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[bioontology-support] Ontology Abbreviations

Natasha Noy noy at stanford.edu
Wed Jul 29 01:01:47 PDT 2009


Dear Eamonn,

> Some ontologies have no abbreviation, which i find strange since a  
> lot of resources are uniquely identified by their Source + the  
> accession for the term, e.g. CHEBI:229231 or whatever. Is there any  
> way to enforce this?

The requirement for abbreviations is an OBO Dounfry requirement, not a  
BioPortal requirement. So we can't really enforce it; and probably  
don't want to.

> Also, on another point, what are you guys using to build the  
> Ontology trees for displaying OWL or OBO files? I am using the  
> mindswap pellet reasoner to perform recursive analysis of each term  
> and it's subsequent subclasses, but it is very slow at classifying  
> ontologies like OBI at times (I say at times because they are  
> spawning off threads in the classification code which are either not  
> working properly, or get locked for extended periods of time  
> depending on time of execution. Sometimes i can process OBI in 13  
> seconds, other times it will take 177 seconds or something  
> ridiculous like that, and sometimes it doesn't complete at all since  
> it runs out of memory). Your input would be very much appreciated!

On the BioPortal side, we don't actually do any DL reasoning. The  
ontology authors, when they submit an ontology, can choose to submit  
an asserted version, or run a classifier before submitting it to us  
and submit an inferred version. We will display whatever they  
submitted to us.

In general, it seems to make more sense to have classification done by  
the ontology authors as they can then verify that the classified  
ontology looks the way they want it to, etc.

So, the performance of pellet or anything similar is not really an  
issue for us at the moment. I hope this helps.

Natasha





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