sssom-py
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mapping-commons
Python toolkit for SSSOM mapping format
We want to make idiot-proof versions of sssom files Context from paper: _Mappings are not idempotent: adding a column to a mapping table could change its semantics. The hardest design...
https://github.com/mapping-commons/sssom-py/blob/master/schema/sssom.yaml#L6-L14 I think the following can be removed: - neuronames - orphanet/ordo
Three core use cases: 1. convert existing formats into SSSOM 2. validate sssom files to encourage high quality FAIR and remixable mappings 3. Export sssom to standard JSON-LD and RDF...
the code in the innermost loop should be a class method on `Mapping` _Originally posted by @cthoyt in https://github.com/mapping-commons/sssom-py/pull/143#discussion_r712853946_
why is the df even allowed to be none? _Originally posted by @cthoyt in https://github.com/mapping-commons/sssom-py/pull/143#discussion_r712854797_ This happens a lot through the codebase - stuff is set as none by default....
TODO indeed. please refactor the code from export_ptable and reuse it _Originally posted by @cthoyt in https://github.com/mapping-commons/sssom-py/pull/143#discussion_r712852570_
See https://github.com/biopragmatics/bioregistry#generating-iris This looks neat, should look into using it!
Currently, there are quite a few that are out of sync - at least the major read/write/from/to ones should be checked and updated.
Right now, only all the other methods can handle URL parameters - `parse` cannot. I would like parse to also handle reading from URL and streams - the best way...
- edges are lost because of the transformation to OWL reification vocabulary, it seems it makes sense it is preserved. - RDFDumper().dumped file cannot be read the same way (roundtrip...