Comments (6)
Great to hear for you, I am aware of BEL, and I have been meaning to try PyBEL for a while. Dexter mentioned your name a while ago and I have been meaning to get in contact.
I wasn't aware of Bio2BEL, awesome!!
PR most welcome.
Note the primary driver for KGX is what I would call simple non-contextual triples. E.g. geneX involved_in processY, geneX interacts_with geneY. To represent contextual associations such as those found in OpenBEL or GO-CAMs a number of different design patterns present themselves, I'm going to have a look at your mapping to nx and may get back with questions.
cc @goodb
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Is there any controlled vocabulary for relations I should use? I started down the rabbit hole of the OBO Relations (ontology?) when I was thinking about that.
I think we can do some post-processing on BEL to take some of the relations that have the context on the edges and make them more simple
Example: p(A) increases p(B, pmod(Ph))
can be converted to p(A) phosphorylates p(B)
and so on
We're actually working this week with some other Fraunhofer colleagues to make the Bio2BEL repos more amenable for representation learning / other ML approaches for knowledge graphs. I will be sure to update you on the results, since they would likely be directly applicable here too
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I believe the RO is exactly the correct rabbit hole to crawl into for this one. Perhaps I can help navigate it? Do you have a list of the relations you want to map tp RO? (I suggest opening it in Protege for an easier time navigating and understanding it.)
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@goodb thanks for the tip. I actually had some fun looking through RO in the OLS at what's possible!
I've begun to write unit tests (no implementation, yet) on how BEL graphs (encoded in PyBEL's internal DSL) would be converted to RO relationships: https://github.com/cthoyt/pybel-obo/blob/master/tests/test_convert.py.
Hopefully the code is self-explanatory, and if it's not trouble I would appreciate feedback in case I missed something important.
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Hi @cthoyt - just doing some triage of issues here, is this still a priority for you?
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this is sort of done, but not a priority since kgx went in a very different direction
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Related Issues (20)
- add documentation to the kgx merge doc that shows when to use cat-merge as well as a set of steps to use merge config
- Dynamic configuration of Biolink Model semantics in KGX validation
- Knowledge Graph Exchange (KGE) Archive Download
- neo_sink.py constraints not created in neo4j v5+
- Do the KGX serialization formats support representation of Biolink qualifiers? HOT 2
- Error occurs when specifying a version starting with "v" in get_biolink_model_schema method HOT 1
- remove pinning of docutils==0.16.0 so that downstream users can also use sphinx
- Option to add un-prefixed labels in neo4j labels
- Automate mapping of infores in primary_knowledge_source HOT 1
- Fetching biolink-model for validate is confused by `v` in biolink version HOT 1
- run kgx validate from inside the project - need scripts defined in pyproject.toml HOT 2
- kgx validate `-o` option writes an empty file, output goes to stderr rather than stdout
- log_error in validation scales poorly HOT 1
- add SQL sink
- When translating kgx tsvs to ntriples, type assertions are wrong
- update KGX to optionally provide "retrieval_source_ids" attribute to collect information retrieval properties
- Relax KGX's `pandas` version dependency.
- KGX merge overwrites "provided_by" property
- Obsolete/Deprecated property is not populated when converting from obojson HOT 15
- Undocumented requirements for input nodes/edges file names?
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