[Biopython-dev] OBO parser & DAG

[Iddo Friedberg]

Hi Bartek,

Thanks. I looked at it a bit.

Any reason why you did your own digraphs instead of using networkx? See
also: http://biopython.org/wiki/Gene_Ontology#GO_Directed_Acyclic_Graph

That said, it seems very mature. But the networkx does many functions for
plotting, interrogating and manipulating graphs.

Your OBO parser seems quite mature. Are you planning to add other edge
types? (E.g. "part_of").

What we are trying to do here, is set up (besides the parser & DAG
implementation) also a measure of DAG similarities. This is due to my
interest in assessing function similarity. That will be a separate module
(perhaps not even useful to Biopython).

So now I am not sure what to do :/ The IO modules seem complete & usable,
but I would have rather seen a DAG implementation using networkx.

Ideas?



On Mon, Jan 6, 2014 at 4:59 PM, Bartek Wilczynski
<bartek at rezolwenta.eu.org>wrote:

> Hi Iddo,
>
> My student has also recently implemented a module for ontologies. Maybe we
> can somehow merge these efforts. His code can be found here:
> https://github.com/tosterovic/biopython
>
> the relevant part is Bio/Ontology
>
> best
> Bartek
>
> On Mon, Jan 6, 2014 at 8:56 PM, Iddo Friedberg <idoerg at gmail.com> wrote:
>
>> Hi all,
>>
>> Is there any effort going on for developing the OBO parser & Bio-ontology
>> DAG? If not, my lab wants to push this. We already have a basic
>> representation using digraph from networkx, and a basic OBO parser. But
>> i'm
>> checking to see if there is no duplicate effort here.
>>
>> All very initial development.
>>
>> Parser:
>> https://github.com/idoerg/go-parser
>>
>> (the relevan module is
>> https://github.com/idoerg/go-parser/blob/master/go_obo_parser.py
>>
>>
>> DAG:
>> https://github.com/osamajomaa/DAGON
>>
>> Thanks,
>>
>> Iddo
>>
>> --
>>
>> Iddo Friedberg
>> http://iddo-friedberg.net/contact.html
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>>
>>
>
>
> --
> Bartek Wilczynski
> ==================
> Institute of Informatics
> University of Warsaw
> http://www.mimuw.edu.pl/~bartek
>



-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html
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++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
.>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
>>----.<--.>++++++.<<<<------------------------------------.