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ebi-chebi / ChEBI

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
https://www.ebi.ac.uk/chebi
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Exact synonyms for CHEBI:91385 represented as related #4471

Open bgyori opened 8 months ago

bgyori commented 8 months ago

Processing ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo, I stumbled upon a case where for CHEBI:91385 (name: PF-00477736), there are two synonyms listed:

synonym: "PF-477736" RELATED [ChEBI]                                            
synonym: "PF 477736" RELATED [ChEBI]

These synonyms are important downstream but should be tagged as EXACT since they are just variants of the standard name for this exact entry rather than corresponding to some related entry.

cmungall commented 1 month ago

I agree - I filed this ticket in 2008 (!) :

As far as I know the situation hasn't changed and the rule that Kirill mentions is still the one used to make synonym scope. IMO the rule is not correct and results in lots of configuration when CHEBI is used alongside other ontologies that make use of synonym scope for NER, search prioritization, etc

Perhaps with the new database structure direct curation of scope will be allowed?