Merge pull request #19 from joerivandervelde/main

Finalized model for v0.2 release
fairgenomes · Jan 13, 2021 · e183484 · e183484
2 parents a5446b4 + 5fd4239
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diff --git a/fair-genomes.yml b/fair-genomes.yml
@@ -1,8 +1,8 @@
 ---
 name: FAIR Genomes metadata model
 description: The FAIR Genomes semantic metadata model to power reuse of NGS data in research and healthcare.
-version: 0.0
-date: 2020-12-19
+version: 0.2
+date: 2021-01-13
 lookupGlobalOptions: lookups/NullFlavors.txt
 modules:
     - name: Study
@@ -248,11 +248,11 @@ modules:
           - name: Family members affected
             description: This term applies to a family member who is diagnosed with the same condition as the individual who is the primary focus of investigation (the proband).
             ontology: HP:0032320 [http://purl.obolibrary.org/obo/HP_0032320]
-            values: String
+            values: LookupMany [lookups/FamilyMembers.txt]
           - name: Family members sequenced
             description: A person related by descent rather than by marriage or law that was also sequenced.
             ontology: NCIT:C71384 [http://purl.obolibrary.org/obo/NCIT_C71384]
-            values: String
+            values: LookupMany [lookups/FamilyMembers.txt]
           - name: Consanguinity
             description: Information on whether the patient is a child from two family members who are second cousins or closer.
             ontology: GSSO:007578 [http://purl.obolibrary.org/obo/GSSO_007578]

