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<p>Dear Ferran,</p>
<p><br>
</p>
<p><br>
</p>
<p>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...</p>
<p><br>
</p>
<p>Disclaimer: I am also a newbie in biopython so I would not know how or where this could be integrated.</p>
<p><br>
</p>
<p><br>
</p>
<p>Best wishes,</p>
<p>Pablo Riesgo Ferreiro</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Biopython <biopython-bounces@biopython.org> on behalf of biopython-request@biopython.org <biopython-request@biopython.org><br>
<b>Sent:</b> 03 January 2022 16:06:49<br>
<b>To:</b> biopython@biopython.org<br>
<b>Subject:</b> Biopython Digest, Vol 227, Issue 1</font>
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Today's Topics:<br>
<br>
1. Bioinformatics master's degree final project (Ferran F?bregas)<br>
2. Re: Bioinformatics master's degree final project<br>
(T?letch?a St?phane)<br>
3. Re: Bioinformatics master's degree final project (Alexey Morozov)<br>
4. Re: Bioinformatics master's degree final project (Ferran F?bregas)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 3 Jan 2022 11:39:40 +0100<br>
From: Ferran F?bregas <ferri.fc@gmail.com><br>
To: biopython@biopython.org<br>
Subject: [Biopython] Bioinformatics master's degree final project<br>
Message-ID:<br>
<CAAJHJUR_EL=9t1CzAk2UNomR-LjYN_83SmbBcnJ8F-Sbm801jQ@mail.gmail.com><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi! My name is Ferran F?bregas and I'm working on my bioinformatics<br>
master?s degree final project. I?m a computer scientist and a Python<br>
veteran but a BioPython newbie.<br>
<br>
I am writing this email because I would like to dedicate the final project<br>
of my master's degree in bioinformatics to the development of a library to<br>
implement gene annotation, pathway enrichment and access to gene ontologies<br>
from Python, similar to how it can be done in R using functions like<br>
enrichPathway from ReactomePA or enrichGo from ClusterProfiler.<br>
<br>
Have any tools been previously developed to do this using BioPython? Are<br>
there any packages similar to Bioconductor's OrgDb, ReactomePA , GOSeq or<br>
ClusterProfiler?<br>
<br>
I?m also working on a BioPython GUI based on PySide6. I've seen some old<br>
projects related to BioPython GUI development but seem to be discontinued.<br>
<br>
I would be very happy to use my time to contribute to the bioPython<br>
project, and I?m open to any suggestions or ideas.<br>
<br>
Thanks in advance,<br>
<br>
Ferran F?bregas<br>
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Message: 2<br>
Date: Mon, 3 Jan 2022 11:49:00 +0100<br>
From: T?letch?a St?phane <stephane.teletchea@univ-nantes.fr><br>
To: biopython@biopython.org<br>
Subject: Re: [Biopython] Bioinformatics master's degree final project<br>
Message-ID: <b9f50908-45ae-985c-c6d8-999938ec5589@univ-nantes.fr><br>
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Message: 3<br>
Date: Mon, 3 Jan 2022 19:45:45 +0800<br>
From: Alexey Morozov <alexeymorozov1991@gmail.com><br>
To: Ferran F?bregas <ferri.fc@gmail.com><br>
Cc: biopython@biopython.org<br>
Subject: Re: [Biopython] Bioinformatics master's degree final project<br>
Message-ID:<br>
<CAK=7cMOBFxgJukRDi2fcR2okMABc9DqNN+JCpOOUzZvZS4dhHQ@mail.gmail.com><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Ferran,<br>
<br>
There is a Python library for GO enrichment called goenrich (<br>
<a href="https://github.com/jdrudolph/goenrich">https://github.com/jdrudolph/goenrich</a>). I haven't used it for the last<br>
couple of years, but it did its job in 2018 or so (despite lacking some<br>
tests available in eg topGO). OTOH, goenrich repo shows that the last<br>
commit was in summer 2020, so maybe they've added something. Back when I<br>
used it, BioPython integration was basically absent, they just used their<br>
own objects for everything.<br>
<br>
There is also a library called goatools (<br>
<a href="https://github.com/tanghaibao/goatools">https://github.com/tanghaibao/goatools</a>), but I haven't actually used it, so<br>
no comments.<br>
<br>
<br>
??, 3 ???. 2022 ?. ? 18:40, Ferran F?bregas <ferri.fc@gmail.com>:<br>
<br>
> Hi! My name is Ferran F?bregas and I'm working on my bioinformatics<br>
> master?s degree final project. I?m a computer scientist and a Python<br>
> veteran but a BioPython newbie.<br>
><br>
> I am writing this email because I would like to dedicate the final project<br>
> of my master's degree in bioinformatics to the development of a library to<br>
> implement gene annotation, pathway enrichment and access to gene ontologies<br>
> from Python, similar to how it can be done in R using functions like<br>
