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The Wonderful World of Wikis for Life Scientists

Submitted by on June 14, 2010 – 12:33 pm 5 Comments

life science social media resource

You may know that the San Diego Biotechnology Network, and its partner company, Comprendia, are dedicated to improving communication between life scientists and the companies that serve them. As part of this objective, we like to pass on resources for both groups to help, check out our video resources for life science and the list of life science companies using social media. Life scientists can use the wiki list below as a reference and to learn and contribute, and companies should realize the potential that resources such as these present for helping their customers put the complex science behind their products in context.

What is a wiki? Many use the term loosely these days, to refer to any web resource. To us, a wiki is a community-driven, content rich website in which many of the pages are interconnected. There are many free software programs to generate wikis, and even a resource which lists wikis and helps you choose which one will best meet your needs.

We’ve been looking into life science wikis, and with help from the Life Scientists group on Friendfeed, came up with the list below. There are a few schools of thought on wikis. Some believe that all content should reside on Wikipedia (only two Wikipedia-based wikis are listed below). Others feel as though wikis specific for life science, outside of wikipedia, offer a more targeted approach. Also, some feel as though they must remain ‘pure’ and have no advertising. However, these wikis require a lot of work, I see no problem with this as long as the companies are transparent with their association with the resource, and are careful to not turn it into solely self-serving.

There is an enormous potential for life science companies to leverage wikis. Why not a signal transduction wiki sponsored by the companies who sell products in that area (in fact, there is a defunct cell signaling portal on Wikipedia which could be rescued)? Enzyme classes, areas of study (e.g. stem cells), disease areas…the possibilities are limitless! See German distributor Biomol’s wiki–they’ve created a wiki-based product listing supplemented with supporting biological information (p.s. search engines love wikis, perhaps for this reason). We see some life science companies creating fancy flash animations to highlight their products…guess what, search engines cannot see the content in flash! In addition, scientists are accustomed to wikis, there is no need to reinvent the wheel with a fancy new application, something we’ve discussed on the Comprendia blog.

If you represent a life science company who would like to learn how to leverage wikis, attend Comprendia’s Social Media for Life Science and Biotechnology Workshop in San Diego June 22nd, where we’ll cover the Basics, Benefits, Best Practices, and Biotech Examples. Don’t live in San Diego? Contact Comprendia to learn about virtual workshops or visits to your area.

Life Science Wikis

Wiki Subject Contributors Sponsors Details
ACS Chemical Biology Community Chemical biology Life scientists ACS A bit confusing because it does not have the standard wiki interface. Hard to tell if it is active.
Biomol Wiki Life science research products Life science companies Biomol GmBH Interesting mix of life science and products. Biomol is a distributor of products from life science vendors, and has created an extensive wiki for their products.
ChemWiki Chemistry Anyone/editors curate UC Davis Chemistry textbook–lots of content.
EcoliWiki All things E. coli Life scientists, with auto-generated content Part of EcoliHub, NIH/NIGMS (Purdue, Oklahoma, SRI, TAMU) Very impressive source of information about genes, proteins, expression levels.
Encyclopedia of Life Biology Anyone/editors curate Harvard University, the Field Museum of Natural
History, the Marine Biological Laboratory, the Smithsonian Institution, the Biodiversity Heritage Library,
and the Missouri Botanical Garden. Funding: John D. and Catherine T.
MacArthur Foundation and the
Alfred P. Sloan Foundation
Collaboration between scientific community and the public. Goal is to disseminate knowledge about the world’s organisms.
Medpedia Health and medicine M.D.’s and Ph.D.’s Harvard, Stanford, UC Berkeley, University of Michigan Nice resource. All content generated by M.D.’s and Ph.D.’s, and each entry has a ‘clinical’ and ‘plain english’ description. Users can ask questions to the editors.
MicrobeWiki Microbiology Life scientists Kenyon College Mostly class material-centric, nicely done with a lot of images.
OpenWetWare Life science laboratories, protocols, and classes Life scientists Individual labs at MIT (NSF grant submitted) Very interesting and popular site. Several different types of entries. Labs can create their own site here to enter their schedules, presentations, and protocols. Class materials can also be organized here.
Protopedia Structural biology Structural biologists, with a large amount of auto-generated content Weizmann Institute, The Israel Structural Proteomics Center Very nicely done–they have created pages for every entry in the protein data bank.
SciTopics General science Scientists Elsevier May be a bit too general for life scientists.
SNPedia SNPs (single nucleotide polymorphisms) Life scientists Independent–started by Michael Cariaso. Catalog of more than 11,000 SNPs. Shows SNPs related to interesting phenotypes such as "sprinting versus endurance muscles." SNPs are downloadable, and there is also a page dedicated to getting your personal SNPs identified.
Subtiwiki All things B. subtilis Life scientists, with auto-generated content University of Gottingen Similar to EcoliWiki.
TOPSAN Structural biology Structural biologists ? “The Open Protein Structure Annotation Network” focusing on sharing information about protein structures determined by structural genomics efforts.
WikiGenes Genes, proteins, chemical compounds, diseases Life scientists Society in Science – The Branco Weiss Fellowship. Original paper published by Robert Hoffmann at MIT. Contains a lot of useful information. Tracks authors of every contribution and allows rating of contributions.
Wikimedia Commons Biology, chemistry sections Anyone Wikimedia foundation May be too general for most life scientists. Focuses on media for download (e.g., images, sound).
Wikipedia: WikiProject Gene Wiki Genes and function Anyone/editors curate NIH/GNF A portal which helps to organize and update entries in Wikipedia involving gene and protein function.
Wikipedia: WikiProject Molecular and Cellular Biology Molecular and cell biology Anyone/editors curate ? A portal which helps to organize and update entries in Wikipedia involving molecular and cell biology. Appears to be stagnant at this point.
Wikispecies Biological species Biologists Wikimedia Foundation May be too general for life scientists.

