Question: UBERON. A way to retrieve relationships?
gravatar for Solowars
2.1 years ago by
Brazil/Porto Alegre/UFRGS
Solowars50 wrote:

Dear community,

I have gene expression data from several animals, which I'd like to compare. These data have UBERON identifiers for the tissues in which they're expressed, however, many tissues belong to different (yet, potentially) comparable anatomical entities (e.g. "kidney" and "adult mammalian kidney"). I know that UBERON, just like GO, has a hierarchical structure, so I thought that perhaps I could compare tissues belonging to the same group within UBERON hierarchy. A way to access such data is through OLS, yet I haven't found an easy way to retrieve the UBERON relationships among anatomical entities. I also investigated R package "rols", but I read that it might not be suitable for such task.

So my question is: Is it a easy-ish way to extract the hierarchical relationships between UBERON terms (from a list of UBERON ids, for example)?

Thanks a lot!

ADD COMMENTlink written 2.1 years ago by Solowars50

Boa noite, conheço bem a Porto Alegre. You just want to extract the hierarchy of a specific UBERON term or keyword? You can do this on the OLS web-page via the search text box. Do you want to find a way to automate it, i.e., programmatically? Have you first contacted the UBERON developers? - they would know the system better than anybody here on Biostars.

ADD REPLYlink written 2.1 years ago by Kevin Blighe59k

Hi Kevin, tudo bom? I was thinking of an automatic way to extract the hierarchy of a list of identifiers. I learnt that for single identifiers, such information can be retrieved via OLS site, but I'm afraid that would be unsuitable for a kinda large number of ids. Contacting the UBERON team seems like a good idea, I'll drop a line to them! Thanks!

ADD REPLYlink written 2.1 years ago by Solowars50

De nada - Please reply back with the information that they give to you, if you ave time. I look at their website and I was able to download a JSon and OWL file of all UBERON terms, but I did not have time to parse them yet. Abraços, Kevin

ADD REPLYlink written 2.1 years ago by Kevin Blighe59k
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