diff --git a/fair-genomes.yml b/fair-genomes.yml index 073fd6a..c0a7566 100644 --- 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 new file mode 100644 index 0000000..6ed0ae5 --- /dev/null +++ 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 b/misc/jrc-cde/compatibility-with-cde.md similarity index 100% rename from misc/compatibility-with-cde.md rename to misc/jrc-cde/compatibility-with-cde.md diff --git a/misc/molgenis/docker/down.sh b/misc/molgenis/docker/down.sh new file mode 100644 index 0000000..d3b3b1d --- /dev/null +++ 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 new file mode 100644 index 0000000..d1b2c0c --- /dev/null +++ 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 new file mode 100644 index 0000000..3a490ee --- /dev/null +++ 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 new file mode 100644 index 0000000..e9ab4ea Binary files /dev/null and b/misc/molgenis/img/analysis.png differ diff --git a/misc/molgenis/img/clinical.png b/misc/molgenis/img/clinical.png new file mode 100644 index 0000000..940ef86 Binary files /dev/null and b/misc/molgenis/img/clinical.png differ diff --git a/misc/molgenis/img/contribute.png b/misc/molgenis/img/contribute.png new file mode 100644 index 0000000..97ea7cb Binary files /dev/null and b/misc/molgenis/img/contribute.png differ diff --git a/misc/molgenis/img/fair_genomes_logo.png b/misc/molgenis/img/fair_genomes_logo.png new file mode 100644 index 0000000..a197f32 Binary files /dev/null and b/misc/molgenis/img/fair_genomes_logo.png differ diff --git a/misc/molgenis/img/fair_genomes_logo_notext.png b/misc/molgenis/img/fair_genomes_logo_notext.png new file mode 100644 index 0000000..cab65b7 Binary files /dev/null and b/misc/molgenis/img/fair_genomes_logo_notext.png differ diff --git a/misc/molgenis/img/individualconsent.png b/misc/molgenis/img/individualconsent.png new file mode 100644 index 0000000..e2c7814 Binary files /dev/null and b/misc/molgenis/img/individualconsent.png differ diff --git a/misc/molgenis/img/info.png b/misc/molgenis/img/info.png new file mode 100644 index 0000000..c906151 Binary files /dev/null and b/misc/molgenis/img/info.png differ diff --git a/misc/molgenis/img/informedconsentform.png b/misc/molgenis/img/informedconsentform.png new file mode 100644 index 0000000..fee0bca Binary files /dev/null and b/misc/molgenis/img/informedconsentform.png differ diff --git a/misc/molgenis/img/lookups.png b/misc/molgenis/img/lookups.png new file mode 100644 index 0000000..d27df31 Binary files /dev/null and b/misc/molgenis/img/lookups.png differ diff --git a/misc/molgenis/img/material.png b/misc/molgenis/img/material.png new file mode 100644 index 0000000..7d24f16 Binary files /dev/null and b/misc/molgenis/img/material.png differ diff --git a/misc/molgenis/img/personal.png b/misc/molgenis/img/personal.png new file mode 100644 index 0000000..50449ed Binary files /dev/null and b/misc/molgenis/img/personal.png differ diff --git a/misc/molgenis/img/samplepreparation.png b/misc/molgenis/img/samplepreparation.png new file mode 100644 index 0000000..5aad35b Binary files /dev/null and b/misc/molgenis/img/samplepreparation.png differ diff --git a/misc/molgenis/img/sequencing.png b/misc/molgenis/img/sequencing.png new file mode 100644 index 0000000..fb89074 Binary files /dev/null and b/misc/molgenis/img/sequencing.png differ diff --git a/misc/molgenis/img/study.png b/misc/molgenis/img/study.png new file mode 100644 index 0000000..2342820 Binary files /dev/null and b/misc/molgenis/img/study.png differ diff --git a/misc/molgenis/other/sys_StaticContent.tsv b/misc/molgenis/other/sys_StaticContent.tsv new file mode 100644 index 0000000..1ee2db2 --- /dev/null +++ b/misc/molgenis/other/sys_StaticContent.tsv @@ -0,0 +1,74 @@ +key_ content +home "
+
+

FAIR Genomes

+

Version 0.2 public demo. This is a prototype for evaluation purposes only. Do not import any sensitive data.

