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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 the mapping_ontologies parameter to specify the ontologies to use when mapping semantic expansion is activated #15

Open jonquet opened 7 years ago

jonquet commented 7 years ago

This task consists of implementing a parameter in the Annotator proxy (this project) that will enable to specify the ontologies to use to expand using the mappings in the case where the &expand_mappings=true is used.

The idea is that &ontologies= will always be used to specify the "ontologies to keep in result" which are the ontologies in which the user do want the final annotations. However, when the mapping semantic expansion is used, instead of using always (which will stay the by default behaviour) the same ontologies to expand with the mappings, we will be able to specify to the Annotator the ones to explicitly used (or all) for mappings.

For example: http://services.bioportal.lirmm.fr/annotator?text=mélanome&ontologies=MDRFRE,MSHFRE&longest_only=false&exclude_numbers=false&whole_word_only=true&exclude_synonyms=false&expand_mappings=true will annotate "mélanome" with MSHFRE and MDRFRE, but if we specify &mapping_ontologies=MEDLINEPLUS,SNMIFRE then this 2 last ontologies will actually be used to generate direct annotations then the mappings MEDLINEPLUS->MSHFRE, SNMIFRE->MSHFRE, MEDLINEPLUS->MDRFRE, SNMIFRE->MDRFRE, will be used to generate new annotations within MSHFRE and MDREFRE.

This will need to be present in the UI also.

syphax-bouazzouni commented 6 months ago

@Bilelkihal is this the thing that you were asked to check if it does work? (mappings expansion) (https://github.com/ontoportal-lirmm/annotators/issues/48)

@jonquet was it implemented ? Same for https://github.com/ontoportal-lirmm/annotators/issues/13

jonquet commented 6 months ago

No this is a different issue but related. We can address this in the proxy.