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[bioontology-support] Get "standard" gene and protein names from "standard" ontologies

John Zobolas john.zobolas at ntnu.no
Tue Mar 19 11:34:09 PDT 2019


Hi,


I have build a web-module that users use and when they type in a box for example a known gene or protein name (e.g. TP53, BRCA1) there is an autocomplete component that fires queries in your REST API asking for terms that match these strings. Now, the thing is, users as they may be, they want to see "standard" ontology names (or standard databases) like uniprot/chebi/ensemble which as far as I can tell they have no equivalent, daily-supporting ontologies.


The closest ontology I found that returns meaningful results is the OGG - though it seems its not actively maintained (and users didn't know about it). Also, the HGNC was another one, which is actively maintained, but the terms lack the synonyms (so its not searchable via the "standard name" - like tp53 for example). In short, this returns nothing (the string on the q parameter is what the user fills in):

http://data.bioontology.org/search?q=TP53&ontologies=HGNC, while this:

http://data.bioontology.org/search?q=HGNC_11998&ontologies=HGNC returns the entry of tp53, but there are no synonyms there, while the entry in the web bioportal interface<https://bioportal.bioontology.org/ontologies/HGNC/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FHugo.owl%23HGNC_11998&jump_to_nav=true> has the aliases and approved symbol that seem reasonable choices to be in the synonyms list of that term (and as such searchable)...


So, my question is first why the above happens?


And what would you suggest me doing?

I made the link to BioPortal because I thought that I wouldn't need to write another dictionary-module to translate from other database/ontologies to my terms/data format, but in the end I may need to do just that? Or it would make more sense to make an .obo file from e.g. uniprot database and to actively maintain it (you pulling it also)?

I thought it better to ask your opinion about this, since you might have come across similar questions/issues in the past and I am fairly new to this ontology business :)


BR, John.

-----------------
John Zobolas
PhD Student
Department of Biology, Faculty of Natural Sciences, NTNU
Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU
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