+

+ A national guideline to promote optimal (re)use of NGS data in research and healthcare.
+

+ + + + + + + + + + + + + + + + + + + + + +
+

+ Study + 		+

+ Personal + 		+

+ Inf. Consent Form +
+

+ Material + 		+

+ Clinical + 		+

+ Individual Consent +
+

+ Sample preparation + 		+

+ Sequencing + 		+

+ Analysis +
+

+ Lookups + 		+

+ Information + 		+

+ Contribute +
+
+
+
+

+ Figure credits: Iconathon, Adrien Coquet, Creative Stall, Anthony Bossard, Eucalyp, Sumit Saengthong, Wichai Wi, Line Icons Pro, Yu-Hsuan Chen and Anita Erica from Noun Project. +

+
+
" \ No newline at end of file diff --git a/src/main/java/org/fairgenomes/transformer/implementations/molgenisemx/ToEMX.java b/src/main/java/org/fairgenomes/transformer/implementations/molgenisemx/ToEMX.java index 45e15b2..cc008ec 100644 --- 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 index 77c71a4..33fc3c2 100644 --- 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 | diff --git a/transformation-output/molgenis-emx/clinical_familymembersaffected.tsv b/transformation-output/molgenis-emx/clinical_familymembersaffected.tsv new file mode 100644 index 0000000..9048c8e --- /dev/null +++ b/transformation-output/molgenis-emx/clinical_familymembersaffected.tsv @@ -0,0 +1,58 @@ +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 +Not available (NAVU, nullflavor) Information is not available at this time (with no expectation regarding whether it will or will not be available in the future). HL7 NAVU http://terminology.hl7.org/CodeSystem/v3-NullFlavor#NAVU +Temporarily unavailable (NAV, nullflavor) Information is not available at this time but it is expected that it will be available later. HL7 NAV http://terminology.hl7.org/CodeSystem/v3-NullFlavor#NAV +Not asked (NASK, nullflavor) This information has not been sought. (e.g., patient was not asked) HL7 NASK http://terminology.hl7.org/CodeSystem/v3-NullFlavor#NASK +Derived (DER, nullflavor) An actual value may exist, but it must be derived from the provided information (usually an EXPR generic data type extension will be used to convey the derivation expression . HL7 DER http://terminology.hl7.org/CodeSystem/v3-NullFlavor#DER +Unknown (UNK, nullflavor) A proper value is applicable, but not known. HL7 UNK http://terminology.hl7.org/CodeSystem/v3-NullFlavor#UNK +Trace (TRC, nullflavor) The content is greater than zero, but too small to be quantified. HL7 TRC http://terminology.hl7.org/CodeSystem/v3-NullFlavor#TRC +Other (OTH, nullflavor) The actual value is not a member of the set of permitted data values in the constrained value domain of a variable.The actual value is not a member of the set of permitted data values in the constrained value domain of a variable. (e.g., concept not provided by required code system). HL7 OTH http://terminology.hl7.org/CodeSystem/v3-NullFlavor#OTH +Masked (MSK, nullflavor) There is information on this item available but it has not been provided by the sender due to security, privacy or other reasons. There may be an alternate mechanism for gaining access to this information. HL7 MSK http://terminology.hl7.org/CodeSystem/v3-NullFlavor#MSK +Negative infinity (NINF, nullflavor) Negative infinity of numbers. HL7 NINF http://terminology.hl7.org/CodeSystem/v3-NullFlavor#NINF +Sufficient quantity (QS, nullflavor) The specific quantity is not known, but is known to be non-zero and is not specified because it makes up the bulk of the material. e.g. 