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Updated generated content for HMD Submission
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joerivandervelde committed Jan 31, 2025
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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">http://purl.allotrope.org/ontologies/role#AFRL_0000449</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">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>
<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="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="2.16.840.1.113883.2.4.3.11.60.120.2.122" 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="2.16.840.1.113883.2.4.3.11.60.120.2.129" 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.
Expand Down
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 & AFRL:0000449 & 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 & DCAT:Collection & 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. }
\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}
17 changes: 16 additions & 1 deletion generated/markdown/fairgenomes-semantic-model.md
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# FAIR Genomes metadata schema

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).

## Module overview

Expand All @@ -15,6 +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 |

## 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).
Expand Down Expand Up @@ -182,6 +183,20 @@ An analysis applies analytical (often computational) methods to existing data of
| Reason for bioinformatic protocol deviation | The rationale for why a deviation from the bioinformatic protocol has occurred. | [NCIT:C93529](http://purl.obolibrary.org/obo/NCIT_C93529) | String |
| 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).

| Element | Description | Ontology | Values |
|---|---|---|---|
| Submitter Role | Role of the Submitter (e.g. Oncologist in charge of the patient, Research Project PI). | [DCAT:Role](https://www.w3.org/ns/dcat#Role) | String |
| Data Center | Refers to the Department in charge of Data Production and/ or analysis | [ADMS:Identifier](https://www.w3.org/TR/vocab-adms/#identifier) | String |
| Clinical Center | Refers to the Clinical Department in charge of the patient. | [ADMS:Identifier](https://www.w3.org/TR/vocab-adms/#identifier) | String |
| 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 |
| Research Consortia | Identifies Research Consortia Involved. | [NCIT:C61538](http://purl.obolibrary.org/obo/NCIT_C61538) | String |

## 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.

Expand Down
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