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Updates for GDI
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joerivandervelde authored Feb 14, 2025
2 parents e17e51e + 457114c commit 3f8d35a
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36 changes: 36 additions & 0 deletions fair-genomes.yml
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Expand Up @@ -575,3 +575,39 @@ modules:
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.
ontology: NCIT:C17564 [http://purl.obolibrary.org/obo/NCIT_C17564]
values: String
- name: HMD Submission
description: Items specific to use in the 1+MG GDI project for metadata submission.
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).
ontology: DCAT:Role [https://www.w3.org/ns/dcat#Role]
values: String
- name: Data Center
description: Refers to the Department in charge of Data Production and/ or analysis
ontology: ADMS:Identifier [https://www.w3.org/TR/vocab-adms/#identifier]
values: String
- name: Clinical Center
description: Refers to the Clinical Department in charge of the patient.
ontology: ADMS:Identifier https://www.w3.org/TR/vocab-adms/#identifier]
values: String
- name: Institution Clinical
description: Identifies the Institution/s involved.
ontology: SIO:000688 [http://semanticscience.org/resource/SIO_000688]
values: LookupMany [lookups/Institutes.txt], ofType [http://semanticscience.org/resource/SIO_000688]
- name: Institution Data Center
description: Identifies the Institution/s involved.
ontology: SIO:000688 [http://semanticscience.org/resource/SIO_000688]
values: LookupMany [lookups/Institutes.txt], ofType [http://semanticscience.org/resource/SIO_000688]
- name: Publication description
description: Linked to the instance of publication_doi; should provide a human-readably description of the publication.
ontology: MS:1001922 [http://purl.obolibrary.org/obo/MS_1001922]
values: String
- name: 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.
ontology: NCIT:C61538 [http://purl.obolibrary.org/obo/NCIT_C61538]
values: String
77 changes: 77 additions & 0 deletions generated/art-decor/fair-genomes_en-US.xml
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Expand Up @@ -253,6 +253,69 @@ href="http://art-decor.org/ADAR/rv/DECOR.sch" type="application/xml" schematypes
</valueDomain>
</concept>
</concept>
<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">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>
<property name="url">https://www.w3.org/TR/vocab-adms/#identifier</property>
<valueDomain type="string">
</valueDomain>
</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">Here goes the description</desc>
<property name="url">https://w3id.org/fair-genomes/resource/FG_0000751</property>
<valueDomain type="string">
</valueDomain>
</concept>
<concept id="2.16.840.1.113883.2.4.3.11.60.120.2.123" statusCode="draft" effectiveDate="2022-02-28T24:00:00" type="item">
<name language="en-US">Data Center</name>
<desc language="en-US">Refers to the Department in charge of Data Production and/ or analysis</desc>
<property name="url">https://www.w3.org/TR/vocab-adms/#identifier</property>
<valueDomain type="string">
</valueDomain>
</concept>
<concept id="2.16.840.1.113883.2.4.3.11.60.120.2.125" statusCode="draft" effectiveDate="2022-02-28T24:00:00" type="item">
<name language="en-US">Institution Clinical</name>
<desc language="en-US">Identifies the Institution/s involved.</desc>
<property name="url">http://semanticscience.org/resource/SIO_000688</property>
<valueDomain type="code">
<conceptList id="2.16.840.1.113883.2.4.3.11.60.120.2.125.20220228000000.0"/>
</valueDomain>
</concept>
<concept id="2.16.840.1.113883.2.4.3.11.60.120.2.126" statusCode="draft" effectiveDate="2022-02-28T24:00:00" type="item">
<name language="en-US">Institution Data Center</name>
<desc language="en-US">Identifies the Institution/s involved.</desc>
<property name="url">http://semanticscience.org/resource/SIO_000688</property>
<valueDomain type="code">
<conceptList id="2.16.840.1.113883.2.4.3.11.60.120.2.126.20220228000000.0"/>
</valueDomain>
</concept>
<concept id="2.16.840.1.113883.2.4.3.11.60.120.2.127" statusCode="draft" effectiveDate="2022-02-28T24:00:00" type="item">
<name language="en-US">Publication description</name>
<desc language="en-US">Linked to the instance of publication_doi; should provide a human-readably description of the publication.</desc>
<property name="url">http://purl.obolibrary.org/obo/MS_1001922</property>
<valueDomain type="string">
</valueDomain>
</concept>
<concept id="2.16.840.1.113883.2.4.3.11.60.120.2.129" statusCode="draft" effectiveDate="2022-02-28T24:00:00" type="item">
<name language="en-US">Research Consortia</name>
<desc language="en-US">Identifies Research Consortia Involved.</desc>