'Add 10mg of ingredient X, 50mg of ingredient Y, and sufficient quantity of water to 100mL.' The null flavor would be used to express the quantity of water. HL7 QS http://terminology.hl7.org/CodeSystem/v3-NullFlavor#QS +Un-encoded (UNC, nullflavor) The actual value has not yet been encoded within the approved value domain. HL7 UNC http://terminology.hl7.org/CodeSystem/v3-NullFlavor#UNC +Invalid (INV, nullflavor) The value as represented in the instance is not a member of the set of permitted data values in the constrained value domain of a variable. HL7 INV http://terminology.hl7.org/CodeSystem/v3-NullFlavor#INV +NoInformation (NI, nullflavor) The value is exceptional (missing, omitted, incomplete, improper). No information as to the reason for being an exceptional value is provided. This is the most general exceptional value. It is also the default exceptional value. HL7 NI http://terminology.hl7.org/CodeSystem/v3-NullFlavor#NI +Not applicable (NA, nullflavor) Known to have no proper value (e.g., last menstrual period for a male). HL7 NA http://terminology.hl7.org/CodeSystem/v3-NullFlavor#NA +Positive infinity (PINF, nullflavor) Positive infinity of numbers. HL7 PINF http://terminology.hl7.org/CodeSystem/v3-NullFlavor#PINF +Asked but unknown (ASKU, nullflavor) Information was sought but not found (e.g., patient was asked but didn't know) HL7 ASKU http://terminology.hl7.org/CodeSystem/v3-NullFlavor#ASKU diff --git a/transformation-output/molgenis-emx/clinical_familymembersaffected_attributes.tsv b/transformation-output/molgenis-emx/clinical_familymembersaffected_attributes.tsv new file mode 100644 index 0000000..98921b1 --- /dev/null +++ b/transformation-output/molgenis-emx/clinical_familymembersaffected_attributes.tsv @@ -0,0 +1,6 @@ +name entity label dataType idAttribute nillable +value clinical_familymembersaffected Value (English) String TRUE FALSE +description clinical_familymembersaffected Description (English) Text FALSE TRUE +codesystem clinical_familymembersaffected The code system (e.g. ontology) this term belongs to String FALSE TRUE +code clinical_familymembersaffected The code within the code system String FALSE TRUE +iri clinical_familymembersaffected The Internationalized Resource Identifier for this term String FALSE TRUE diff --git a/transformation-output/molgenis-emx/clinical_familymemberssequenced.tsv b/transformation-output/molgenis-emx/clinical_familymemberssequenced.tsv new file mode 100644 index 0000000..9048c8e --- /dev/null +++ b/transformation-output/molgenis-emx/clinical_familymemberssequenced.tsv @@ -0,0 +1,58 @@ +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 +Not available (NAVU, nullflavor) Information is not available at this time (with no expectation regarding whether it will or will not be available in the future). HL7 NAVU http://terminology.hl7.org/CodeSystem/v3-NullFlavor#NAVU +Temporarily unavailable (NAV, nullflavor) Information is not available at this time but it is expected that it will be available later. HL7 NAV http://terminology.hl7.org/CodeSystem/v3-NullFlavor#NAV +Not asked (NASK, nullflavor) This information has not been sought. (e.g., patient was not asked) HL7 NASK http://terminology.hl7.org/CodeSystem/v3-NullFlavor#NASK +Derived (DER, nullflavor) An actual value may exist, but it must be derived from the provided information (usually an EXPR generic data type extension will be used to convey the derivation expression . HL7 DER http://terminology.hl7.org/CodeSystem/v3-NullFlavor#DER +Unknown (UNK, nullflavor) A proper value is applicable, but not known. HL7 UNK http://terminology.hl7.org/CodeSystem/v3-NullFlavor#UNK +Trace (TRC, nullflavor) The content is greater than zero, but too small to be quantified. HL7 TRC http://terminology.hl7.org/CodeSystem/v3-NullFlavor#TRC +Other (OTH, nullflavor) The actual value is not a member of the set of permitted data values in the constrained value domain of a variable.The actual value is not a member of the set of permitted data values in the constrained value domain of a variable. (e.g., concept not provided by required code system). HL7 OTH http://terminology.hl7.org/CodeSystem/v3-NullFlavor#OTH +Masked (MSK, nullflavor) There is information on this item available but it has not been provided by the sender due to security, privacy or other reasons. There may be an alternate mechanism for gaining access to this information. HL7 MSK http://terminology.hl7.org/CodeSystem/v3-NullFlavor#MSK +Negative infinity (NINF, nullflavor) Negative infinity of numbers. HL7 NINF http://terminology.hl7.org/CodeSystem/v3-NullFlavor#NINF +Sufficient quantity (QS, nullflavor) The specific quantity is not known, but is known to be non-zero and is not specified because it makes up the bulk of the material. e.g. 