Activate the use of inter-portal mappings when using the Annotator

[jonquet]

We have reconciled multilingual mappings between the french ontologies on the SIFR BioPortal and their english counterparts on the NCBO BioPortal;
http://www.lirmm.fr/~jonquet/publications/documents/Article_WIMS2016_Reconciliation_Annane.pdf
and
https://github.com/sifrproject/multilingual_mappings

This ticket concerns the implementation of the feature that will enable to use those interportal mappings to annotate the original french text with ontology concepts from the NCBO BioPortal ontologies.

This means a new parameter expand_interportal_mappings={true|false} (and a small change in the UI to use it)

[twktheainur]

@jonquet For the implementation, I have a few questions regarding how to interpret the task at hand:

• Should this be added to NCBO_Annotator or to the proxy? An implementation in the proxy may be more involved depending on how it currently works in the ncbo_annotator.

• Scenario 1: Interportal mappings are loaded in the NCBO already and are retrieved already by ontologies_linked_data (mappings/mappings.rb). Question: how to distinguish between regular mappings and interportal mappings.

  • 1.a Proxy implementation: filtering the annotation to replace annotatedClasses with mapping classes if and only if the mapping in question is an interportal mapping.
  • 1.b -- NCBO_Annotator implementation, same process as above.

• Scenario 2: Interportal mappings are not currently included at all:

  • Implementing the retrieval of interportal mappings in ontologies_linkeddata in a new method (say Models.interportal_mappings_for_classids)
  • Writing the filtering code in the NCBO_Annotator

[jonquet]

Because the interportal and external mappings feature has been added into the main NCBO code, I would not recommend to use the proxy for this.
We should find where the mapping expansion happen, then activate the expansions with interportal mappings that are yes, indeed distinguished from others.

For instance:
http://data.bioportal.lirmm.fr/ontologies/SNMIFRE/classes/http%3A%2F%2Fchu-rouen.fr%2Fcismef%2FSNOMED_int.%23P2-00100/mappings
returns 2 different of mappings.

@vemonet How do you distinguish the interportal one from the normal one using the JSON info ?

@twktheainur I think we can ignore scenario 2 has we will only deal with this the boxes where the mappings are. ie the SIFR BioPortal appliance.