WikiPathway/PathVisio Newsletter
Kelder Thomas (BIGCAT)
- New Features
- Wikipathways in the press
- PathVisio article published in BMC Bioinformatics
- Micronutrient genomics project adopts portal at WikiPathways
- New Pathways
== New Features ==
We implemented several new features in WikiPathways and PathVisio that make it easier to draw, curate and access pathways.
- Curation tags:
Curation tags are short messages that can be added to a pathway to notify the community about the state of the pathway. For example, pathways with missing or inappropriate content can be tagged to notify the authors. Or you could tag your draft pathway to notify other users that it is still work in progress. See the documentation page for more information:
http://wikipathways.org/index.php/Help:CurationTags
- Author list:
To give contributors proper credit for their work, each pathway page now displays an author list on top of the page. The author list shows users who have edited the pathway, sorted by the number of contributions they made.
- Web service:
WikiPathways can now be accessed through a SOAP web service. The web service can be used by software developers to include WikiPathways data in their software, see http://www.wikipathways.org/index.php/Help:WikiPathways_Webservice
for more details. You can now also use WikiPathways in your Taverna workflows, see http://www.myexperiment.org/packs/30 for examples.
- Protein complexes:
It is now possible to specify protein complexes in the pathway editor. See the following video for a demo:
http://www.youtube.com/watch?v=A7ryJwV4Y00&fmt=18
- Grouping pathway objects:
The grouping function in the pathway editor has been improved. You can now select and modify individual elements within a group. See the following video for a
demo:
http://www.youtube.com/watch?v=mAultpJCLJk&fmt=18
== Wikipathways in the press ==
WikiPathways is featured in Nature's "Big Data" issue. In this article, Mitch Waldrop examines how different groups are experimenting with Wiki's to manage the flow of scientific data. Nature. 2008 Sep 4;455(7209):22-5.
http://www.nature.com/news/2008/080903/full/455022a.html
== PathVisio article published ==
An article on PathVisio has been published in BMC Bioinformatics:
Presenting and exploring biological pathways with PathVisio. Martijn P van Iersel, Thomas Kelder, Alexander R Pico, Kristina Hanspers, Susan Coort, Bruce R Conklin and Chris Evelo. BMC Bioinformatics 2008, 9:399 (25 Sep 2008)
http://www.biomedcentral.com/1471-2105/9/399
== Micronutrient genomics project adopts portal at WikiPathways ==
The micronutrient genomics project (http://www.nugo.org/micronutrient) aims to build and provide a bioinformatics portal to assist micronutrient researchers in finding and working with omics data and results. The project will provide an integrated biological network for all micronutrients which allows to
* access all relevant genetic variations related to the biological activity,
* visualize transcriptome results,
* visualize plasma metabolomics results.
The project adopted a portal a WikiPathways as their main resource for pathway information about micronutrients to support their visualization initiatives.
== New pathways ==
Several pathways have been added to WikiPathways recently:
- Wnt Signaling (Caenorhabditis elegans)
http://www.wikipathways.org/index.php/Pathway:Caenorhabditis_elegans:Wnt_Signaling
- NLR proteins (Homo sapiens)
http://www.wikipathways.org/index.php/Pathway:Homo_sapiens:NLR_proteins
- Neural retinal development (Mus musculus)
http://www.wikipathways.org/index.php/Pathway:Mus_musculus:neural_retinal_development
- Sex determination (Caenorhabditis elegans)
http://www.wikipathways.org/index.php/Pathway:Caenorhabditis_elegans:Sex_determination
- Toll Like Receptor signaling (Mus musculus)
http://www.wikipathways.org/index.php/Pathway:Mus_musculus:Toll_Like_Receptor_signaling