diff --git a/lookups/FamilyMembers.txt b/lookups/FamilyMembers.txt
@@ -0,0 +1,42 @@
+value	description	codesystem	code	iri
+Biological Daughter	A female progeny with genetic makeup inherited from the parent.	NCIT	C150887	http://purl.obolibrary.org/obo/NCIT_C150887
+Biological Son	A male progeny with genetic makeup inherited from the parent.	NCIT	C150888	http://purl.obolibrary.org/obo/NCIT_C150888
+Biological Maternal Grandfather	A male relative who is the biological father of the biological mother.	NCIT	C96577	http://purl.obolibrary.org/obo/NCIT_C96577
+Biological Paternal Grandfather	A male relative who is the biological father of the biological father.	NCIT	C96583	http://purl.obolibrary.org/obo/NCIT_C96583
+Biological Paternal Grandmother	A female relative who is the biological mother of the biological father.	NCIT	C96584	http://purl.obolibrary.org/obo/NCIT_C96584
+Biological Maternal Grandmother	A female relative who is the biological mother of the biological mother.	NCIT	C96578	http://purl.obolibrary.org/obo/NCIT_C96578
+Biological Maternal Cousin	A relative who is the offspring of a sibling of the biological mother and thus sharing a common ancestor.	NCIT	C96576	http://purl.obolibrary.org/obo/NCIT_C96576
+Biological Paternal Cousin	A relative who is the offspring of a sibling of the biological father and thus sharing a common ancestor.	NCIT	C96582	http://purl.obolibrary.org/obo/NCIT_C96582
+Biological Paternal Aunt	A female relative who is a sibling of the biological father, and who both share a common ancestor.	NCIT	C96581	http://purl.obolibrary.org/obo/NCIT_C96581
+Biological Maternal Aunt	A female relative who is a sibling of the biological mother, and who both share a common ancestor.	NCIT	C96575	http://purl.obolibrary.org/obo/NCIT_C96575
+Biological Father	A male who contributes to the genetic makeup of his offspring through the fertilization of an ovum by his sperm.	NCIT	C96572	http://purl.obolibrary.org/obo/NCIT_C96572
+Biological Mother	A female who contributes to the genetic makeup of her offspring from the fertilization of her ovum.	NCIT	C96580	http://purl.obolibrary.org/obo/NCIT_C96580
+Half-brother with Father as Common Parent	A male sibling who shares the genetic makeup inherited from only the biological father.	NCIT	C96655	http://purl.obolibrary.org/obo/NCIT_C96655
+Half-sister with Father as Common Parent	A female sibling who shares the genetic makeup inherited from only the biological father.	NCIT	C96657	http://purl.obolibrary.org/obo/NCIT_C96657
+Half-brother with Mother as Common Parent	A male sibling who shares the genetic makeup inherited from only the biological mother.	NCIT	C96656	http://purl.obolibrary.org/obo/NCIT_C96656
+Half-sister with Mother as Common Parent	A female sibling who shares the genetic makeup inherited from only the biological mother.	NCIT	C96658	http://purl.obolibrary.org/obo/NCIT_C96658
+Fraternal Twin Brother	A male full sibling that developed from a separately fertilized ova during the same pregnancy.	NCIT	C165796	http://purl.obolibrary.org/obo/NCIT_C165796
+Fraternal Twin Sister	A female full sibling that developed from a separately fertilized ova during the same pregnancy.	NCIT	C165797	http://purl.obolibrary.org/obo/NCIT_C165797
+Identical Twin Brother	A male full sibling that developed from a shared ovum.	NCIT	C165848	http://purl.obolibrary.org/obo/NCIT_C165848
+Identical Twin Sister	A female full sibling that developed from a shared ovum.	NCIT	C165849	http://purl.obolibrary.org/obo/NCIT_C165849
