.obolibrary.org/obo/MS_1001922]
             values: String
           - name: Collection
-            description: Identifies collection (Biobank, Collection, Cohort, other types of projects) in which data are part of.
-            ontology: DCAT:Collection [http://www.w3.org/ns/prov#Collection]
+            description: Here goes the description
+            ontology: FG:0000751 [https://w3id.org/fair-genomes/resource/FG_0000751]
             values: String
           - name: Research Consortia
             description: Identifies Research Consortia Involved.

generated/art-decor/fair-genomes_en-US.xml

@@ -256,7 +256,7 @@ href="http://art-decor.org/ADAR/rv/DECOR.sch" type="application/xml" schematypes
 <concept id="2.16.840.1.113883.2.4.3.11.60.120.2.121" statusCode="draft" effectiveDate="2022-02-28T24:00:00" type="group">
 <name language="en-US">HMD Submission</name>
 <desc language="en-US">Items specific to use in the 1+MG GDI project for metadata submission.</desc>
-<property name="url">http://purl.allotrope.org/ontologies/role#AFRL_0000449</property>
+<property name="url">https://w3id.org/fair-genomes/resource/FG_0000750</property>
 <concept id="2.16.840.1.113883.2.4.3.11.60.120.2.124" statusCode="draft" effectiveDate="2022-02-28T24:00:00" type="item">
 <name language="en-US">Clinical Center</name>
 <desc language="en-US">Refers to the Clinical Department in charge of the patient.</desc>
@@ -266,8 +266,8 @@ href="http://art-decor.org/ADAR/rv/DECOR.sch" type="application/xml" schematypes
 </concept>
 <concept id="2.16.840.1.113883.2.4.3.11.60.120.2.128" statusCode="draft" effectiveDate="2022-02-28T24:00:00" type="item">
 <name language="en-US">Collection</name>
-<desc language="en-US">Identifies collection (Biobank, Collection, Cohort, other types of projects) in which data are part of.</desc>
-<property name="url">http://www.w3.org/ns/prov#Collection</property>
+<desc language="en-US">Here goes the description</desc>
+<property name="url">https://w3id.org/fair-genomes/resource/FG_0000751</property>
 <valueDomain type="string">
 </valueDomain>
 </concept>
@@ -1155,14 +1155,14 @@ href="http://art-decor.org/ADAR/rv/DECOR.sch" type="application/xml" schematypes
 <terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.118" conceptFlexibility="2022-02-28T24:00:00" code="C50996" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.0" codeSystemName="NCIT" displayName="Bioinformatic protocol deviation" effectiveDate="2022-02-28T24:00:00"/>
 <terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.119" conceptFlexibility="2022-02-28T24:00:00" code="C93529" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.0" codeSystemName="NCIT" displayName="Reason for bioinformatic protocol deviation" effectiveDate="2022-02-28T24:00:00"/>
 <terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.120" conceptFlexibility="2022-02-28T24:00:00" code="C17564" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.0" codeSystemName="NCIT" displayName="WGS guideline followed" effectiveDate="2022-02-28T24:00:00"/>
-<terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.121" conceptFlexibility="2022-02-28T24:00:00" code="0000449" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.32" codeSystemName="AFRL" displayName="HMD Submission" effectiveDate="2022-02-28T24:00:00"/>
+<terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.121" conceptFlexibility="2022-02-28T24:00:00" code="0000750" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.12" codeSystemName="FG" displayName="HMD Submission" effectiveDate="2022-02-28T24:00:00"/>
 <terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.122" conceptFlexibility="2022-02-28T24:00:00" code="Role" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.39" codeSystemName="DCAT" displayName="Submitter Role" effectiveDate="2022-02-28T24:00:00"/>
 <terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.123" conceptFlexibility="2022-02-28T24:00:00" code="Identifier" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.40" codeSystemName="ADMS" displayName="Data Center" effectiveDate="2022-02-28T24:00:00"/>
 <terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.124" conceptFlexibility="2022-02-28T24:00:00" code="Identifier" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.40" codeSystemName="ADMS" displayName="Clinical Center" effectiveDate="2022-02-28T24:00:00"/>
 <terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.125" conceptFlexibility="2022-02-28T24:00:00" code="000688" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.19" codeSystemName="SIO" displayName="Institution Clinical" effectiveDate="2022-02-28T24:00:00"/>
 <terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.126" conceptFlexibility="2022-02-28T24:00:00" code="000688" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.19" codeSystemName="SIO" displayName="Institution Data Center" effectiveDate="2022-02-28T24:00:00"/>
 <terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.127" conceptFlexibility="2022-02-28T24:00:00" code="1001922" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.41" codeSystemName="MS" displayName="Publication description" effectiveDate="2022-02-28T24:00:00"/>
-<terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.128" conceptFlexibility="2022-02-28T24:00:00" code="Collection" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.39" codeSystemName="DCAT" displayName="Collection" effectiveDate="2022-02-28T24:00:00"/>
+<terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.128" conceptFlexibility="2022-02-28T24:00:00" code="0000751" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.12" codeSystemName="FG" displayName="Collection" effectiveDate="2022-02-28T24:00:00"/>
 <terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.129" conceptFlexibility="2022-02-28T24:00:00" code="C61538" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.0" codeSystemName="NCIT" displayName="Research Consortia" effectiveDate="2022-02-28T24:00:00"/>
 <codeSystem ref="2.16.840.1.113883.6.96" name="SNOMED_CT" displayName="SNOMED CT"/>
 <codeSystem ref="2.16.840.1.113883.5.1008" name="NullFlavor" displayName="NullFlavor"/>

