[Biopython-dev] OBO parser & DAG

[Bartek Wilczynski]

Hi,

I will meet with Kamil sometime this week and we will discuss options for
switching to networkx or at least adding some compatibility layer for it. I
think the information about the edge type is preserved in the DAG after
parsing, so I'm not sure what you mean by "supporting" other types of
relationships. Our interest was mostly in ontology term enrichment
analysis, which Kamil implemented, and his version is also usable for
parsing, but I think we are quite open to changes still at this point and
I'm sure we will be able to come up with a good version merging the
important features from both versions.

best
Bartek


On Mon, Jan 6, 2014 at 11:17 PM, Iddo Friedberg <idoerg at gmail.com> wrote:

> 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
>>> ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
>>> ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
>>> .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
>>> >>----.<--.>++++++.<<<<------------------------------------.
>>> _______________________________________________
>>> Biopython-dev mailing list
>>> Biopython-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biopython-dev
>>>
>>>
>>
>>
>> --
>> Bartek Wilczynski
>> ==================
>> Institute of Informatics
>> University of Warsaw
>> http://www.mimuw.edu.pl/~bartek
>>
>
>
>
> --
> Iddo Friedberg
> http://iddo-friedberg.net/contact.html
> ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
> ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
> .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
> >>----.<--.>++++++.<<<<------------------------------------.
>



-- 
Bartek Wilczynski
==================
Institute of Informatics
University of Warsaw
http://www.mimuw.edu.pl/~bartek