[Biopython-dev] OBO parser & DAG

Tue Jan 7 20:51:19 UTC 2014

Hi,

I've talked with Kamil today and we've looked through some of your code.

We have actually evaluated networkx before implementing our library and
thought it was unnecessary for our purposes to make it a requirement for
biopython as the enrichment analysis is using a relatively small subset of
graph operations.

However it would be very easy to make functions for converting our
ontologies to networkx digraphs, either with or without gene annotations as
additional attributes.

As for support for different types of transitivity in relations of
different type (as in your inference of ancestry for is_a and part_of
relations) we are currently not supporting it, but after thinking about it,
we will make a change to support this feature. Probably we will let the
user to (optionally) define the transitivity between relationship types
(i.e. is_a + part_of becomes part_of, etc).

In general, it would be very helpful if you could give us some rough idea
about your expected use cases. For example: are you expecting to modify the
graphs in the networkx objects? What will you use the inferred ancestor
lists for? So that the changes we make will be as useful to the community
as possible.

Naturally, if anyone else wants to contribute their ideas or use-cases, you
are most welcome...

best
Bartek

On Mon, Jan 6, 2014 at 11:42 PM, Iddo Friedberg <idoerg at gmail.com> wrote:

> I will meet with my student tomorrow (cc'd) and we can continue this
> further.
>
> Osama: Bartek Wilczynski's group has been working on a OBO parser / GO
> module too. Their parser seems complete & useful. Their digraph
> implementation is not in networkx, so I'm not sure about adopting that as
> is. In any case, let's meet tomorrow and talk, and maybe the four of us can
> work out a collaborative plan if we feel it's useful.
>
> Cheers,
>
> Iddo
>
>
> On Mon, Jan 6, 2014 at 5:26 PM, Bartek Wilczynski <
> bartek at rezolwenta.eu.org> wrote:
>
>> 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
>>
>
>
>
> --
> Iddo Friedberg
> http://iddo-friedberg.net/contact.html
> ++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
> ++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
> .>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
> >>----.<--.>++++++.<<<<------------------------------------.
>

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