generated/latex/fair-genomes.tex

@@ -21,7 +21,7 @@
 Sample preparation & OBI:0001902 & 9 \\
 Sequencing & EDAM:topic\_3168 & 12 \\
 Analysis & EDAM:operation\_2945 & 11 \\
-HMD Submission & AFRL:0000449 & 8 \\
+HMD Submission & FG:0000750 & 8 \\
 \hline
 \end{tabular}
 \caption[Module overview]{\label{table:table1} FAIR Genomes metadata schema v1.3-SNAPSHOT overview of all modules.}
@@ -230,11 +230,11 @@
 Institution Clinical & SIO:000688 & Institutes lookup (219 choices) \\
 Institution Data Center & SIO:000688 & Institutes lookup (219 choices) \\
 Publication description & MS:1001922 & String \\
-Collection & DCAT:Collection & String \\
+Collection & FG:0000751 & String \\
 Research Consortia & NCIT:C61538 & String \\
 \hline
 \end{tabular}
-\caption[Module: HMD Submission]{\label{table:table11} Module: HMD Submission. Items specific to use in the 1+MG GDI project for metadata submission. Ontology: AFRL:0000449. }
+\caption[Module: HMD Submission]{\label{table:table11} Module: HMD Submission. Items specific to use in the 1+MG GDI project for metadata submission. Ontology: FG:0000750. }
 \end{table}
 
 \begin{table}[htb]

generated/markdown/fairgenomes-semantic-model.md

@@ -15,7 +15,7 @@ The FAIR Genomes semantic metadata schema to power reuse of NGS data in research
 | [Sample preparation](#module-sample-preparation) | A sample preparation for a nucleic acids sequencing assay. | [OBI:0001902](http://purl.obolibrary.org/obo/OBI_0001902) | 9 |
 | [Sequencing](#module-sequencing) | The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes. | [EDAM:topic_3168](http://edamontology.org/topic_3168) | 12 |
 | [Analysis](#module-analysis) | An analysis applies analytical (often computational) methods to existing data of a specific type to produce some desired output. | [EDAM:operation_2945](http://edamontology.org/operation_2945) | 11 |
-| [HMD Submission](#module-hmd-submission) | Items specific to use in the 1+MG GDI project for metadata submission. | [AFRL:0000449](http://purl.allotrope.org/ontologies/role#AFRL_0000449) | 8 |
+| [HMD Submission](#module-hmd-submission) | Items specific to use in the 1+MG GDI project for metadata submission. | [FG:0000750](https://w3id.org/fair-genomes/resource/FG_0000750) | 8 |
 
