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SynBioHub / synbiohub-lab

SynBioHub is a Web-based repository for synthetic biology, enabling users to browse, upload, and share synthetic biology designs.
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Mapping ontology terms to human readable names/descriptions #6

Open jamesamcl opened 6 years ago

jamesamcl commented 6 years ago

I see two easy ways to do this:

  1. Extract the names and descriptions from OWL and make a URI -> { name, desc } mapping in LevelDB

or

  1. Load the OWL into the triplestore and retrieve names/descriptions using SPARQL in the view

So far I've explored option 2 and Virtuoso died a horrible death when I tried to upload the gene ontology (172 MB of RDF/XML). I'm now leaning towards option 1, which would also be faster at render time.

jamesamcl commented 6 years ago

Example ontologies, both of which we need:

https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/so.owl (small) http://purl.obolibrary.org/obo/go.owl (big)

jamesamcl commented 6 years ago

@chrisAta We could use the same leveldb to map URIs of taxonomy IDs to names.

jamesamcl commented 6 years ago

Also SBO

http://www.ebi.ac.uk/sbo/exports/Main/SBO_OWL.owl