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renaud / neuroNER

named entity recognizer for neuronal cells, based on UIMA Ruta rules
GNU Lesser General Public License v3.0
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export uberon structure name as exact synonym .obo file #59

Closed stripathy closed 8 years ago

stripathy commented 8 years ago

@tgbugs I noticed the following:

UBERON:0000411 visual cortex MBA:669 Visual areas ------ABA SYNS------ VIS Visual areas visual areas visual cortex -----UBERON SYNS----- --Related-- higher-order visual cortex visual areas

but in the .obo files you prepared for me:

[Term] id: ABA_REGION:669 name: Visual areas synonym: "higher-order visual cortex" RELATED [] synonym: "visual areas" RELATED []

In other words, we need to explicitly export the Uberon term name as an exact synonym (in the above example, visual cortex) when we're doing the conversion to .obo for parsing by neuroNER/sherlok

tgbugs commented 8 years ago

Ah yep, I'll add it.

tgbugs commented 8 years ago

@stripathy done via 4f07c5c3cc4e3bdbef1d6854f98da31bcde2ec27, note that sometimes this results in duplicate synonyms but that should be ok.

tgbugs commented 8 years ago

Do this with the the brain slim.

tgbugs commented 8 years ago

@stripathy files are here https://github.com/renaud/neuroNER/blob/master/ontology_merge/ns_stripped_e.obo according to the usual naming pattern.