[Biopython] Biopython Digest, Vol 227, Issue 1

Mon Jan 3 15:36:06 EST 2022

Dear Ferran,

>From my experience of querying biomart from python, I found the implementations I used not very intuitive. It seems to me that some details of the biomart REST API (eg: XML) have leaked into the Python API. Maybe having a better Python API around biomart would add some value? Not saying it will be easy...

Disclaimer: I am also a newbie in biopython so I would not know how or where this could be integrated.

Best wishes,

Pablo Riesgo Ferreiro

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Sent: 03 January 2022 16:06:49
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Subject: Biopython Digest, Vol 227, Issue 1

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Today's Topics:

   1. Bioinformatics master's degree final project (Ferran F?bregas)
   2. Re: Bioinformatics master's degree final project
      (T?letch?a St?phane)
   3. Re: Bioinformatics master's degree final project (Alexey Morozov)
   4. Re: Bioinformatics master's degree final project (Ferran F?bregas)

----------------------------------------------------------------------

Message: 1
Date: Mon, 3 Jan 2022 11:39:40 +0100
From: Ferran F?bregas <ferri.fc at gmail.com>
To: biopython at biopython.org
Subject: [Biopython] Bioinformatics master's degree final project
Message-ID:
        <CAAJHJUR_EL=9t1CzAk2UNomR-LjYN_83SmbBcnJ8F-Sbm801jQ at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi! My name is Ferran F?bregas and I'm working on my bioinformatics
master?s degree final project. I?m a computer scientist and a Python
veteran but a BioPython newbie.

I am writing this email because I would like to dedicate the final project
of my master's degree in bioinformatics to the development of a library to
implement gene annotation, pathway enrichment and access to gene ontologies
from Python, similar to how it can be done in R using functions like
enrichPathway from ReactomePA or enrichGo from ClusterProfiler.

Have any tools been previously developed to do this using BioPython? Are
there any packages similar to Bioconductor's OrgDb, ReactomePA , GOSeq or
ClusterProfiler?

I?m also working on a BioPython GUI based on PySide6. I've seen some old
projects related to BioPython GUI development but seem to be discontinued.

I would be very happy to use my time to contribute to the bioPython
project, and I?m open to any suggestions or ideas.

Thanks in advance,

Ferran F?bregas
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Message: 2
Date: Mon, 3 Jan 2022 11:49:00 +0100
From: T?letch?a St?phane  <stephane.teletchea at univ-nantes.fr>
To: biopython at biopython.org
Subject: Re: [Biopython] Bioinformatics master's degree final project
Message-ID: <b9f50908-45ae-985c-c6d8-999938ec5589 at univ-nantes.fr>
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Message: 3
Date: Mon, 3 Jan 2022 19:45:45 +0800
From: Alexey Morozov <alexeymorozov1991 at gmail.com>
To: Ferran F?bregas <ferri.fc at gmail.com>
Cc: biopython at biopython.org
Subject: Re: [Biopython] Bioinformatics master's degree final project
Message-ID:
        <CAK=7cMOBFxgJukRDi2fcR2okMABc9DqNN+JCpOOUzZvZS4dhHQ at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear Ferran,

There is a Python library for GO enrichment called goenrich (
https://github.com/jdrudolph/goenrich). I haven't used it for the last
couple of years, but it did its job in 2018 or so (despite lacking some
tests available in eg topGO). OTOH, goenrich repo shows that the last
commit was in summer 2020, so maybe they've added something. Back when I
used it, BioPython integration was basically absent, they just used their
own objects for everything.

There is also a library called goatools (
https://github.com/tanghaibao/goatools), but I haven't actually used it, so
no comments.

