Functional mock-up of a wiki editable 'genome assembly'.

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Dan Bolser

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Apr 20, 2011, 8:59:21 PM4/20/11
to GSoD, rm...@cornell.edu

GMoD project idea #9 [1] is related to community editing of a genome
assembly. The AGP file format is one way of representing a genome
assembly [2]. Using SMW/SF [3,4], I put together an AGP editing
'package' in the bifx.org/wiki [5,6]. To see the mock-up in action,
use the following links:

* A wiki page representing one 'AGP object'
** http://goo.gl/hRKiV

* An 'ask query' that returns AGP data from the wiki
** http://goo.gl/NU49S

* A form that can be used to easily edit the AGP object page
** http://goo.gl/qcq8M in edit mode, and
** http://goo.gl/zb8uo


Using this 'mock-up', you can already create and edit AGP files and
see the wiki history of the page. Please feel free to play around with
and improve these dummy examples (it's a wiki!). For reference, I've
tried to keep all the 'package' pages categorized here [6].


Having got this far, a few interesting possibilities present
themselves:

1) Develop "Semantic Forms Inputs" to improve the form editing
experience (e.g. see http://goo.gl/7ycvh and
http://www.mediawiki.org/wiki/Extension:Semantic_Forms_Inputs).

2) Export AGP data from the wiki in DAS format (e.g. see http://www.dasregistry.org/
and http://das.referata.com/).

3) Use the wiki to support the DAS write-back protocol (see
http://www.mail-archive.com/d...@lists.open-bio.org/msg00400.html).

4) Visualize the assembly data in the wiki using an embedded GBrowse?


Any feedback welcome,
Dan.

References:

[1] http://gmod.org/wiki/GSoC
[2] http://www.ncbi.nlm.nih.gov/projects/genome/assembly/agp/AGP_Specification.shtml
[3] http://semantic-mediawiki.org/
[4] http://www.mediawiki.org/wiki/Extension:Semantic_Forms
[5] http://www.bioinformatics.org/wiki/Main_Page
[6] http://www.bioinformatics.org/wiki/AGP

irc://irc.freenode.net/#gmod

Dan Bolser

unread,
Apr 21, 2011, 8:31:21 AM4/21/11
to GSoD, Robert Buels


On Apr 21, 1:59 am, Dan Bolser <dan.bol...@gmail.com> wrote:
> GMoD project idea #9 [1] is related to community editing of a genome
> assembly. The AGP file format is one way of representing a genome
> assembly [2]. Using SMW/SF [3,4], I put together an AGP editing
> 'package' in the bifx.org/wiki [5,6]. To see the mock-up in action,
> use the following links:
>
> * A wiki page representing one 'AGP object'
> **http://goo.gl/hRKiV
>
> * An 'ask query' that returns AGP data from the wiki
> **http://goo.gl/NU49S
>
> * A form that can be used to easily edit the AGP object page
> **http://goo.gl/qcq8Min edit mode, and
> **http://goo.gl/zb8uo
>
> Using this 'mock-up', you can already create and edit AGP files and
> see the wiki history of the page. Please feel free to play around with
> and improve these dummy examples (it's a wiki!). For reference, I've
> tried to keep all the 'package' pages categorized here [6].
>
> Having got this far, a few interesting possibilities present
> themselves:
>
> 1) Develop "Semantic Forms Inputs" to improve the form editing
> experience (e.g. seehttp://goo.gl/7ycvhandhttp://www.mediawiki.org/wiki/Extension:Semantic_Forms_Inputs).
>
> 2) Export AGP data from the wiki in DAS format (e.g. seehttp://www.dasregistry.org/
> andhttp://das.referata.com/).
>
> 3) Use the wiki to support the DAS write-back protocol (see
> http://www.mail-archive.com/...@lists.open-bio.org/msg00400.html).
>
> 4) Visualize the assembly data in the wiki using an embedded GBrowse?

See: http://goo.gl/MDGdy



> Any feedback welcome,
> Dan.
>
> References:
>
> [1]http://gmod.org/wiki/GSoC
> [2]http://www.ncbi.nlm.nih.gov/projects/genome/assembly/agp/AGP_Specific...
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