'Add 10mg of ingredient X, 50mg of ingredient Y, and sufficient quantity of water to 100mL.' The null flavor would be used to express the quantity of water. HL7 QS http://terminology.hl7.org/CodeSystem/v3-NullFlavor#QS +Un-encoded (UNC, nullflavor) The actual value has not yet been encoded within the approved value domain. HL7 UNC http://terminology.hl7.org/CodeSystem/v3-NullFlavor#UNC +Invalid (INV, nullflavor) The value as represented in the instance is not a member of the set of permitted data values in the constrained value domain of a variable. HL7 INV http://terminology.hl7.org/CodeSystem/v3-NullFlavor#INV +NoInformation (NI, nullflavor) The value is exceptional (missing, omitted, incomplete, improper). No information as to the reason for being an exceptional value is provided. This is the most general exceptional value. It is also the default exceptional value. HL7 NI http://terminology.hl7.org/CodeSystem/v3-NullFlavor#NI +Not applicable (NA, nullflavor) Known to have no proper value (e.g., last menstrual period for a male). HL7 NA http://terminology.hl7.org/CodeSystem/v3-NullFlavor#NA +Positive infinity (PINF, nullflavor) Positive infinity of numbers. HL7 PINF http://terminology.hl7.org/CodeSystem/v3-NullFlavor#PINF +Asked but unknown (ASKU, nullflavor) Information was sought but not found (e.g., patient was asked but didn't know) HL7 ASKU http://terminology.hl7.org/CodeSystem/v3-NullFlavor#ASKU diff --git a/transformation-output/molgenis-emx/clinical_familymemberssequenced_attributes.tsv b/transformation-output/molgenis-emx/clinical_familymemberssequenced_attributes.tsv new file mode 100644 index 0000000..aff842c --- /dev/null +++ b/transformation-output/molgenis-emx/clinical_familymemberssequenced_attributes.tsv @@ -0,0 +1,6 @@ +name entity label dataType idAttribute nillable +value clinical_familymemberssequenced Value (English) String TRUE FALSE +description clinical_familymemberssequenced Description (English) Text FALSE TRUE +codesystem clinical_familymemberssequenced The code system (e.g. ontology) this term belongs to String FALSE TRUE +code clinical_familymemberssequenced The code within the code system String FALSE TRUE +iri clinical_familymemberssequenced The Internationalized Resource Identifier for this term String FALSE TRUE diff --git a/transformation-output/molgenis-emx/setup.sh b/transformation-output/molgenis-emx/setup.sh index ecec251..3e553f1 100644 --- a/transformation-output/molgenis-emx/setup.sh +++ b/transformation-output/molgenis-emx/setup.sh @@ -1,41 +1,87 @@ -mcmd import -p sys_md_Package.tsv -mcmd import -p personal_lookup_gender_attributes.tsv --as attributes --in fair-genomes -mcmd import -p personal_lookup_genotypicsex_attributes.tsv --as attributes --in fair-genomes -mcmd import -p personal_lookup_countryofresidence_attributes.tsv --as attributes --in fair-genomes -mcmd import -p personal_lookup_ethnicity_attributes.tsv --as attributes --in fair-genomes -mcmd import -p personal_lookup_countryofbirth_attributes.tsv --as attributes --in fair-genomes -mcmd import -p personal_lookup_inclusionstatus_attributes.tsv --as attributes --in fair-genomes -mcmd import -p personal_lookup_primaryaffiliatedinstitute_attributes.tsv --as attributes --in fair-genomes -mcmd import -p personal_lookup_dataavailableinotherinstitutes_attributes.tsv --as attributes --in fair-genomes -mcmd import -p informedconsentform_lookup_consentformcreator_attributes.tsv --as attributes --in