<property name="url">http://purl.obolibrary.org/obo/NCIT_C61538</property>
<valueDomain type="string">
</valueDomain>
</concept>
<concept id="2.16.840.1.113883.2.4.3.11.60.120.2.122" statusCode="draft" effectiveDate="2022-02-28T24:00:00" type="item">
<name language="en-US">Submitter Role</name>
<desc language="en-US">Role of the Submitter (e.g. Oncologist in charge of the patient, Research Project PI).</desc>
<property name="url">https://www.w3.org/ns/dcat#Role</property>
<valueDomain type="string">
</valueDomain>
</concept>
</concept>
<concept id="2.16.840.1.113883.2.4.3.11.60.120.2.35" statusCode="draft" effectiveDate="2022-02-28T24:00:00" type="group">
<name language="en-US">Individual consent</name>
<desc language="en-US">Consent given by a patient to a surgical or medical procedure or participation in a study, examination or analysis after achieving an understanding of the relevant medical facts and the risks involved.</desc>
Expand Down Expand Up @@ -969,6 +1032,8 @@ href="http://art-decor.org/ADAR/rv/DECOR.sch" type="application/xml" schematypes
<terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.102.20220228000000.0" valueSet="2.16.840.1.113883.2.4.3.11.60.120.11.27" flexibility="2022-02-28T24:00:00" effectiveDate="2022-02-28T24:00:00"/>
<terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.114.20220228000000.0" valueSet="2.16.840.1.113883.2.4.3.11.60.120.11.28" flexibility="2022-02-28T24:00:00" effectiveDate="2022-02-28T24:00:00"/>
<terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.116.20220228000000.0" valueSet="2.16.840.1.113883.2.4.3.11.60.120.11.29" flexibility="2022-02-28T24:00:00" effectiveDate="2022-02-28T24:00:00"/>
<terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.125.20220228000000.0" valueSet="2.16.840.1.113883.2.4.3.11.60.120.11.7" flexibility="2022-02-28T24:00:00" effectiveDate="2022-02-28T24:00:00"/>
<terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.126.20220228000000.0" valueSet="2.16.840.1.113883.2.4.3.11.60.120.11.7" flexibility="2022-02-28T24:00:00" effectiveDate="2022-02-28T24:00:00"/>
<terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.0" conceptFlexibility="2022-02-28T24:00:00" code="C63536" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.0" codeSystemName="NCIT" displayName="Study" effectiveDate="2022-02-28T24:00:00"/>
<terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.1" conceptFlexibility="2022-02-28T24:00:00" code="0000006" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.1" codeSystemName="OMIABIS" displayName="Identifier" effectiveDate="2022-02-28T24:00:00"/>
<terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.2" conceptFlexibility="2022-02-28T24:00:00" code="0000037" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.1" codeSystemName="OMIABIS" displayName="Name" effectiveDate="2022-02-28T24:00:00"/>
Expand Down Expand Up @@ -1090,6 +1155,15 @@ 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="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="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"/>
<codeSystem ref="2.16.840.1.113883.6.1" name="LOINC" displayName="LOINC"/>
Expand Down Expand Up @@ -1139,6 +1213,9 @@ href="http://art-decor.org/ADAR/rv/DECOR.sch" type="application/xml" schematypes
<codeSystem ref="2.16.840.1.113883.2.4.3.11.60.120.5.36" name="SWO" displayName="SWO"/>
<codeSystem ref="2.16.840.1.113883.2.4.3.11.60.120.5.37" name="GCF" displayName="GCF"/>
<codeSystem ref="2.16.840.1.113883.2.4.3.11.60.120.5.38" name="GCA" displayName="GCA"/>
<codeSystem ref="2.16.840.1.113883.2.4.3.11.60.120.5.39" name="DCAT" displayName="DCAT"/>
<codeSystem ref="2.16.840.1.113883.2.4.3.11.60.120.5.40" name="ADMS" displayName="ADMS"/>
<codeSystem ref="2.16.840.1.113883.2.4.3.11.60.120.5.41" name="MS" displayName="MS"/>
<valueSet name="Inclusioncriteria_Opts" displayName="Inclusion criteria Options" versionLabel="1.3" id="2.16.840.1.113883.2.4.3.11.60.120.11.0" effectiveDate="2022-02-28T24:00:00" statusCode="draft">
<desc language="en-US">
Options for The conditions which, if met, make an person eligible for participation in this study.
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1 change: 1 addition & 0 deletions generated/java/org/fairgenomes/generated/FAIRGenomesRoot.java
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Expand Up @@ -12,4 +12,5 @@ public class FairgenomesRoot {
public Map<String, SamplePreparation> SamplePreparation;
public Map<String, Sequencing> Sequencing;
public Map<String, Analysis> Analysis;
public Map<String, HmdSubmission> HmdSubmission;
}
14 changes: 14 additions & 0 deletions generated/java/org/fairgenomes/generated/HmdSubmission.java
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@@ -0,0 +1,14 @@
package org.fairgenomes.generated;