What are your opinions about these ‘free standing’ wikis, outside of wikipedia? Is the redundance found on the wikis troubling, are these private efforts confusing and contrary to the objectives of NCBI, RCSB, etc.? Also, how would you feel if life science companies started to sponsor more wikis? Leave a comment below, and let the discussion begin!

To share easily, cut and paste: The Wonderful World of Wikis for Life Scientists http://bit.ly/apZTOs

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5 Comments »

  • Mr. Gunn says:

    The problem of redundant content falls in to the category of problems that are nice to have. It would be a very good thing if too much content were a bigger problem than not enough. It would also make a very good case for semantic markup, as that would allow an entry found on one wiki to be automatically imported to another, in the proper context.

  • Paul Gardner says:

    There are many advantages to using/contributing directly to Wikipedia. There are lovely bots that will trawl through WP fixing citations (Citation_bot_1), there are masses of people who spend a lot of time correcting spelling, grammar and fixing dead links (eg. Woohookitty). With a free-standing wiki you miss out on these things as well as the famous extra long tail of editors who drop in, make a contribtution and then disappear again. Remember the top google hit for many scientific terms is now Wikipedia, therefore contributions there are going to be a lot more visible.

    Finally, the MCB wikiproject you mention is far from stagnant as you suggest. Look at the discussion page.

  • The Wikipedia, as the central depository for all information, is a laudable goal, but this one-size-fits-all approach does not work for handling all requirements of knowledge transfer. For example, the primary goal of the ChemWiki is to supplant chemistry textbooks (to reduce educational costs and to provide flexibility for instructors course materials). The ChemWiki does not strive to be a “chemistry-pedia”, which Wikipedia has mastered (somewhat). Our approach requires a different structure with aspects like clear flow between topics, consistency, redundancy in some part and secondary aspects like homework questions and exercises. This is a outside the current infrastructure of Wikipedia (as powerful as it is).

    There is a definite niche for non-Wikipedia Wikis to be supported. By the way, the ChemWiki (occasionally, but not often) ranks higher than Wikipedia in some Chemistry searches on Google.

  • Thanks for your article. It’s been very helpful.
    Dan Gilliland

  • I think its clear that there will and should be many wikis. Wikipedia is great for what it is but what it is isn’t always what everyone needs. That being said, I think there are elements of Wikipedia articles that could be re-used in the context of other wikis. When there is already a great summary of a gene’s function on its Wikipedia entry, another wiki or other website should be able to import that summary into their own context. Preferably other open editing platforms should also be allowed to contribute back to Wikipedia directly in a straightforward way. This kind of transfer already happens via cutting and pasting.. it will be a great step forward when the APIs that underlie wikis and related systems start intentionally supporting dynamic integration and thus stimulating a bounty of inter-related, non-redundant, purpose-built knowledge repositories.

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