fair-genomes -mcmd import -p informedconsentform_lookup_consentformrestrictedto_attributes.tsv --as attributes --in fair-genomes -mcmd import -p individualconsent_lookup_restrictedto_attributes.tsv --as attributes --in fair-genomes -mcmd import -p material_lookup_materialtype_attributes.tsv --as attributes --in fair-genomes -mcmd import -p material_lookup_anatomicalsource_attributes.tsv --as attributes --in fair-genomes -mcmd import -p material_lookup_storageconditions_attributes.tsv --as attributes --in fair-genomes -mcmd import -p samplepreparation_lookup_librarypreparationkit_attributes.tsv --as attributes --in fair-genomes -mcmd import -p samplepreparation_lookup_targetenrichmentkit_attributes.tsv --as attributes --in fair-genomes -mcmd import -p sequencing_lookup_sequencingplatform_attributes.tsv --as attributes --in fair-genomes -mcmd import -p sequencing_lookup_sequencinginstrumentmodel_attributes.tsv --as attributes --in fair-genomes -mcmd import -p sequencing_lookup_sequencingtype_attributes.tsv --as attributes --in fair-genomes -mcmd import -p analysis_lookup_physicaldatalocation_attributes.tsv --as attributes --in fair-genomes -mcmd import -p personal_lookup_gender.tsv --as fair-genomes_personal_lookup_gender --in fair-genomes -mcmd import -p personal_lookup_genotypicsex.tsv --as fair-genomes_personal_lookup_genotypicsex --in fair-genomes -mcmd import -p personal_lookup_countryofresidence.tsv --as fair-genomes_personal_lookup_countryofresidence --in fair-genomes -mcmd import -p personal_lookup_ethnicity.tsv --as fair-genomes_personal_lookup_ethnicity --in fair-genomes -mcmd import -p personal_lookup_countryofbirth.tsv --as fair-genomes_personal_lookup_countryofbirth --in fair-genomes -mcmd import -p personal_lookup_inclusionstatus.tsv --as fair-genomes_personal_lookup_inclusionstatus --in fair-genomes -mcmd import -p personal_lookup_primaryaffiliatedinstitute.tsv --as fair-genomes_personal_lookup_primaryaffiliatedinstitute --in fair-genomes -mcmd import -p personal_lookup_dataavailableinotherinstitutes.tsv --as fair-genomes_personal_lookup_dataavailableinotherinstitutes --in fair-genomes -mcmd import -p informedconsentform_lookup_consentformcreator.tsv --as fair-genomes_informedconsentform_lookup_consentformcreator --in fair-genomes -mcmd import -p informedconsentform_lookup_consentformrestrictedto.tsv --as fair-genomes_informedconsentform_lookup_consentformrestrictedto --in fair-genomes -mcmd import -p individualconsent_lookup_restrictedto.tsv --as fair-genomes_individualconsent_lookup_restrictedto --in fair-genomes -mcmd import -p material_lookup_materialtype.tsv --as fair-genomes_material_lookup_materialtype --in fair-genomes -mcmd import -p material_lookup_anatomicalsource.tsv --as fair-genomes_material_lookup_anatomicalsource --in fair-genomes -mcmd import -p material_lookup_storageconditions.tsv --as fair-genomes_material_lookup_storageconditions --in fair-genomes -mcmd import -p samplepreparation_lookup_librarypreparationkit.tsv --as fair-genomes_samplepreparation_lookup_librarypreparationkit --in fair-genomes -mcmd import -p samplepreparation_lookup_targetenrichmentkit.tsv --as fair-genomes_samplepreparation_lookup_targetenrichmentkit --in fair-genomes -mcmd import -p sequencing_lookup_sequencingplatform.tsv --as fair-genomes_sequencing_lookup_sequencingplatform --in fair-genomes -mcmd import -p sequencing_lookup_sequencinginstrumentmodel.tsv --as fair-genomes_sequencing_lookup_sequencinginstrumentmodel --in fair-genomes -mcmd import -p sequencing_lookup_sequencingtype.tsv --as fair-genomes_sequencing_lookup_sequencingtype --in fair-genomes -mcmd import -p analysis_lookup_physicaldatalocation.tsv --as fair-genomes_analysis_lookup_physicaldatalocation --in fair-genomes +mcmd import -p sys_md_Package.tsv +mcmd import -p personal_gender_attributes.tsv --as attributes --in fair-genomes +mcmd import -p