import java.util.List;

public class HmdSubmission {
public String SubmitterRole;
public String DataCenter;
public String ClinicalCenter;
public List<String> InstitutionClinical;
public List<String> InstitutionDataCenter;
public String PublicationDescription;
public String Collection;
public String ResearchConsortia;
}
22 changes: 20 additions & 2 deletions generated/latex/fair-genomes.tex
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Expand Up @@ -6,7 +6,7 @@
\textbf{FAIR Genomes metadata schema}
\newline

The FAIR Genomes semantic metadata schema to power reuse of NGS data in research and healthcare. Version 1.3-SNAPSHOT, 2022-02-28. This model consists of 9 modules that contain 112 metadata elements and 85367 lookups in total (excluding null flavors).
The FAIR Genomes semantic metadata schema to power reuse of NGS data in research and healthcare. Version 1.3-SNAPSHOT, 2022-02-28. This model consists of 10 modules that contain 120 metadata elements and 85805 lookups in total (excluding null flavors).

\begin{table}[htb]
\begin{tabular}{lll}
Expand All @@ -21,6 +21,7 @@
Sample preparation & OBI:0001902 & 9 \\
Sequencing & EDAM:topic\_3168 & 12 \\
Analysis & EDAM:operation\_2945 & 11 \\
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.}
Expand Down Expand Up @@ -219,6 +220,23 @@
\caption[Module: Analysis]{\label{table:table10} Module: Analysis. An analysis applies analytical (often computational) methods to existing data of a specific type to produce some desired output. Ontology: EDAM:operation\_2945. }
\end{table}

\begin{table}[htb]
\begin{tabular}{lll}
Name & Ontology & Values \\
\hline
Submitter Role & DCAT:Role & String \\
Data Center & ADMS:Identifier & String \\
Clinical Center & ADMS:Identifier & String \\
Institution Clinical & SIO:000688 & Institutes lookup (219 choices) \\
Institution Data Center & SIO:000688 & Institutes lookup (219 choices) \\
Publication description & MS:1001922 & 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: FG:0000750. }
\end{table}

\begin{table}[htb]
\begin{tabular}{ll}
Value & Ontology \\
Expand All @@ -241,7 +259,7 @@
Trace & HL7:TRC \\
\hline
\end{tabular}
\caption[NullFlavors]{\label{table:table11} Overview of null flavors. Each lookup is supplemented with so-called 'null flavors' from HL7. These can be used to indicate precisely why a particular value could not be entered into the system, providing substantially more insight than simply leaving a field empty. }
\caption[NullFlavors]{\label{table:table12} Overview of null flavors. Each lookup is supplemented with so-called 'null flavors' from HL7. These can be used to indicate precisely why a particular value could not be entered into the system, providing substantially more insight than simply leaving a field empty. }
\end{table}

\end{document}
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