+Full Brother	A male who shares with his sibling the genetic makeup inherited from both of the biological parents.	NCIT	C111201	http://purl.obolibrary.org/obo/NCIT_C111201
+Full Sister	A female who shares with her sibling the genetic makeup inherited from both of the biological parents.	NCIT	C111202	http://purl.obolibrary.org/obo/NCIT_C111202
+Grandson	A male grandchild.	NCIT	C71398	http://purl.obolibrary.org/obo/NCIT_C71398
+Granddaughter	A female grandchild.	NCIT	C71399	http://purl.obolibrary.org/obo/NCIT_C71399
+Biological Maternal Uncle	A male relative who is a sibling of the biological mother, and who both share a common ancestor.	NCIT	C96579	http://purl.obolibrary.org/obo/NCIT_C96579
+Biological Paternal Uncle	A male relative who is a sibling of the biological father, and who both share a common ancestor.	NCIT	C96585	http://purl.obolibrary.org/obo/NCIT_C96585
+Niece	A daughter of your brother or sister.	NCIT	C71408	http://purl.obolibrary.org/obo/NCIT_C71408
+Nephew	A son of your brother or sister.	NCIT	C71409	http://purl.obolibrary.org/obo/NCIT_C71409
+Ancestor	Someone from whom you are descended (but usually more remote than a grandparent).	NCIT	C42609	http://purl.obolibrary.org/obo/NCIT_C42609
+Maternal First Cousin Once Removed	A child of one's first cousin who is related by lineage through the mother's side of the family.	NCIT	C165851	http://purl.obolibrary.org/obo/NCIT_C165851
+Paternal First Cousin Once Removed	A child of one's first cousin who is related by lineage through the father's side of the family.	NCIT	C165852	http://purl.obolibrary.org/obo/NCIT_C165852
+Descendent	Someone deriving or descending from an ancestor.	NCIT	C42674	http://purl.obolibrary.org/obo/NCIT_C42674
+Great Grandchild	A child of one's grandchild.	NCIT	C165847	http://purl.obolibrary.org/obo/NCIT_C165847
+Maternal Great Grandparent	A parent of one's maternal grandparent.	NCIT	C166127	http://purl.obolibrary.org/obo/NCIT_C166127
+Paternal Great Grandparent	A parent of one's paternal grandparent.	NCIT	C166128	http://purl.obolibrary.org/obo/NCIT_C166128
+Great Nephew	A male child of one's niece or nephew.	NCIT	C165798	http://purl.obolibrary.org/obo/NCIT_C165798
+Great Niece	A female child of one's niece or nephew.	NCIT	C165846	http://purl.obolibrary.org/obo/NCIT_C165846
+Maternal Great Aunt	The aunt of one's mother.	NCIT	C165853	http://purl.obolibrary.org/obo/NCIT_C165853
+Maternal Great Uncle	The uncle of one's mother.	NCIT	C165854	http://purl.obolibrary.org/obo/NCIT_C165854
+Paternal Great Aunt	The aunt of one's father.	NCIT	C165856	http://purl.obolibrary.org/obo/NCIT_C165856
+Paternal Great Uncle	The uncle of one's father.	NCIT	C165857	http://purl.obolibrary.org/obo/NCIT_C165857
diff --git a/misc/compatibility-with-cde.md → misc/jrc-cde/compatibility-with-cde.md b/misc/compatibility-with-cde.md → misc/jrc-cde/compatibility-with-cde.md
diff --git a/misc/molgenis/docker/down.sh b/misc/molgenis/docker/down.sh
@@ -0,0 +1,3 @@
+cd ~/github/docker/molgenis/8.3/
+docker-compose down
+docker volume prune
diff --git a/misc/molgenis/docker/nuke.sh b/misc/molgenis/docker/nuke.sh
@@ -0,0 +1 @@
+docker system prune --all --force --volumes
diff --git a/misc/molgenis/docker/up.sh b/misc/molgenis/docker/up.sh
@@ -0,0 +1,2 @@
+cd ~/github/docker/molgenis/8.3/
+docker-compose up
diff --git a/misc/molgenis/img/analysis.png b/misc/molgenis/img/analysis.png
diff --git a/misc/molgenis/img/clinical.png b/misc/molgenis/img/clinical.png
diff --git a/misc/molgenis/img/contribute.png b/misc/molgenis/img/contribute.png
diff --git a/misc/molgenis/img/fair_genomes_logo.png b/misc/molgenis/img/fair_genomes_logo.png
