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[bioontology-support] Problem with synonyms

Michael Dorf mdorf at stanford.edu
Mon Nov 7 12:12:03 PST 2016


Hi Luis,

Thank you so much for reporting this issue to us. I've identified the issue and fixed it. The synonym property attribute was incorrectly set for RadLex in our system. I've corrected it and re-processed the ontology. Your query the Annotator service below should now yield both annotations:

http://data.bioontology.org/annotator?text=fifth%20digit%20dig%205&ontologies=RADLEX&longest_only=true&exclude_numbers=false&whole_word_only=true&exclude_synonyms=false

Thanks!

Michael


On Nov 4, 2016, at 08:55, Luís Campos <luis.filipe.lcampos at gmail.com<mailto:luis.filipe.lcampos at gmail.com>> wrote:

Hi!

Isn't BioPortal annotator suppose to annotate also synonyms of classes? I was assuming that yes, because there is an "Exclude Synonyms" parameter.

But it's not what is happening.

For example, the class "fifth digit" from RadLex (http://bioportal.bioontology.org/ontologies/RADLEX/?p=classes&conceptid=http%3A%2F%2Fwww.owl-ontologies.com%2FOntology1447432460.owl%23RID28760&jump_to_nav=true) has the synonym "dig 5" but this term is not annotated, although the preferred term "fifth digit" is.

http://data.bioontology.org/annotator?text=fifth%20digit%20dig%205&ontologies=RADLEX&longest_only=true&exclude_numbers=false&whole_word_only=true&exclude_synonyms=false

Thanks!
Luis Campos
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