> enrichPathway from ReactomePA or enrichGo from ClusterProfiler.<br>
><br>
> Have any tools been previously developed to do this using BioPython? Are<br>
> there any packages similar to Bioconductor's OrgDb, ReactomePA , GOSeq or<br>
> ClusterProfiler?<br>
><br>
> I?m also working on a BioPython GUI based on PySide6. I've seen some old<br>
> projects related to BioPython GUI development but seem to be discontinued.<br>
><br>
> I would be very happy to use my time to contribute to the bioPython<br>
> project, and I?m open to any suggestions or ideas.<br>
><br>
> Thanks in advance,<br>
><br>
> Ferran F?bregas<br>
> _______________________________________________<br>
> Biopython mailing list - Biopython@biopython.org<br>
> <a href="https://mailman.open-bio.org/mailman/listinfo/biopython">https://mailman.open-bio.org/mailman/listinfo/biopython</a><br>
><br>
<br>
<br>
-- <br>
Alexey Morozov,<br>
LIN SB RAS, bioinformatics group.<br>
Irkutsk, Russia.<br>
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<br>
Message: 4<br>
Date: Mon, 3 Jan 2022 16:06:36 +0100<br>
From: Ferran F?bregas <ferri.fc@gmail.com><br>
To: biopython@biopython.org<br>
Subject: Re: [Biopython] Bioinformatics master's degree final project<br>
Message-ID:<br>
<CAAJHJUTDdomZWABVB5ZPugC0rO4jm+S7yhC=cw0vUoXZ8a3ovA@mail.gmail.com><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Thanks for your replies, it seems that the community prefers to use<br>
different bioinformatics related modules for different functionalities<br>
instead of one big, more complex module :)<br>
<br>
A couple of questions about that:<br>
<br>
Do you think that it makes sense adding some enrichment functions to<br>
biopython?<br>
<br>
Do you think that it can be useful to create a modular Python GUI that<br>
integrates biopython functionalities plus Bioservices / GoEnrich / etc...<br>
? Or maybe it is not useful at all because you can already use some servers<br>
like the Galaxy project website (<a href="https://galaxyproject.org/">https://galaxyproject.org/</a>)?<br>
<br>
What do you think about that?<br>
<br>
Thanks in advance,<br>
<br>
F<br>
<br>
<br>
On Mon, Jan 3, 2022 at 12:45 PM Alexey Morozov <alexeymorozov1991@gmail.com><br>
wrote:<br>
<br>
> Dear Ferran,<br>
><br>
> There is a Python library for GO enrichment called goenrich (<br>
> <a href="https://github.com/jdrudolph/goenrich">https://github.com/jdrudolph/goenrich</a>). I haven't used it for the last<br>
> couple of years, but it did its job in 2018 or so (despite lacking some<br>
> tests available in eg topGO). OTOH, goenrich repo shows that the last<br>
> commit was in summer 2020, so maybe they've added something. Back when I<br>
> used it, BioPython integration was basically absent, they just used their<br>
> own objects for everything.<br>
><br>
> There is also a library called goatools (<br>
> <a href="https://github.com/tanghaibao/goatools">https://github.com/tanghaibao/goatools</a>), but I haven't actually used it,<br>
> so no comments.<br>
><br>
><br>
> ??, 3 ???. 2022 ?. ? 18:40, Ferran F?bregas <ferri.fc@gmail.com>:<br>
><br>
>> Hi! My name is Ferran F?bregas and I'm working on my bioinformatics<br>
>> master?s degree final project. I?m a computer scientist and a Python<br>
>> veteran but a BioPython newbie.<br>
>><br>
>> I am writing this email because I would like to dedicate the final<br>
>> project of my master's degree in bioinformatics to the development of a<br>
>> library to implement gene annotation, pathway enrichment and access to gene<br>
>> ontologies from Python, similar to how it can be done in R using functions<br>
>> like enrichPathway from ReactomePA or enrichGo from ClusterProfiler.<br>
>><br>
>> Have any tools been previously developed to do this using BioPython? Are<br>
>> there any packages similar to Bioconductor's OrgDb, ReactomePA , GOSeq or<br>
>> ClusterProfiler?<br>
>><br>
>> I?m also working on a BioPython GUI based on PySide6. I've seen some old<br>
>> projects related to BioPython GUI development but seem to be discontinued.<br>
>><br>
>> I would be very happy to use my time to contribute to the bioPython<br>
>> project, and I?m open to any suggestions or ideas.<br>
>><br>
>> Thanks in advance,<br>
>><br>
>> Ferran F?bregas<br>
>> _______________________________________________<br>
>> Biopython mailing list - Biopython@biopython.org<br>
>> <a href="https://mailman.open-bio.org/mailman/listinfo/biopython">https://mailman.open-bio.org/mailman/listinfo/biopython</a><br>
>><br>
><br>
><br>
> --<br>
> Alexey Morozov,<br>
> LIN SB RAS, bioinformatics group.<br>
> Irkutsk, Russia.<br>
><br>
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