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OpenBEL / resource-generator

Python modules to generate BEL resource documents.
Apache License 2.0
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Allow for term synonyms to be parsed from the data. #8

Closed jhourani closed 10 years ago

jhourani commented 11 years ago

We would like to be able to get back a term and all of its synonyms for each dataset. This has a use in SDP-Web also.

jhourani commented 11 years ago

Synonyms can now be parsed from most datasets. It would be very easy to add them for the other datasets, once we knew where to pull them from. The synonyms version of the code can be found on the synonyms branch. Simply run gp_baseline.py and a synonyms.json file will be written to the specified directory.

ncatlett commented 11 years ago

synonyms.json output not written

ncatlett commented 11 years ago

synonym_dict only contains MeSH and ChEBI synonyms (+ empty dictionaries for entrez, mgi, hgnc, and swissprot). Need synonyms for each namespace as relevant.

ncatlett commented 10 years ago

Synonyms are now parsed from all applicable data sets, but not output as part of gp_baseline

For each namespace-generating data set: get_synonym_names() and get_synonym_symbols() returns a synonym dictionary (or None) as applicable

ncatlett commented 10 years ago

A set of synonyms is now obtained for a given id with get_alt_names(id) and/or get_alt_symbols(id). This is used for the output of rdf.py, for all namespaces, as applicable.