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ontoportal-lirmm / annotators

Web service to add functionalities to the http://bioportal.bioontology.org and similar ontology annotators
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implement score old on mappings #5

Closed julien-diener closed 9 years ago

vemonet commented 9 years ago

http://tubo.lirmm.fr:8080/annotators/ncbo_annotator_plus?text=Melanoma+is+a+malignant+tumor&apikey=24e03810-54e0-11e0-9d7b-005056aa3316&ontologies=MESH,SNOMEDCT&expand_mappings=true&score=old Score for mapping should be 7 (not 8).

vemonet commented 9 years ago

http://tubo.lirmm.fr:8080/annotators/ncbo_annotator_plus?text=Melanoma+is+a+malignant+tumor&apikey=24e03810-54e0-11e0-9d7b-005056aa3316&ontologies=MESH,SNOMEDCT&expand_mappings=true&score=old Some Mappings (in this case 3 of them) don't have a score For example the mapping annotatedClass with id http://purl.bioontology.org/ontology/SNOMEDCT/20376005 has no score.

julien-diener commented 9 years ago

The score is not computed for mapping (this is the issue actually) but if an annotatedClass appears anywhere else, it will still get some score. Remember that the score of an annotatedClass, where ever it appears, is the sum of all scores it get throughout the whole json doc. So

vemonet commented 9 years ago

Ok, for the score I was just putting what Clément said in his mail in GitHub (more convenient to track issues)

julien-diener commented 9 years ago

You were right, and I answered in order to be clear.

jonquet commented 9 years ago

Just to precise... score 8 should not occur by itself... It is either 10+7=17 (if the other match has been done with preferred name) or 8+7=15 (if other match has been done with synonym) or something decimal (if other match was a hierachy) but not 8 itself... no ?

julien-diener commented 9 years ago

That's what I meant: where there is 8 currently, it should be 8+7*number-of-appearance-in-mappings. However, mappings are still not implemented. So it's only 8 for now.

julien-diener commented 9 years ago

To end all discussions about how it is supposed to work when the mappings are not implemented, I implemented it.

Could you guys check that this is the expected results (e.g. using the url given above by @vemonet)? So I can close this issue.