personal_genotypicsex_attributes.tsv --as attributes --in fair-genomes +mcmd import -p personal_countryofresidence_attributes.tsv --as attributes --in fair-genomes +mcmd import -p personal_ethnicity_attributes.tsv --as attributes --in fair-genomes +mcmd import -p personal_countryofbirth_attributes.tsv --as attributes --in fair-genomes +mcmd import -p personal_inclusionstatus_attributes.tsv --as attributes --in fair-genomes +mcmd import -p personal_inclusioncriteria_attributes.tsv --as attributes --in fair-genomes +mcmd import -p personal_primaryaffiliatedinstitute_attributes.tsv --as attributes --in fair-genomes +mcmd import -p personal_resourcesinotherinstitutes_attributes.tsv --as attributes --in fair-genomes +mcmd import -p informedconsentform_consentformcreator_attributes.tsv --as attributes --in fair-genomes +mcmd import -p informedconsentform_consentformrestrictedto_attributes.tsv --as attributes --in fair-genomes +mcmd import -p individualconsent_restrictedto_attributes.tsv --as attributes --in fair-genomes +mcmd import -p clinical_phenotype_attributes.tsv --as attributes --in fair-genomes +mcmd import -p clinical_unobservedphenotype_attributes.tsv --as attributes --in fair-genomes +mcmd import -p clinical_phenotypicdataavailable_attributes.tsv --as attributes --in fair-genomes +mcmd import -p clinical_clinicaldiagnosis_attributes.tsv --as attributes --in fair-genomes +mcmd import -p clinical_moleculardiagnosisgene_attributes.tsv --as attributes --in fair-genomes +mcmd import -p clinical_medication_attributes.tsv --as attributes --in fair-genomes +mcmd import -p clinical_familymembersaffected_attributes.tsv --as attributes --in fair-genomes +mcmd import -p clinical_familymemberssequenced_attributes.tsv --as attributes --in fair-genomes +mcmd import -p clinical_medicalhistory_attributes.tsv --as attributes --in fair-genomes +mcmd import -p material_materialtype_attributes.tsv --as attributes --in fair-genomes +mcmd import -p material_anatomicalsource_attributes.tsv --as attributes --in fair-genomes +mcmd import -p material_storageconditions_attributes.tsv --as attributes --in fair-genomes +mcmd import -p samplepreparation_librarypreparationkit_attributes.tsv --as attributes --in fair-genomes +mcmd import -p samplepreparation_targetenrichmentkit_attributes.tsv --as attributes --in fair-genomes +mcmd import -p sequencing_sequencingplatform_attributes.tsv --as attributes --in fair-genomes +mcmd import -p sequencing_sequencinginstrumentmodel_attributes.tsv --as attributes --in fair-genomes +mcmd import -p sequencing_sequencingtype_attributes.tsv --as attributes --in fair-genomes +mcmd import -p analysis_dataformatsstored_attributes.tsv --as attributes --in fair-genomes +mcmd import -p personal_gender.tsv --as fair-genomes_personal_gender --in fair-genomes +mcmd import -p personal_genotypicsex.tsv --as fair-genomes_personal_genotypicsex --in fair-genomes +mcmd import -p personal_countryofresidence.tsv --as fair-genomes_personal_countryofresidence --in fair-genomes +mcmd import -p personal_ethnicity.tsv --as fair-genomes_personal_ethnicity --in fair-genomes +mcmd import -p personal_countryofbirth.tsv --as fair-genomes_personal_countryofbirth --in fair-genomes +mcmd import -p personal_inclusionstatus.tsv --as fair-genomes_personal_inclusionstatus --in fair-genomes +mcmd import -p personal_inclusioncriteria.tsv --as fair-genomes_personal_inclusioncriteria --in fair-genomes +mcmd import -p personal_primaryaffiliatedinstitute.tsv --as fair-genomes_personal_primaryaffiliatedinstitute --in fair-genomes +mcmd import -p personal_resourcesinotherinstitutes.tsv --as fair-genomes_personal_resourcesinotherinstitutes --in fair-genomes +mcmd import -p informedconsentform_consentformcreator.tsv --as fair-genomes_informedconsentform_consentformcreator --in fair-genomes +mcmd import -p informedconsentform_consentformrestrictedto.tsv --as