 ## Module: Study
 A detailed examination, analysis, or critical inspection of one or multiple subjects designed to discover facts. Ontology: [NCIT:C63536](http://purl.obolibrary.org/obo/NCIT_C63536).
@@ -184,7 +184,7 @@ An analysis applies analytical (often computational) methods to existing data of
 | WGS guideline followed | Any followed systematic statement of policy rules or principles. Guidelines may be developed by government agencies at any level, institutions, professional societies, governing boards, or by convening expert panels. | [NCIT:C17564](http://purl.obolibrary.org/obo/NCIT_C17564) | String |
 
 ## Module: HMD Submission
-Items specific to use in the 1+MG GDI project for metadata submission. Ontology: [AFRL:0000449](http://purl.allotrope.org/ontologies/role#AFRL_0000449).
+Items specific to use in the 1+MG GDI project for metadata submission. Ontology: [FG:0000750](https://w3id.org/fair-genomes/resource/FG_0000750).
 
 | Element | Description | Ontology | Values |
 |---|---|---|---|
@@ -194,7 +194,7 @@ Items specific to use in the 1+MG GDI project for metadata submission. Ontology:
 | Institution Clinical | Identifies the Institution/s involved. | [SIO:000688](http://semanticscience.org/resource/SIO_000688) | [Institutes](../../lookups/Institutes.txt) lookup (219 choices [of type](http://semanticscience.org/resource/SIO_000688)) |
 | Institution Data Center | Identifies the Institution/s involved. | [SIO:000688](http://semanticscience.org/resource/SIO_000688) | [Institutes](../../lookups/Institutes.txt) lookup (219 choices [of type](http://semanticscience.org/resource/SIO_000688)) |
 | Publication description | Linked to the instance of publication_doi; should provide a human-readably description of the publication. | [MS:1001922](http://purl.obolibrary.org/obo/MS_1001922) | String |
-| Collection | Identifies collection (Biobank, Collection, Cohort, other types of projects) in which data are part of. | [DCAT:Collection](http://www.w3.org/ns/prov#Collection) | String |
+| Collection | Here goes the description | [FG:0000751](https://w3id.org/fair-genomes/resource/FG_0000751) | String |
 | Research Consortia | Identifies Research Consortia Involved. | [NCIT:C61538](http://purl.obolibrary.org/obo/NCIT_C61538) | String |
 
 ## Null flavors

generated/molgenis-emx/HmdSubmission_attributes.tsv

@@ -5,5 +5,5 @@ ClinicalCenter	Clinical Center	Refers to the Clinical Department in charge of th
 InstitutionClinical	Institution Clinical	Identifies the Institution/s involved. (SIO:000688)	HmdSubmission	mref	FALSE	FALSE	TRUE	TRUE	fair-genomes_HmdSubmission_InstitutionClinical
 InstitutionDataCenter	Institution Data Center	Identifies the Institution/s involved. (SIO:000688)	HmdSubmission	mref	FALSE	FALSE	TRUE	TRUE	fair-genomes_HmdSubmission_InstitutionDataCenter
 PublicationDescription	Publication description	Linked to the instance of publication_doi; should provide a human-readably description of the publication. (MS:1001922)	HmdSubmission	string	FALSE	FALSE	TRUE	TRUE	
-Collection	Collection	Identifies collection (Biobank, Collection, Cohort, other types of projects) in which data are part of. (DCAT:Collection)	HmdSubmission	string	FALSE	FALSE	TRUE	TRUE	
+Collection	Collection	Here goes the description (FG:0000751)	HmdSubmission	string	FALSE	FALSE	TRUE	TRUE	
 ResearchConsortia	Research Consortia	Identifies Research Consortia Involved. (NCIT:C61538)	HmdSubmission	string	FALSE	FALSE	TRUE	TRUE	