??, 3 ???. 2022 ?. ? 18:40, Ferran F?bregas <ferri.fc at gmail.com>:

> Hi! My name is Ferran F?bregas and I'm working on my bioinformatics
> master?s degree final project. I?m a computer scientist and a Python
> veteran but a BioPython newbie.
>
> I am writing this email because I would like to dedicate the final project
> of my master's degree in bioinformatics to the development of a library to
> implement gene annotation, pathway enrichment and access to gene ontologies
> from Python, similar to how it can be done in R using functions like
> enrichPathway from ReactomePA or enrichGo from ClusterProfiler.
>
> Have any tools been previously developed to do this using BioPython? Are
> there any packages similar to Bioconductor's OrgDb, ReactomePA , GOSeq or
> ClusterProfiler?
>
> I?m also working on a BioPython GUI based on PySide6. I've seen some old
> projects related to BioPython GUI development but seem to be discontinued.
>
> I would be very happy to use my time to contribute to the bioPython
> project, and I?m open to any suggestions or ideas.
>
> Thanks in advance,
>
> Ferran F?bregas
> _______________________________________________
> Biopython mailing list  -  Biopython at biopython.org
> https://mailman.open-bio.org/mailman/listinfo/biopython
>

--
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
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Message: 4
Date: Mon, 3 Jan 2022 16:06:36 +0100
From: Ferran F?bregas <ferri.fc at gmail.com>
To: biopython at biopython.org
Subject: Re: [Biopython] Bioinformatics master's degree final project
Message-ID:
        <CAAJHJUTDdomZWABVB5ZPugC0rO4jm+S7yhC=cw0vUoXZ8a3ovA at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Thanks for your replies, it seems that the community prefers to use
different bioinformatics related modules for different functionalities
instead of one big, more complex module :)

A couple of questions about that:

Do you think that it makes sense adding some enrichment functions to
biopython?

Do you think that it can be useful to create a modular Python GUI that
integrates biopython functionalities plus Bioservices / GoEnrich / etc...
? Or maybe it is not useful at all because you can already use some servers
like the Galaxy project website (https://galaxyproject.org/)?

What do you think about that?

Thanks in advance,

F

On Mon, Jan 3, 2022 at 12:45 PM Alexey Morozov <alexeymorozov1991 at gmail.com>
wrote:

> Dear Ferran,
>
> There is a Python library for GO enrichment called goenrich (
> https://github.com/jdrudolph/goenrich). I haven't used it for the last
> couple of years, but it did its job in 2018 or so (despite lacking some
> tests available in eg topGO). OTOH, goenrich repo shows that the last
> commit was in summer 2020, so maybe they've added something. Back when I
> used it, BioPython integration was basically absent, they just used their
> own objects for everything.
>
> There is also a library called goatools (
> https://github.com/tanghaibao/goatools), but I haven't actually used it,
> so no comments.
>
>
> ??, 3 ???. 2022 ?. ? 18:40, Ferran F?bregas <ferri.fc at gmail.com>:
>
>> Hi! My name is Ferran F?bregas and I'm working on my bioinformatics
>> master?s degree final project. I?m a computer scientist and a Python
>> veteran but a BioPython newbie.
>>
>> I am writing this email because I would like to dedicate the final
>> project of my master's degree in bioinformatics to the development of a
>> library to implement gene annotation, pathway enrichment and access to gene
>> ontologies from Python, similar to how it can be done in R using functions
>> like enrichPathway from ReactomePA or enrichGo from ClusterProfiler.
>>
>> Have any tools been previously developed to do this using BioPython? Are
>> there any packages similar to Bioconductor's OrgDb, ReactomePA , GOSeq or
>> ClusterProfiler?
>>
>> I?m also working on a BioPython GUI based on PySide6. I've seen some old
>> projects related to BioPython GUI development but seem to be discontinued.
>>
>> I would be very happy to use my time to contribute to the bioPython
>> project, and I?m open to any suggestions or ideas.
>>
>> Thanks in advance,
>>
>> Ferran F?bregas
>> _______________________________________________
>> Biopython mailing list  -  Biopython at biopython.org
>> https://mailman.open-bio.org/mailman/listinfo/biopython
>>
>
>
> --
> Alexey Morozov,
> LIN SB RAS, bioinformatics group.
> Irkutsk, Russia.
>
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