List of custom OntoTools installations - SemLookP

rombaum commented 3 years ago

Hi @matentzn ,

sadly I'm a little bit late with my response, but I would love to contribute how we would like to use OLS and OxO for our research for your overview.

SemLookP

The Semantic Lookup Platform SemLookP hosted by the ZB MED - Information Centre for Life Sciences should be used in the biomedical domain. We want to use the system as a backbone service for different other services. SemLookP should help us in the following task:

Create (semi-)automatic annotations for research data
Set up an enriched semantic search service
Give additional information about a specific terminology resource

Our SemLookP services are accessible under:

terminology service: https://semanticlookup.zbmed.de/ols/index
mapping service: https://semanticlookup.zbmed.de/mappings/

One of our first use cases where we use SemLookP to show additional information for a concept is our COVID-19 preprint viewer preVIEW.

I hope the content fits the page. If you need anything else just contact me.

Best,

Roman

matentzn commented 3 years ago

@rombaum Roman, this is great! Thanks for sharing. I assume you are not using docker, but a completely customised fork of OLS/OxO right? Would you be able to describe a bit the kind of changes you did in the source code to enable your customised version?

rombaum commented 3 years ago

Hi @matentzn Nico,

we created a fork in December 2018 and created an own docker. But I also tested it last week with the docker of OLS on my local machine. To run OLS just with an individual frontend you just have to change the following two files:

The value of line 24 in the docker-compose file
Add a new module for the customized frontend in the pom.xml

Next to this to small changes you could start to create your own frontend by duplicating the module 'ols-web'. So if there are any changed in the original code we only have to adapt the changed of our customized frontend module 'ols-web'.

Some highlights we did:

ordered the database cross references in alphanumerical order
- Also hyperlinks will appear at the beginning of the list
added a hyperlink functionality when the creators of an ontology are hyperlinks
- possible to use FAIR identifiers
- it is also more interactive
made the frontend also a little bit more responsive

Independently from these frontend changes we also played a little bit around and updated some technologies inside of our OLS version:

upgraded MongoDB Java Driver from 2.14.3 to the newest version 3.12.3
- sadly it was never merged into your code
we also updated the embedded Neo4j version from 2.2.2 to 2.3.12
- but was I already spotted that you want to update this old version to a much newer version of Neo4j. That would be awesome.

edit: we created our fork in December 2018

matentzn commented 3 years ago

Thank you so much for the detailed response! Very nice work!

matentzn commented 3 years ago

Check https://github.com/EBISPOT/OLS/pull/482

matentzn commented 3 years ago

REMOVED https://ols.ccdh.io/ontologies/ncit_plus

matentzn commented 3 years ago

https://terminology.nfdi4chem.de/ts

matentzn commented 3 months ago

https://ols.monarchinitiative.org/

matentzn commented 3 months ago