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:
Please try the public demo at give us feedback.
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.
To upload to molgenis-emx2, make a zip of the generated/molgenis-emx2 and upload.