Custom Ontology shows in OLS but not in OXO

[rpandey19]

I am working on a POC to integrate a custom ontology into OLS/OXO.
To achieve this I have a local installation of OLS / OXO and have created an OBO file. It shows in OLS fine but the mapping doesn't show in OXO. For this custom ontology I am having mappings with BAO as xrefs. Not sure if I am missing some steps here. I tried to find some instruction on custom ontologies but was unsuccessful.

Here is the snippet from my obo file-
[Term]
id: RFA:00021
name:Genomic Dna
is_a:RFA:00020
xref:EFO:0008479
xref:BAO:0000316

[Term]
id: RFA:00022
name:cDNA
is_a:RFA:00021
xref:BAO:0000315
xref:EFO:0008481

[Term]
id: RFA:00023
name:inhibition
is_a:RFA:00018
xref:BAO:0000091

screenshot of search

[matentzn]

I have had a lot of trouble with this as well. It is possible that OxO somehow does not understand your RFA: namespace.. Just out of curiosity for trouble shooting, I would try to change the namespace to a known namespace (say, EFO:) and see whether OxO recognises that. If it does, at least we know its about the RFA, if it does not we can look further.

But just to touch the basics:

1. The RFA ontology was correctly loaded into OLS, before you run the OxO loader
2. OLS was running at the time of the OxO load, and it was definitely looking at your OLS, not EBIs OLS

(I am just a user so not sure how far I can help)

[rpandey19]

Changing namespace doesn't help either.

1. Yes the ontology shows correctly in OLS
2. OLS is indexed and running at the time OXO loads. It is pointing locally. Pointing to EBIs OLS times out for me.
   Are you also trying to test custom ontology in OXO? I have tried so many things including comparing my obo to obo files from other ontologies but couldn't figure out yet :(

config-
[Basics]
oxoUrl=http://localhost:8081
oxoAPIkey=key
olsSolrBaseUrl=http://localhost:8983/solr
solrChunks=5000
neoURL=bolt://localhost:7687
neoUser=neo4j
neoPass=dba
olsurl=http://localhost:8080/api
oboDbxrefUrl=https://raw.githubusercontent.com/geneontology/go-site/master/metadata/db-xrefs.yaml

[matentzn]

So when changing the namespace to something known, the xrefs do not show up on OxO?

Well then unfortunately, I have bad news: I have been using this branch: https://github.com/EBISPOT/OXO/pull/43/files

But there is no resources allocated to cleaning this up and merging this into the main OxO (it requires extensive testing due to its hackyness).

for my OxO deployments, and its technically possible that this what is required to run custom ontologies like yours (I ran dozens of custom ontologies).

Feel free to try the image I am using:
https://hub.docker.com/r/ihcc/oxo-web
https://hub.docker.com/r/ihcc/oxo-loader

[matentzn]

And just to be clear - I do not know whether it fixes your problem! I just seem to remember something!

[jamesamcl]

We will be making some changes to the loader soon for SNOMED so I will bear this in mind. Maybe I can find a way to merge @matentzn 's branch if it fixes the problem.

[rpandey19]

@matentzn Thanks for the links. I tried the images you mentioned and it works fine. Actually it resolves 2 issues. The custom ontology shows in OXO, as well as the term labels are displayed correctly. There is only one issue I can see now is that the evidence link is broken. I have to dig into that more next week.

[matentzn]

Sounds good @rpandey19

Can you share an example that shows the broken evidence link (e.g. here if your instance is not public)

[rpandey19]

@matentzn This example has one evidence but when clicked on link it gives following error.
mappings.txt

[matentzn]

Uuuu never noticed that.. yeah this will probably not be fixed really fast. Feel free to dig into it yourself and make a pull request though!

[rpandey19]

I will try it. In case you find a solution please tag me.