generated/molgenis-emx2/molgenis.csv

@@ -120,12 +120,12 @@ tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,ref
 "Analysis","","BioinformaticProtocolDeviation","string","","","","","","","","http://purl.obolibrary.org/obo/NCIT_C50996","A variation from processes or procedures defined in the bioinformatic protocol. Deviations usually do not preclude the overall evaluability of subject data for either efficacy or safety, and are often acknowledged and accepted in advance by the sponsor.","FAIR Genomes"
 "Analysis","","ReasonForBioinformaticProtocolDeviation","string","","","","","","","","http://purl.obolibrary.org/obo/NCIT_C93529","The rationale for why a deviation from the bioinformatic protocol has occurred.","FAIR Genomes"
 "Analysis","","WgsGuidelineFollowed","string","","","","","","","","http://purl.obolibrary.org/obo/NCIT_C17564","Any followed systematic statement of policy rules or principles. Guidelines may be developed by government agencies at any level, institutions, professional societies, governing boards, or by convening expert panels.","FAIR Genomes"
-"HmdSubmission","","","","","","","","","","","http://purl.allotrope.org/ontologies/role#AFRL_0000449","Items specific to use in the 1+MG GDI project for metadata submission.","FAIR Genomes"
+"HmdSubmission","","","","","","","","","","","https://w3id.org/fair-genomes/resource/FG_0000750","Items specific to use in the 1+MG GDI project for metadata submission.","FAIR Genomes"
 "HmdSubmission","","SubmitterRole","string","","","","","","","","https://www.w3.org/ns/dcat#Role","Role of the Submitter (e.g. Oncologist in charge of the patient, Research Project PI).","FAIR Genomes"
 "HmdSubmission","","DataCenter","string","","","","","","","","https://www.w3.org/TR/vocab-adms/#identifier","Refers to the Department in charge of Data Production and/ or analysis","FAIR Genomes"
 "HmdSubmission","","ClinicalCenter","string","","","","","","","","https://www.w3.org/TR/vocab-adms/#identifier","Refers to the Clinical Department in charge of the patient.","FAIR Genomes"
 "HmdSubmission","","InstitutionClinical","ontology_array","","","","InstitutionClinical","","","","http://semanticscience.org/resource/SIO_000688","Identifies the Institution/s involved.","FAIR Genomes"
 "HmdSubmission","","InstitutionDataCenter","ontology_array","","","","InstitutionDataCenter","","","","http://semanticscience.org/resource/SIO_000688","Identifies the Institution/s involved.","FAIR Genomes"
 "HmdSubmission","","PublicationDescription","string","","","","","","","","http://purl.obolibrary.org/obo/MS_1001922","Linked to the instance of publication_doi; should provide a human-readably description of the publication.","FAIR Genomes"
-"HmdSubmission","","Collection","string","","","","","","","","http://www.w3.org/ns/prov#Collection","Identifies collection (Biobank, Collection, Cohort, other types of projects) in which data are part of.","FAIR Genomes"
+"HmdSubmission","","Collection","string","","","","","","","","https://w3id.org/fair-genomes/resource/FG_0000751","Here goes the description","FAIR Genomes"
 "HmdSubmission","","ResearchConsortia","string","","","","","","","","http://purl.obolibrary.org/obo/NCIT_C61538","Identifies Research Consortia Involved.","FAIR Genomes"

generated/ontology/fair-genomes.ttl

@@ -828,7 +828,7 @@ fg:Analysis_WGS_guideline_followed a owl:DatatypeProperty;
   dc:description "Any followed systematic statement of policy rules or principles. Guidelines may be developed by government agencies at any level, institutions, professional societies, governing boards, or by convening expert panels." .
 
 fg:HMD_Submission a owl:Class;
-  rdfs:isDefinedBy <http://purl.allotrope.org/ontologies/role#AFRL_0000449>;
+  rdfs:isDefinedBy <https://w3id.org/fair-genomes/resource/FG_0000750>;
   rdfs:label "HMD Submission";
   dc:description "Items specific to use in the 1+MG GDI project for metadata submission." .
 