diff --git a/misc/molgenis/img/fair_genomes_logo_notext.png b/misc/molgenis/img/fair_genomes_logo_notext.png
diff --git a/misc/molgenis/img/individualconsent.png b/misc/molgenis/img/individualconsent.png
diff --git a/misc/molgenis/img/info.png b/misc/molgenis/img/info.png
diff --git a/misc/molgenis/img/informedconsentform.png b/misc/molgenis/img/informedconsentform.png
diff --git a/misc/molgenis/img/lookups.png b/misc/molgenis/img/lookups.png
diff --git a/misc/molgenis/img/material.png b/misc/molgenis/img/material.png
diff --git a/misc/molgenis/img/personal.png b/misc/molgenis/img/personal.png
diff --git a/misc/molgenis/img/samplepreparation.png b/misc/molgenis/img/samplepreparation.png
diff --git a/misc/molgenis/img/sequencing.png b/misc/molgenis/img/sequencing.png
diff --git a/misc/molgenis/img/study.png b/misc/molgenis/img/study.png
diff --git a/misc/molgenis/other/sys_StaticContent.tsv b/misc/molgenis/other/sys_StaticContent.tsv
@@ -0,0 +1,74 @@
+key_	content
+home	"<div class=""jumbotron jumbotron-fluid"">
+<div class=""container"">
+	<h1 class=""display-4"" style=""color: #353535;font-size: 8.5em; ""><img src=""/logo/fair_genomes_logo_notext.png"" style=""height: 100px;""/>FAIR Genomes</h1>
+	<h4>Version 0.2 public demo. This is a prototype for evaluation purposes only. Do not import any sensitive data.</h4>
+	<p class=""lead"">
+		<i>A national guideline to promote optimal (re)use of NGS data in research and healthcare</i>.<br/>
+	</p>
+	<table style=""table-layout: fixed; width: 700px; height: 800px;"">
+		<tr>
+			<td style=""text-align: center; vertical-align: bottom; width:100px; height: 100px;"">
+				<p><a href=""/menu/main/dataexplorer?entity=fair-genomes_study""><img alt=""study"" src=""/logo/study.png"" style=""height: 100px;""/></a></p>
+				<a class=""btn btn-primary btn-lg"" href=""/menu/main/dataexplorer?entity=fair-genomes_study"" role=""button"">Study</a>
+			</td>
+			<td style=""text-align: center; vertical-align: bottom; width:100px; height: 100px;"">
+				<p><a href=""/menu/main/dataexplorer?entity=fair-genomes_personal""><img alt=""personal"" src=""/logo/personal.png"" style=""height: 100px;""/></a></p>
+				<a class=""btn btn-primary btn-lg"" href=""/menu/main/dataexplorer?entity=fair-genomes_personal"" role=""button"">Personal</a>
+			</td>
+			<td style=""text-align: center; vertical-align: bottom; width:100px; height: 100px;"">
+				<p><a href=""/menu/main/dataexplorer?entity=fair-genomes_informedconsentform""><img alt=""informedconsentform"" src=""/logo/informedconsentform.png"" style=""height: 100px;""/></a></p>
+				<a class=""btn btn-primary btn-lg"" href=""/menu/main/dataexplorer?entity=fair-genomes_informedconsentform"" role=""button"">Inf. Consent Form</a>
+			</td>
+		</tr>
+		<tr>
+			<td style=""text-align: center; vertical-align: bottom; width:100px; height: 100px;"">
+				<p><a href=""/menu/main/dataexplorer?entity=fair-genomes_material""><img alt=""material"" src=""/logo/material.png"" style=""width: 100px;""/></a></p>
+				<a class=""btn btn-primary btn-lg"" href=""/menu/main/dataexplorer?entity=fair-genomes_material"" role=""button"">Material</a>
+			</td>
+			<td style=""text-align: center; vertical-align: bottom; width:100px; height: 100px;"">
+				<p><a href=""/menu/main/dataexplorer?entity=fair-genomes_clinical""><img alt=""clinical"" src=""/logo/clinical.png"" style=""height: 100px;""/></a></p>
+				<a class=""btn btn-primary btn-lg"" href=""/menu/main/dataexplorer?entity=fair-genomes_clinical"" role=""button"">Clinical</a>
+			</td>
+			<td style=""text-align: center; vertical-align: bottom; width:100px; height: 100px;"">
