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

[David Hill]

This would certainly free Tanya and I up to do a lot of other stuff. We 
edit the regulation graph by hand a lot! In fact, we will be doing it 
this afternoon.

David

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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