Comments (3)
cthoyt
commented on May 9, 2024
Actually this is a good place to think about what other features of the aetionomy database in terms of data import we want to make public with pybel, or keep in a different project. Also, see Indra from the Sorger lab
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LeKono
commented on May 9, 2024
How about providing the namespace-mapping db as sqlite with the project? Maybe we could also provide the precompiled mapping dictionary?
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cthoyt
commented on May 9, 2024
I don't think that's a good idea. That puts the burden of maintaining data with us, and the nice people at UniProt and other sources are already doing that.
Also, if we include the scripts that grab the data from their sources so users have to download stuff on their own the first time, we can prove data provenance
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Related Issues (20)
- pybel.tokens.parse_result_to_dsl doesn't capture 'concept' information
- UnicodeDecodeError: 'charmap' codec can't decode byte 0x8d in position 8815866: character maps to <undefined> HOT 11
- Switch from Travis-CI to GitHub Actions
- Add postgres and mysql container tests to GitHub Actions
- pybel.to_indra_statements() fails on KEGG COVID pathway BEL script HOT 2
- Variable name typo
- collapse_nodes does not apply to members of ListAbundance HOT 3
- Update EMMAA downloader
- Named reactions
- Convert .Molecule or OBMol to SMILES HOT 1
- How to convert files in SMILES or MOL format to MOL2 3D structure HOT 1
- Add HTML summary for better jupyter notebook output
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- Challenge writing INDRA statements to nodelink and reading it back in to pybel HOT 2
- Problem getting a BEL graph from the Fraunhofer OrientDB HOT 2
- Cannot write the graph in any extension
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- attribute error for pybel HOT 1
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