PathVisio and WikiPathways newsletter
Thomas Kelder
WikiPathways, the pathway visualization tool and collaborative pathway
curation website.
In this newsletter:
* New drawing capabilities
* New species support: Zea Mays
* BridgeDb identifier mapping framework released and published
* Metabolite database update
* Curation Jamboree results
* New Pathways in WikiPathways
= New drawing capabilities =
Our pathway drawing tool now supports a lot of new capabilities. There
are more choices for shapes, fonts and font attributes, background
colors, text alignment ec. With these you can make your pathways look
better without hassle.
= New species support: Zea Mays =
We're happy to introduce a new species to the WikiPathways collection:
Zea Mays, also known as Maize. Maize is of course a crop of major
importance, and is now the third plant species added after Arabidopsis
and Rice. There are currently no pathways for Maize, although we
expect new pathways to be created soon. Your help would be much
appreciated.
= BridgeDb paper published, BridgeDb 1.0 released =
BridgeDb is the identifier mapping subsystem employed by PathVisio and
WikiPathways. We've recently spun-off this into a separate framework
to be used by other applications. BridgeDb is targeted at
bioinformatics tool developers. You can find the project page at
http://www.bridgedb.org. There is now also a publication on BridgeDb:
van Iersel et al., BMC Bioinformatics 2010 11(1):5.
= Metabolite database updated =
Our database for metabolomics analysis in PathVisio has been updated.
The new version includes 7985 metabolites, an increase of 13.7%. The
new database can be downloaded at
http://www.pathvisio.org/data/gene_databases.
= Curation Jamboree =
On February 10-11 2010 We organized a Curation Jamboree to start a
focused effort to increase the quality of our pathway collecytion. In
total, a description was added to 450 pathways and 261 pathways were
given at least one literature reference. The number of approved
pathways in the analysis collection increased from 578 to 770 and the
featured pathways collection increased from 22 to 50 pathways. Great
job everyone and thanks for your contributions! It is to be expected
that we'll organize another curation jamboree in a few months time,
watch this mailinglist for an announcement.
= New Pathways in WikiPathways =
The following major pathways have recently been contributed by the
WikiPathways community:
- Valine, leucine and isoleucine degradation (Caenorhabditis elegans),
created by Pieter Giesbertz
http://www.wikipathways.org/index.php/Pathway:WP1451
- Vulval development (Caenorhabditis elegans), created by kyook
http://www.wikipathways.org/index.php/Pathway:WP1453
- Photosynthetic Carbon Reduction (Arabidopsis thaliana), created by
Martijn van Iersel
http://www.wikipathways.org/index.php/Pathway:WP1461
- TOR signaling (Homo sapiens), created by Pieter Giesbertz
http://www.wikipathways.org/index.php/Pathway:WP1471
- Interactions between CFTR and other ion channels (Rattus
norvegicus), created by p
http://www.wikipathways.org/index.php/Pathway:WP1485
- Intracellular trafficking of CFTR (Rattus norvegicus), created by
Thomas Theelen
http://www.wikipathways.org/index.php/Pathway:WP1486
- TNF-alpha and mucus production in lung epythelium (Rattus
norvegicus), created by Julia139
http://www.wikipathways.org/index.php/Pathway:WP1487
- CFTR activity in the plasma membrane (Rattus norvegicus), created by Karin
http://www.wikipathways.org/index.php/Pathway:WP1488