EBISPOT / OLS

Ontology Lookup Service from SPOT at EBI

http://www.ebi.ac.uk/ols

Apache License 2.0

95 stars 40 forks source link

ECO tree view using OLS tree view code not working #565

Open nsuvarnaiari opened 2 years ago

nsuvarnaiari commented 2 years ago

Hi OLS Team,

ECO (Evidence and Conclusion Ontology) is using OLS tree view code for displaying ECO tree for searched terms in our website (https://evidenceontology.org/browse/). A user reported the tree view is not displaying the tree for a searched term "ECO:0007295" - inference by association of genotype from phenotype used in automatic assertion. Instead "Loading" is displaying. Trying different terms yield the same "Loading" message.

Interestingly, the tree loads and can be traversed by clicking [+] or [-] and the tree displays for terms 'evidence' and 'assertion method'.

Wanted to check with you if there is a known issue with OLS tree view that could be breaking ECO tree view.

Thanks, Suvvi #

@dolleyj @mgiglio99

https://github.com/evidenceontology/evidenceontology/issues/288

henrietteharmse commented 2 years ago

We are not aware of any issues in this regard. I have tested this now as well on EBI OLS and did not encounter any problems.

Let us know if the user is experiencing it again. May be also ask the user to make a note of the time and time zone they did this at. That can help us link it back to any potential infrastructure issues.

henrietteharmse commented 2 years ago

May be also ask the user whether they did the search via the UI or the API.

dolleyj commented 2 years ago

I found the problem is with our handling of the data after we query the API. We have been filtering out non-ECO terms, so we display a tree containing only ECO terms. Up until now this has worked for us. I believe this particular term may have a connection to a non-ECO term that got filtered out. This consequently orphaned the term and broke the tree.

Do the OLS API allow for filtering - meaning can I set a flag to have only ECO terms returned? This is an example of our call to the API for the term mentioned above: https://www.ebi.ac.uk/ols/api/ontologies/eco/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FECO_0007295/jstree?viewMode=All&siblings=true

henrietteharmse commented 2 years ago

@dolleyj There is no way to filter out terms when retrieving tree information.

The only way to achieve this will be to do the query and filter out undesired terms and rebuild the tree on your side.