famplex
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sorgerlab
Resources for grounding protein families and complexes from text and describing their hierarchical relationships.
This script will canonicalize the order of entries in the famplex files. This will make it easier to curate since you can put new entries anywhere, as well as hopefully...
It looks like the part of the test workflow responsible for checking up-to-date exports is having issues: ``` /home/runner/work/_temp/d8686b5f-ab1e-4937-8e9f-e3a808b63639.sh: line 4: /usr/bin/egrep: Argument list too long /home/runner/work/_temp/d8686b5f-ab1e-4937-8e9f-e3a808b63639.sh: line 4: echo:...
Currently there isn't a single parent entry for heat shock proteins. This comes up in text as e.g., "HSPs" and could be mapped to e.g., NCIT:C16672 and MESH:D006360.
From @bgyori > Classification of entities: I think this classification can be automatically inferred from membership so I'm not sure if it should be something that is curated/modifiable or something...
I found that there is a large number of equivalences in `equivalences.csv` that are not exact matches, for instance, in the case of InterPro mappings. As an example, take `FPLX:Hedgehog`...
Currently FamPlex IDs are name-like but there isn't a specific resource file to assign standard names for entries. In some exports, e.g., OBO, names are automatically constructed by doing some...
Currently the FamPlex grounding map contains mappings for entities that aren't actually protein families or complexes, and are therefore not directly relevant to the main role of FamPlex. These mappings...
Members are PRKD1 and PRKD2 as far as I can tell. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201600/ Grounding may be problematic because PKD is an alias of PRKD1 (https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:9407) and is also ambiguous with other...