@@ -873,8 +873,8 @@ fg:HMD_Submission_Publication_description a owl:DatatypeProperty;
 fg:HMD_Submission_Collection a owl:DatatypeProperty;
   rdfs:label "Collection";
   rdfs:domain fg:HMD_Submission;
-  rdfs:isDefinedBy <http://www.w3.org/ns/prov#Collection>;
-  dc:description "Identifies collection (Biobank, Collection, Cohort, other types of projects) in which data are part of." .
+  rdfs:isDefinedBy <https://w3id.org/fair-genomes/resource/FG_0000751>;
+  dc:description "Here goes the description" .
 
 fg:HMD_Submission_Research_Consortia a owl:DatatypeProperty;
   rdfs:label "Research Consortia";

generated/palga-codebook/CODEBOOK.tsv

@@ -120,12 +120,12 @@ Bioinformatic protocol used	A human-readable collection of information about abo
 Bioinformatic protocol deviation	A variation from processes or procedures defined in the bioinformatic protocol. Deviations usually do not preclude the overall evaluability of subject data for either efficacy or safety, and are often acknowledged and accepted in advance by the sponsor.	NCIT	C50996	ST	Bioinformatic protocol deviation		text	{url=http://purl.obolibrary.org/obo/NCIT_C50996}	Analysis	
 Reason for bioinformatic protocol deviation	The rationale for why a deviation from the bioinformatic protocol has occurred.	NCIT	C93529	ST	Reason for bioinformatic protocol deviation		text	{url=http://purl.obolibrary.org/obo/NCIT_C93529}	Analysis	
 WGS guideline followed	Any followed systematic statement of policy rules or principles. Guidelines may be developed by government agencies at any level, institutions, professional societies, governing boards, or by convening expert panels.	NCIT	C17564	ST	WGS guideline followed		text	{url=http://purl.obolibrary.org/obo/NCIT_C17564}	Analysis	
-HMD Submission	Items specific to use in the 1+MG GDI project for metadata submission.	AFRL	0000449	ST	HMD Submission		multi-select	{url=http://purl.allotrope.org/ontologies/role#AFRL_0000449}		
+HMD Submission	Items specific to use in the 1+MG GDI project for metadata submission.	FG	0000750	ST	HMD Submission		multi-select	{url=https://w3id.org/fair-genomes/resource/FG_0000750}		
 Submitter Role	Role of the Submitter (e.g. Oncologist in charge of the patient, Research Project PI).	DCAT	Role	ST	Submitter Role		text	{url=https://www.w3.org/ns/dcat#Role}	HMD Submission	
 Data Center	Refers to the Department in charge of Data Production and/ or analysis	ADMS	Identifier	ST	Data Center		text	{url=https://www.w3.org/TR/vocab-adms/#identifier}	HMD Submission	
 Clinical Center	Refers to the Clinical Department in charge of the patient.	ADMS	Identifier	ST	Clinical Center		text	{url=https://www.w3.org/TR/vocab-adms/#identifier}	HMD Submission	
 Institution Clinical	Identifies the Institution/s involved.	SIO	000688	ST	Institution Clinical	Institutes	multi-select	{url=http://semanticscience.org/resource/SIO_000688}	HMD Submission	
 Institution Data Center	Identifies the Institution/s involved.	SIO	000688	ST	Institution Data Center	Institutes	multi-select	{url=http://semanticscience.org/resource/SIO_000688}	HMD Submission	
 Publication description	Linked to the instance of publication_doi; should provide a human-readably description of the publication.	MS	1001922	ST	Publication description		text	{url=http://purl.obolibrary.org/obo/MS_1001922}	HMD Submission	
-Collection	Identifies collection (Biobank, Collection, Cohort, other types of projects) in which data are part of.	DCAT	Collection	ST	Collection		text	{url=http://www.w3.org/ns/prov#Collection}	HMD Submission	
+Collection	Here goes the description	FG	0000751	ST	Collection		text	{url=https://w3id.org/fair-genomes/resource/FG_0000751}	HMD Submission	
 Research Consortia	Identifies Research Consortia Involved.	NCIT	C61538	ST	Research Consortia		text	{url=http://purl.obolibrary.org/obo/NCIT_C61538}	HMD Submission