+				<p><a href=""/menu/main/dataexplorer?entity=fair-genomes_individualconsent""><img alt=""individualconsent"" src=""/logo/individualconsent.png"" style=""height: 100px;""/></a></p>
+				<a class=""btn btn-primary btn-lg"" href=""/menu/main/dataexplorer?entity=fair-genomes_individualconsent"" role=""button"">Individual Consent</a>
+			</td>
+		</tr>
+		<tr>
+			<td style=""text-align: center; vertical-align: bottom; width:100px; height: 100px;"">
+				<p><a href=""/menu/main/dataexplorer?entity=fair-genomes_samplepreparation""><img alt=""samplepreparation"" src=""/logo/samplepreparation.png"" style=""height: 100px;""/></a></p>
+				<a class=""btn btn-primary btn-lg"" href=""/menu/main/dataexplorer?entity=fair-genomes_samplepreparation"" role=""button"">Sample preparation</a>
+			</td>
+			<td style=""text-align: center; vertical-align: bottom; width:100px; height: 100px;"">
+				<p><a href=""/menu/main/dataexplorer?entity=fair-genomes_sequencing""><img alt=""sequencing"" src=""/logo/sequencing.png"" style=""height: 100px;""/></a></p>
+				<a class=""btn btn-primary btn-lg"" href=""/menu/main/dataexplorer?entity=fair-genomes_sequencing"" role=""button"">Sequencing</a>
+			</td>
+			<td style=""text-align: center; vertical-align: bottom; width:100px; height: 100px;"">
+				<p><a href=""/menu/main/dataexplorer?entity=fair-genomes_analysis""><img alt=""analysis"" src=""/logo/analysis.png"" style=""height: 100px;""/></a></p>
+				<a class=""btn btn-primary btn-lg"" href=""/menu/main/dataexplorer?entity=fair-genomes_analysis"" role=""button"">Analysis</a>
+			</td>
+		</tr>
+		<tr>
+			<td style=""text-align: center; vertical-align: bottom; width:100px; height: 100px;"">
+				<p><a href=""/menu/main/navigator/fair-genomes""><img alt=""lookups"" src=""/logo/lookups.png"" style=""height: 100px;""/></a></p>
+				<a class=""btn btn-warning btn-lg"" href=""/menu/main/navigator/fair-genomes"" role=""button"">Lookups</a>
+			</td>
+			<td style=""text-align: center; vertical-align: bottom; width:100px; height: 100px;"">
+				<p><a href=""https://www.zonmw.nl/nl/onderzoek-resultaten/geneesmiddelen/programmas/project-detail/personalised-medicine/fair-genomes-a-national-guideline-to-promote-optimal-reuse-of-ngs-data-in-research-and-healthcare""><img alt=""info"" src=""/logo/info.png"" style=""height: 100px;""/></a></p>
+				<a class=""btn btn-warning btn-lg"" href=""https://www.zonmw.nl/nl/onderzoek-resultaten/geneesmiddelen/programmas/project-detail/personalised-medicine/fair-genomes-a-national-guideline-to-promote-optimal-reuse-of-ngs-data-in-research-and-healthcare"" role=""button"">Information</a>
+			</td>
+			<td style=""text-align: center; vertical-align: bottom; width:100px; height: 100px;"">
+				<p><a href=""https://github.com/fairgenomes""><img alt=""contribute"" src=""/logo/contribute.png"" style=""height: 100px;""/></a></p>
+				<a class=""btn btn-warning btn-lg"" href=""https://github.com/fairgenomes"" role=""button"">Contribute</a>
+			</td>
+		</tr>
+	</table>
+	<br/>
+	<br/>
+	<br/>
+	<p style=""font-size:10px"">
+		Figure credits: Iconathon, Adrien Coquet, Creative Stall, Anthony Bossard, Eucalyp, Sumit Saengthong, Wichai Wi, Line Icons Pro, Yu-Hsuan Chen and Anita Erica from <a href=""https://thenounproject.com/"">Noun Project</a>.
+	</p>
+</div>
+</div>"
diff --git a/src/main/java/org/fairgenomes/transformer/implementations/molgenisemx/ToEMX.java b/src/main/java/org/fairgenomes/transformer/implementations/molgenisemx/ToEMX.java
@@ -17,7 +17,7 @@ public class ToEMX {
 
