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From GOC meeting in Cambridge, Oct 2017:
Spaceholder ticket. Please formulate the issue(s); make a proposal for next GOC mtg at NYU 2018.
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I would like to suggest replacing the boolean representation of GPR associations with a true Gene-Protein-Reaction association schema.
Here are few reasons for this:
1. Gene expression is not bo…
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### Description of the issue:
HMR2 GPRs were updated with enzyme complex information (i.e., "AND" expressions) using a process that combined importing rules from other models (iHsa and Recon3D) with …
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As part of the doc drafted at https://docs.google.com/document/d/1j1zO-JHMaXi4ESrjTm_X1amLKdm3vO4szUaeB5LvxvA/edit#heading=h.25jngq5vebjo and the draft at https://github.com/geneontology/geneontology.…
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The atomic convolutions currently take in an entire protein-ligand complex. This makes working with them very gnarly since proteins get large (tens of thousands of atoms easily). Since the coordinates…
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In the file huintaf2-main/data/HuRI-uniprot-mapping.csv
There are many mappings that mapped the ensemble to isoform-2 of a protein, e.g. `ENSG00000072682,O15460-2`
However, in the file `HuRI-mer…
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The work is incredibly constructive, particularly for RFdiffusion, which traditionally struggles to produce stable short peptides in the range of 10 to 30 amino acids.
Despite this, after a week of …
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Wrt cleaning up protein complex terms that may be too species-specific
(hint: if they have only one annotation...)
make sure that when a strategy is set in place, this is very clearly communicated to …
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Working with @nmarkari, a basic table of GO-CAM to gene data should be generated as an input to enrichment test.
Some detail from @nmarkari:
> I'd like a table that for all causal models in prod…