We’re pleased to introduce the first in a series of blog posts highlighting specific BioGPS plugins. If you have suggestions on who we should profile in the future and what we should ask, let us know. Without further ado, this week’s subject is the UCSD/Nature Signaling Gateway, also available as a BioGPS plugin.
2. Why is your database unique?
Two words: Peer review. Each Molecule Page that we publish (550 and counting!) undergoes a rigorous peer and editorial review process prior to publication on the Signaling Gateway website. Nature Publishing Group editors invite experts to prepare new Molecule Pages and ensure that the information provided is accurate and unbiased. Each published page therefore provides a reliable and comprehensive view of the functional and biological activity of a specific signaling protein.
In addition to the text-based review article, published Molecule Pages are supplemented with database entries that list a protein’s localization, post-translational modifications (with catalysts, if known) and interactions. Each entry in the highly structured database contains at least one citation to the primary literature, which we hope helps speed and streamline background reading. Data are also available for export as an XML file.
For Molecule Pages that are not yet published, we import and provide links to publicly available databases such as the NCBI, GEO, ArrayExpress, IntAct, and many others. This ‘automated data’ is available for each of the nearly 4,000 proteins in the database. All data within the Molecule Pages database are available for free.
Finally, the Signaling Gateway also contains a rich variety of editorial content in the form of highlights of recently published articles, news stories, a library of cell-signaling papers and a calendar of upcoming conferences. The Signaling Gateway aims to keep cell-signaling researchers informed of the latest advances in the field, and provide a trusted resource for detailed information on all cell signaling proteins.
3. What improvements are coming in the future?
We are currently developing custom PDFs for all published Molecule Pages. These PDFs will contain the review article, tables of the protein’s biological and biochemical activity, and a figure of the molecule’s interactions, post-translational modifications and subcellular localizations. We also hope to provide Molecule Page authors with the ability to update their previously published pages in the near future. The updated information will also undergo peer and editorial review, and will be available as a new ‘version’ of the Molecule Page.
In addition, we are planning to launch a Molecule Page Wiki that will allow the signaling community to add, edit and annotate information about their proteins of interest. We also regularly add new databases to the automated data section and encourage researchers to tell us about databases that we should consider linking to.
4. Who is the team behind your project?
At Nature Publishing Group, associate editors Emily Chenette and Brenda Riley, senior editors Bernd Pulverer (chief editor, Nature Cell Biology) and Barbara Marte (senior editor, Nature), and publisher Matt Day coordinate peer review and manage the editorial side of the Signaling Gateway. Members of our esteemed editorial board provide advice on potential new authors and perform an initial check of new Molecule Page submissions in their subject areas. Long-term advice and guidance for the project comes from our editorial advisory board members: Drs Pat Casey, Michael Berridge, Vishva Dixit, Robin Irvine, Ravi Iyengar and Tony Hunter. Our collaborator at the San Diego Supercomputer Center (SDSC) at the University of California, San Diego (UCSD) is Prof Shankar Subramaniam, who heads a group of bioinformaticians and data analysts including Brian Saunders, Ashok Reddy Dinasarapu and Prasad V Burra.
The Signaling Gateway and Molecule Pages database is available free of charge thanks to generous support from Genentech and the National Institute of General Medical Sciences (NIGMS) at the National Institutes of Heath (NIH).
Thanks to the Signaling Gateway team for registering their site as a BioGPS plugin, and for agreeing to participate in our first Spotlight feature.