fair-genomes_informedconsentform_consentformrestrictedto --in fair-genomes +mcmd import -p individualconsent_restrictedto.tsv --as fair-genomes_individualconsent_restrictedto --in fair-genomes +mcmd import -p clinical_phenotype.tsv --as fair-genomes_clinical_phenotype --in fair-genomes +mcmd import -p clinical_unobservedphenotype.tsv --as fair-genomes_clinical_unobservedphenotype --in fair-genomes +mcmd import -p clinical_phenotypicdataavailable.tsv --as fair-genomes_clinical_phenotypicdataavailable --in fair-genomes +mcmd import -p clinical_clinicaldiagnosis.tsv --as fair-genomes_clinical_clinicaldiagnosis --in fair-genomes +mcmd import -p clinical_moleculardiagnosisgene.tsv --as fair-genomes_clinical_moleculardiagnosisgene --in fair-genomes +mcmd import -p clinical_medication.tsv --as fair-genomes_clinical_medication --in fair-genomes +mcmd import -p clinical_familymembersaffected.tsv --as fair-genomes_clinical_familymembersaffected --in fair-genomes +mcmd import -p clinical_familymemberssequenced.tsv --as fair-genomes_clinical_familymemberssequenced --in fair-genomes +mcmd import -p clinical_medicalhistory.tsv --as fair-genomes_clinical_medicalhistory --in fair-genomes +mcmd import -p material_materialtype.tsv --as fair-genomes_material_materialtype --in fair-genomes +mcmd import -p material_anatomicalsource.tsv --as fair-genomes_material_anatomicalsource --in fair-genomes +mcmd import -p material_storageconditions.tsv --as fair-genomes_material_storageconditions --in fair-genomes +mcmd import -p samplepreparation_librarypreparationkit.tsv --as fair-genomes_samplepreparation_librarypreparationkit --in fair-genomes +mcmd import -p samplepreparation_targetenrichmentkit.tsv --as fair-genomes_samplepreparation_targetenrichmentkit --in fair-genomes +mcmd import -p sequencing_sequencingplatform.tsv --as fair-genomes_sequencing_sequencingplatform --in fair-genomes +mcmd import -p sequencing_sequencinginstrumentmodel.tsv --as fair-genomes_sequencing_sequencinginstrumentmodel --in fair-genomes +mcmd import -p sequencing_sequencingtype.tsv --as fair-genomes_sequencing_sequencingtype --in fair-genomes +mcmd import -p analysis_dataformatsstored.tsv --as fair-genomes_analysis_dataformatsstored --in fair-genomes +mcmd import -p study_attributes.tsv --as attributes --in fair-genomes +mcmd import -p personal_attributes.tsv --as attributes --in fair-genomes +mcmd import -p informedconsentform_attributes.tsv --as attributes --in fair-genomes +mcmd import -p individualconsent_attributes.tsv --as attributes --in fair-genomes +mcmd import -p clinical_attributes.tsv --as attributes --in fair-genomes +mcmd import -p material_attributes.tsv --as attributes --in fair-genomes +mcmd import -p samplepreparation_attributes.tsv --as attributes --in fair-genomes +mcmd import -p sequencing_attributes.tsv --as attributes --in fair-genomes +mcmd import -p analysis_attributes.tsv --as attributes --in fair-genomes +mcmd import -p ../../misc/molgenis/other/sys_StaticContent.tsv +mcmd add logo -p ../../misc/molgenis/img/analysis.png +mcmd add logo -p ../../misc/molgenis/img/lookups.png +mcmd add logo -p ../../misc/molgenis/img/clinical.png +mcmd add logo -p ../../misc/molgenis/img/informedconsentform.png +mcmd add logo -p ../../misc/molgenis/img/individualconsent.png +mcmd add logo -p ../../misc/molgenis/img/contribute.png +mcmd add logo -p ../../misc/molgenis/img/info.png +mcmd add logo -p ../../misc/molgenis/img/material.png +mcmd add logo -p ../../misc/molgenis/img/personal.png +mcmd add logo -p ../../misc/molgenis/img/samplepreparation.png +mcmd add logo -p ../../misc/molgenis/img/sequencing.png +mcmd add logo -p ../../misc/molgenis/img/study.png +mcmd add logo -p ../../misc/molgenis/img/fair_genomes_logo_notext.png +mcmd add logo -p ../../misc/molgenis/img/fair_genomes_logo.png +mcmd make --role ANONYMOUS fair-genomes_EDITOR +mcmd give anonymous view sys_md