Discover the full schema at the interactive overview.
The source of the schema is located at fair-genomes.yml. The reference lookup lists are available at lookups.
Representations of the schema for specific systems/users are generated from the schema. The following outputs are available:
- MOLGENIS EMX1 database setup at molgenis-emx.
- PALGA Codebook at palga-codebook.
- ART-DECOR at art-decor. The ART-DECOR XML is uploaded to NICTIZ made available for iCRF Generator. FAIR Genomes interoperable case report forms can be created by iCRF Generator in these EDC formats:
- Castor - Step
- Castor - Report
- Castor - Survey
- REDCap
- OpenClinica 3
- Interactive overview at markdown. View it here.
- Typesetted LaTeX/PDF at latex and pdf. View it here.
- LODE page at lode. View it here.
Please try the public demo at give us feedback.
- Persistent namespace is provided by W3ID, linking to ontology and resources.
- Find us on FAIRSharing.
- Available on BioPortal.
The Research Organization Registry (https://ror.org/) provides a unique identifier for every research organization in the world. The 2021-09-23 ROR Data release (see https://zenodo.org/communities/ror-data) has been transformed in a FAIR Genomes compatible lookup list. This list, available at InstitutesROR.txt, can be used to supplement or replace the default Institutes.txt. The ROR institute data is currently not generated into apps because everything would become much bigger and slower than necessary under most circumstances.
The YAML format used to contain the FAIR Genomes schema is documented at YamlFormat.md.
The FAIR Genomes application ontology TTL files can be converted to other RDF serialization formats including OWL-XML, RDF-XML, RDF-JSON, JSON-LD, N-Triples, TriG, TriX, Thrift, Manchester syntax and Functional syntax using Ontology Converter.
For example, conversion to OWL-XML can be accomplished by running:
java -jar ont-converter.jar -i /path/to/fairgenomes-semantic-model/generated/ontology/fair-genomes.ttl -if TURTLE -o fair-genomes.owl -of OWL_XML
Please be aware that the original TTL format is highly efficient. Other RDF formats typically consume more disk space. Conversions using the FAIR Genomes TTL of 25-02-2021 as a reference results in the following relative file size differences:
Format | Difference |
---|---|
TTL | 0% (reference) |
OWL-XML | +660% |
RDF-XML | +107% |
RDF-JSON | +176% |
JSON-LD | +13% |
N-Triples | +357% |
TriG | -1% |
TriX | +696% |
Thrift | +284% |
Manchester | +435% |
Functional | +300% |
The ART-DECOR XML is validated using Saxon, requiring these resources:
http://art-decor.org/ADAR/rv/DECOR.sch
https://github.com/Schematron/stf/blob/master/iso-schematron-xslt2/iso_svrl_for_xslt2.xsl
https://github.com/Schematron/stf/blob/master/iso-schematron-xslt2/iso_schematron_skeleton_for_saxon.xsl
The Schematron must first be converted to XSLT:
java -jar saxon-he-10.3.jar -o:DECOR.xsl -s:DECOR.sch iso_svrl_for_xslt2.xsl
The XML can then be validated as follows:
java -jar saxon-he-10.3.jar -o:warnings.xml -s:/path/to/fairgenomes-semantic-model/generated/art-decor/fair-genomes_en-US.xml DECOR.xsl
Finally, warnings.xml
is inspected for any errors or warnings.
- Set correct date, version number and release type in YAML file.
- Generate outputs (by running Main.java).
- Validate implementations:
- Run ART-DECOR XML validation
- Run MOLGENIS setup script
- Import application ontology into GraphDB
- Check Markdown rendering
- Update PDF (run toPDF.sh in generated/latex).
- Update version in sys_StaticContent.tsv.
- Update version in pom.xml.
- Update Docker prepare at misc/molgenis/docker based on setup.sh.
- Create a new Excel file at misc/excel.
- Make commits and push to fork.
- Pull request and merge with main (i.e. fairgenomes organization).
- Create updated LODE page by following the link to TTL file in main repo.
- Commit LODE page to fork, then again PR and merge with main.
- Create Github release on main.
- Prepare for further development: increment version in fair-genomes.yml and set to SNAPSHOT. Also update pom.xml and sys_StaticContent.tsv.
- Use Ontology Converter to convert to OWL and publish new version on BioPortal.
- Reset demo server and import new app.