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geneontology / noctua

Graph-based modeling environment for biology, including prototype editor and services
http://noctua.geneontology.org/
BSD 3-Clause "New" or "Revised" License
38 stars 12 forks source link

Noctua URL + access to various file formats #712

Closed lpalbou closed 2 years ago

lpalbou commented 3 years ago

http://noctua.geneontology.org/download/gomodel:R-HSA-71064/owl

Will get you the OWL. It would be nice that

http://noctua.geneontology.org/download/gomodel:R-HSA-71064/ttl

Gets you the TTL and same principles for json, causaltab, sif, etc

balhoff commented 3 years ago

FYI, the OWL is the TTL, and the TTL is the OWL. 😉 I don't think we have a means within Minerva to generate the other formats, do we?

lpalbou commented 3 years ago

Oops, I meant owl (ttl) vs owl (xml).

For the other formats, it's related to the possible refactoring of some codes in minerva for the "business logic" layer and the PPT which is circulating regarding go cam graphs.

lpalbou commented 3 years ago

So to clarify further, the proposal would be to have:

http://noctua.geneontology.org/download/gomodel:R-HSA-71064/gpad (already here) http://noctua.geneontology.org/download/gomodel:R-HSA-71064/owl.ttl (same as current /owl) http://noctua.geneontology.org/download/gomodel:R-HSA-71064/owl.xml http://noctua.geneontology.org/download/gomodel:R-HSA-71064/json (could be the Cytoscape format) http://noctua.geneontology.org/download/gomodel:R-HSA-71064/tsv (discussed in go cam graph PPT) http://noctua.geneontology.org/download/gomodel:R-HSA-71064/sif

Note: why http://noctua.geneontology.org/download/gomodel:R-HSA-71064/owl is not the same as https://raw.githubusercontent.com/geneontology/noctua-models/master/models/R-HSA-71064.ttl ? It's probably the same annotations but the files are different. The /owl files seems better formatted, why not flush them on GH noctua-models ?

balhoff commented 3 years ago

Note: why http://noctua.geneontology.org/download/gomodel:R-HSA-71064/owl is not the same as https://raw.githubusercontent.com/geneontology/noctua-models/master/models/R-HSA-71064.ttl ?

The first is an export from the in-memory (and possibly not saved) OWL ontology object via OWL API. The second is a direct export from the triplestore, which is much faster in bulk.

cmungall commented 3 years ago

There are some good ideas here, but let us park this issue for now until we prioritize this

vanaukenk commented 2 years ago

Closing for now; we can reopen if we want to do this as part of a more general export file project.