[Ontology-editors] Automating regulation terms (and combinatorial terms in general)

[Jennifer Deegan (nee Clark)]

Hi Chris,

This sounds good. I'd be interested to see a demo of the OBO-Edit 
features you mention as well.

If you think that the cvs system is the more sensible for now then that 
sounds good to me. It would be much quicker than editing by hand.

Jen

Chris Mungall wrote:

> I'm kind of embarassed that poor curators like Ruth have to type out  
> sourceforge requests like this:
> 
> * 
> https://sourceforge.net/tracker/index.php?func=detail&aid=2045154&group_id=36855&atid=440764 
> 
> 
> And then someone has to manually add this into the graph being careful  
> to get the is_a links correct
> 
> Regulation term creation (and much xp creation in general) should be  
> far more automatable. This will be easier with OE2 when we can have  the 
> intersection_of lines live in the main ontology, but I think there  is a 
> lot we can do now.
> 
> The current methodology is to parse terms into xp defs, run the  
> reasoner via script, and have people look through reports. I don't  
> think this is scalable. The first time we did this, we ended up having  
> to fix 1000 links. Looking at the current reports[*] there are nearly  
> 1000 more links needing fixed. This translates to an alarmingly high  
> rate of false negatives in search results and analyses.
> 
> David and Tanya like to look through the reports as examining the  
> reasoner results individually allows them to find errors in the source  
> graph. This happens if someone puts the biologically correct link in  
> the regulation graph but neglects to do the equivalent in the source  
> graph. The fact this is happening at all is worrying - no one should  be 
> editing the regulation graph manually!
> 
> It would be really easy to automate things more, even whilst waiting  
> for OE2.
> 
> One idea would be to have a file in CVS that just contains a list of  
> terms or term requests. E.g.
> 
>     regulation of blood vessel remodeling
>     negative regulation of blood vessel remodeling
>     positive regulation of blood vessel remodeling
> 
> Or it could just be the source term, with the request for 3 regulation  
> terms being implicit
> 
> A nightly script would generate obo including synonyms, standard defs  
> and correct placement in the obo file. It would write the unparseables  
> to a report file. It could even be automatically merged but I'm  
> guessing folks would prefer some kind of oversight. Either way it  
> should just be a simple script to merge the results in. We could  
> probably use obomerge.
> 
> Folks should also be aware that as far as "standard" regulation terms  
> go OE2 has a lot of useful functionality. For example, you can just  
> create a bunch of regulation terms under biological process, run the  
> semantic parser (under the reasoner menu) to generate the xp defs, run  
> the reasoner, then select "assert implied links". The main fiddly step  
> here is that the intersection_of lines have to be stripped before  going 
> into the editors version. Should be possible with save filters.
> 
> I'm leaning towards doing this out of oboedit. The file-in-cvs  approach 
> fits well with the annotator submission model. It's easily  extensible 
> beyond standard regulation terms. It does introduce a  "fork" in the 
> term submission process, but I think it creates less  work and less 
> errors all round. I could also implement the whole thing  in < 5 mins.
> 
> A variation is a web form that allows you to build xps and then submit  
> them.
> 
> Thoughts? Call?
> 
> Cheers
> Chris
> 
> [*] 
> http://wiki.geneontology.org/index.php/XP:biological_process_xp_regulation#Availability 
> 
> 
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-- 
Jennifer Deegan (nee Clark)
EMBL-European Bioinformatics Institute
Gene Ontology Consortium