     FAIRGenomes fg;
     File outputFolder;
-    static final String RN = "\r\n";
+    static final String RN = "\n";
     public static final String PACKAGE_NAME = "fair-genomes";
 
     public ToEMX(FAIRGenomes fg, File outputFolder) throws Exception {
@@ -118,8 +118,6 @@ Write model attributes for the modules (the actual tables that people use to ent
             bw = new BufferedWriter(fw);
             bw.write("name\tlabel\tdescription\tentity\tdataType\tidAttribute\tlabelAttribute\tvisible\tnillable\trefEntity" + RN);
 
-            // todo: auto ID + label ?
-
             for (Element e : m.elements) {
                 if(e.valueTypeEnum.equals(ValueType.UniqueID))
                 {
@@ -134,6 +132,22 @@ Write model attributes for the modules (the actual tables that people use to ent
             MCMDbw.write("mcmd import -p " + fileName + " --as attributes --in " + PACKAGE_NAME + RN);
         }
 
+        /*
+        Landing page
+         */
+        MCMDbw.write("mcmd import -p ../../misc/molgenis/other/sys_StaticContent.tsv" + RN);
+        String[] imgs = new String[]{"analysis", "lookups", "clinical", "informedconsentform", "individualconsent", "contribute", "info", "material", "personal", "samplepreparation", "sequencing", "study", "fair_genomes_logo_notext", "fair_genomes_logo"};
+        for(String img : imgs)
+        {
+            MCMDbw.write("mcmd add logo -p ../../misc/molgenis/img/"+img+".png" + RN);
+        }
+
+        /*
+        Demo permissions
+         */
+        MCMDbw.write("mcmd make --role ANONYMOUS fair-genomes_EDITOR" + RN);
+        MCMDbw.write("mcmd give anonymous view sys_md" + RN);
+
 
         /*
         Flush and close MOLGENIS Commander script

diff --git a/transformation-output/markdown/fairgenomes-semantic-model.md b/transformation-output/markdown/fairgenomes-semantic-model.md
@@ -1,6 +1,6 @@
 # FAIR Genomes semantic metadata model
 
-The FAIR Genomes semantic metadata model to power reuse of NGS data in research and healthcare. Version 0.0, 2020-12-19. This model consists of __9 modules__ that contain __107 metadata elements__ in total.
+The FAIR Genomes semantic metadata model to power reuse of NGS data in research and healthcare. Version 0.2, 2021-01-13. This model consists of __9 modules__ that contain __107 metadata elements__ in total.
 
 ## Module overview
 
@@ -100,8 +100,8 @@ Data obtained through patient examination or treatment. Ontology: [NCIT:C15783](
 | Age at last screening | Age of the patient at the moment of the most recent screening. | [NCIT:C81258](http://purl.obolibrary.org/obo/NCIT_C81258) | Integer |
 | Medication | Unique identifier of a drug conforming to the Anatomical Therapeutic Chemical (ATC) Classification System, a drug classification system controlled by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC). | [EDAM:data_3103](http://edamontology.org/data_3103) | [Drugs](../../lookups/Drugs.txt) lookup (5632 choices) |
 | Drug regimen | The specific way a therapeutic drug is to be taken, including formulation, route of administration, dose, dosing interval, and treatment duration. | [NCIT:C142516](http://purl.obolibrary.org/obo/NCIT_C142516) | Text |
-| Family members affected | This term applies to a family member who is diagnosed with the same condition as the individual who is the primary focus of investigation (the proband). | [HP:0032320](http://purl.obolibrary.org/obo/HP_0032320) | String |
-| Family members sequenced | A person related by descent rather than by marriage or law that was also sequenced. | [NCIT:C71384](http://purl.obolibrary.org/obo/NCIT_C71384) | String |
+| Family members affected | This term applies to a family member who is diagnosed with the same condition as the individual who is the primary focus of investigation (the proband). | [HP:0032320](http://purl.obolibrary.org/obo/HP_0032320) | [FamilyMembers](../../lookups/FamilyMembers.txt) lookup (41 choices) |
+| Family members sequenced | A person related by descent rather than by marriage or law that was also sequenced. | [NCIT:C71384](http://purl.obolibrary.org/obo/NCIT_C71384) | [FamilyMembers](../../lookups/FamilyMembers.txt) lookup (41 choices) |
 | Consanguinity | Information on whether the patient is a child from two family members who are second cousins or closer. | [GSSO:007578](http://purl.obolibrary.org/obo/GSSO_007578) | String |
 | Medical history | A record of a person's background regarding health, occurrence of disease events and surgical procedures. | [NCIT:C18772](http://purl.obolibrary.org/obo/NCIT_C18772) | [MedicalHistory](../../lookups/MedicalHistory.txt) lookup (1167 choices) |
 | Age of onset | Age of onset of clinical manifestations related to a clinical entity. | [Orphanet:C023](http://www.orpha.net/ORDO/Orphanet_C023) | Integer |