jonquet
commented
2 years ago This issue is inherently linked to the fact that our mapping creation strategy (LOOM and sameURI) has never really considered "re-uses". Which means that every-time a new ontology is built using e.g. BFO we end up generating a tons of mappings (typically for "continuant") to every other ontologies relaying on BFO too. Those objects are not really "mappings" (an equivalent term/concept/class in another ontology) as they are exactly the same term (same URI).
We have discussed differences between term reuses, term overlap and mappings here : https://dx.doi.org/10.1007/978-3-030-61244-3_5
A solution is to implement a way in BioPortal to distinguish :
- term reuses => mostly get rid of the sameURI mappings and just find a way to "stay" on BioPortal when a user click on an URI from BioPortal that resolves to somewhere else.
- term overlap => get rid of term overlap (LOOM mappings) when an ontology reuses terms from another ontology
- focus on LOOM mapping only for term not reused
- focus on REST created mappings
There are a lot of ontologies in BioPortal that have a set of classes at or near the root with identical preferred labels, e.g., "entity", "continuant", "occurant", etc. One example is the HTN ontology where the root class of "entity" has 676 class-level mappings to "entity" classes in other ontologies:
https://data.bioontology.org/ontologies/HTN/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000001/mappings?display_links=false&display_context=false
Selecting these classes in the class trees in the Rails applications is becoming a performance bottleneck:
https://bioportal.bioontology.org/ontologies/HTN/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000001
We should consider adding paging to this endpoint.