RE: Table Information extraction tools in DebianMed?
Hello,
Thank you for the reply. I created an wiki account and I will go on creating account alioth.debian.org. However, I would have one question regarding binary code from my source. I have used quite a few libraries as .jar files, such as weka, openNLP, JENA, MetaMap, etc. Does what you said mean that I need to package all these .jars before I package mine? Also, what happens if some package, such as MetaMap is not open source? I cannot make a package that will build it, but rather it is dependent on NLM and their schedule of building it. Can you explain more?
Thank you,
Nikola Milosevic
-----Original Message-----
From: Andreas Tille [mailto:andreas@an3as.eu]
Sent: 19 July 2016 20:56
To: debian-med@lists.debian.org
Subject: Re: Table Information extraction tools in DebianMed?
Hi Nikola,
thanks for your interest in Debian Med.
On Tue, Jul 19, 2016 at 12:15:34PM +0000, Nikola Milosevic wrote:
>
> I am a PhD student at the University of Manchester and during my PhD, I have developed a set of tools for processing, annotating and information extraction from tables in biomedical literature (currently supported XML formats of PubMedCentral and DailyMed). The tools can be found on GitHub and create a pipeline (one uses the output of the other):
> - https://github.com/nikolamilosevic86/TableAnnotator
> - https://github.com/nikolamilosevic86/Marvin
> -
> https://github.com/nikolamilosevic86/WIET---Wizard-for-Information-Ext
> raction-from-Tables
>
> They are still under development, but are now quite stable and ready to be used. I would like to package these tools and include them into DebianMed distribution. I read the following page https://wiki.debian.org/DebianMed/MoM and I would be happy if someone can help me to start.
Fine. You can easily get the next MoM slot with one of the programs of yours - preferably the most basic one. Please note: For Debian packaging you need to get rid of *all* binary code from your source tarball which are also *.jar files. I have not checked yet but usually it happens that you need to start with packaging some Java precondition.
So feel free to add your name to the MoM table and start following the Debian Med policy to create an account on alioth.debian.org to gain commit permissions.
Kind regards
Andreas.
--
http://fam-tille.de
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