Add new properties to HMD Submission

fairgenomes · Feb 14, 2025 · d0bdcf0 · d0bdcf0
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diff --git a/fair-genomes.yml b/fair-genomes.yml
@@ -576,38 +576,38 @@ modules:
             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.
+      description: A class specific for the 1+MG GDI project containing items 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]
+            ontology: FG:0000752 [https://w3id.org/fair-genomes/resource/FG_0000752]
             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]
+            ontology: FG:0000753 [https://w3id.org/fair-genomes/resource/FG_0000753]
             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]
+            ontology: FG:0000754 [https://w3id.org/fair-genomes/resource/FG_0000754]
             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]
+            ontology: FG:0000755 [https://w3id.org/fair-genomes/resource/FG_0000755]
+            values: LookupMany [lookups/InstitutesROR.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]
+            ontology: FG:0000756 [https://w3id.org/fair-genomes/resource/FG_0000756]
+            values: LookupMany [lookups/InstitutesROR.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]
+            ontology: FG:0000757 [https://w3id.org/fair-genomes/resource/FG_0000757]
             values: String
           - name: Collection
-            description: Here goes the description
+            description: Identifies collection (Biobank, Collection, Cohort, other types of projects) in which data are part of.
             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]
+            ontology: FG:0000758 [https://w3id.org/fair-genomes/resource/FG_0000758]
             values: String
diff --git a/generated/art-decor/fair-genomes_en-US.xml b/generated/art-decor/fair-genomes_en-US.xml
diff --git a/generated/latex/fair-genomes.tex b/generated/latex/fair-genomes.tex
@@ -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 10 modules that contain 120 metadata elements and 85805 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 290151 lookups in total (excluding null flavors).
 
 \begin{table}[htb]
 \begin{tabular}{lll}
@@ -224,17 +224,17 @@
 \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 \\
+Submitter Role & FG:0000752 & String \\
+Data Center & FG:0000753 & String \\
+Clinical Center & FG:0000754 & String \\
+Institution Clinical & FG:0000755 & InstitutesROR lookup (102392 choices) \\
+Institution Data Center & FG:0000756 & InstitutesROR lookup (102392 choices) \\
+Publication description & FG:0000757 & String \\
 Collection & FG:0000751 & String \\
-Research Consortia & NCIT:C61538 & String \\
+Research Consortia & FG:0000758 & 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. }
+\caption[Module: HMD Submission]{\label{table:table11} Module: HMD Submission. A class specific for the 1+MG GDI project containing items for metadata submission. Ontology: FG:0000750. }
 \end{table}
 
 \begin{table}[htb]

diff --git a/generated/markdown/fairgenomes-semantic-model.md b/generated/markdown/fairgenomes-semantic-model.md
@@ -1,6 +1,6 @@
 # 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 __10 modules__ that contain __120 metadata elements__ and __85805 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 __290151 lookups__ in total (excluding null flavors).
 
 ## Module overview
 
@@ -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. | [FG:0000750](https://w3id.org/fair-genomes/resource/FG_0000750) | 8 |
+| [HMD Submission](#module-hmd-submission) | A class specific for the 1+MG GDI project containing items 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).
@@ -184,18 +184,18 @@ 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: [FG:0000750](https://w3id.org/fair-genomes/resource/FG_0000750).
+A class specific for the 1+MG GDI project containing items for metadata submission. Ontology: [FG:0000750](https://w3id.org/fair-genomes/resource/FG_0000750).
 
 | 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 | 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 |
+| Submitter Role | Role of the Submitter (e.g. Oncologist in charge of the patient, Research Project PI). | [FG:0000752](https://w3id.org/fair-genomes/resource/FG_0000752) | String |
+| Data Center | Refers to the Department in charge of Data Production and/ or analysis | [FG:0000753](https://w3id.org/fair-genomes/resource/FG_0000753) | String |
+| Clinical Center | Refers to the Clinical Department in charge of the patient. | [FG:0000754](https://w3id.org/fair-genomes/resource/FG_0000754) | String |
+| Institution Clinical | Identifies the Institution/s involved. | [FG:0000755](https://w3id.org/fair-genomes/resource/FG_0000755) | [InstitutesROR](../../lookups/InstitutesROR.txt) lookup (102392 choices [of type](http://semanticscience.org/resource/SIO_000688)) |
+| Institution Data Center | Identifies the Institution/s involved. | [FG:0000756](https://w3id.org/fair-genomes/resource/FG_0000756) | [InstitutesROR](../../lookups/InstitutesROR.txt) lookup (102392 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. | [FG:0000757](https://w3id.org/fair-genomes/resource/FG_0000757) | String |
+| Collection | Identifies collection (Biobank, Collection, Cohort, other types of projects) in which data are part of. | [FG:0000751](https://w3id.org/fair-genomes/resource/FG_0000751) | String |
+| Research Consortia | Identifies Research Consortia Involved. | [FG:0000758](https://w3id.org/fair-genomes/resource/FG_0000758) | 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.