Tag Archives: wikipedia

Friday SNPets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

A biological wikis conference: NETTAB 2010

Boy, I wish I could go to this. I would love to know where and how the successes are happening in this arena.  From the Biocurator mailing list:

Joint NETTAB 2010 and BBCC 2010 workshop Biological Wikis

November 29 – December 1, 2010

Congress Center, University of Naples “Federico II”, Naples, Italy http://www.nettab.org/2010/

The joint NETTAB and BBCC 2010 workshop on “Biological Wikis” promises to be a great meeting for all researchers involved in the exploitation of wikis in biology.

Come and discuss your ideas and doubts with such scientists as Alex Bateman, Alexander Pico, Andrew Su, Dan Bolser, Robert Hoffmann, Thomas Kelder, Mike Cariaso, Adam Godzik, Luca Toldo and many other who, we hope, will join the workshop.

It’s a great chance to follow smart tutorials and lectures on WikiPathways, WikiGenes, Semantic Wiki, PDBWiki, Gene Wiki and a proficient use of Wikipedia.

See a list of keynote speakers and tutorials at http://www.nettab.org/2010/progr.html .

There still is time to submit abstracts for posters and software demonstrations until next October 17, 2010!

The complete Call is available on-line at http://www.nettab.org/2010/call.html .

Registration is open at http://www.nettab.org/2010/rform.html .

Register within next October 29, 2010 and take profit of early registration fees.

A reduction of 20 euro applies to all fees for members of ISCB and other societies and networks.

More reductions are foreseen for PhD students.

Further information is available at http://www.nettab.org/2010/ .

Looking forward to seeing you soon in Naples.

Paolo Romano

I’ll be watching for tweets and meeting reports, please!

Community Annotation; Beyond Reference Genomes

I’m catching up with some mailing lists and news and I came across this interesting tidbit from our friends in the GMOD community. We are huge supporters of curation by humans for a couple of reasons: 1) we know the quality of that information can be the best and it captures so much of the information biologists need beyond sequence info; and 2) some of us have done curation and we know that it’s underappreciated but far from trivial :) .

We’ve also followed attempts by various groups to get the wider community involved to do a couple of things–to get authoritative and active researchers to put in stuff they know, and to reduce the burden on the overwhelmed professionals.  There have been a variety of ambitious attempts to get people involved in curation. UCSC has a wiki they rolled out. Some journals required Wiki updates. Seeding Wikipedia with some information and encouraging community input has been attempted. Separate new wikis on some topics have been initiated like WikiPathways.  We have been “skeptical optimists” about how some of these would go. We understand the need–but we know that end users of data are busy, they don’t get any work-related credit or time to do this sort of thing, and sometimes they don’t understand the finer points of curation.  But we like to see how the efforts work out and we’d like to see success.

Well–I’ve seen some results on various efforts that you ought to see. The GMOD community recently had a Community Annotation meeting that brought several groups together to discuss their experiences and outcomes. I’m not going to give it away–you need to go read it. One group had a 90% success rate with a strategy they attempted!!  Some groups are using curation as a student project. Others report on things they’ve tried that haven’t had as much success. Anyway: it’s all very interesting to know about–what works and what doesn’t.  And what about communities that don’t have MOD (model organism database)? They touched issues on that too.

There was another meeting too that took on a separate topic: Post Reference Genome Tools.  The premise is this:

How are we going to visualize and exploit (or even cope with) the world three years from now, when small labs may be able to fully sequence 500 individuals or species (or more) in a month? How can we visualize and link together 500, 1000, or 10,000 genomes? Many existing tools assume a reference genome. Will a reference make sense in the future, or will it hold us back?

We know a lot about the volume of data that we’ve already got that so many people aren’t aware of.  As I was just saying the other day: the data’s not in the papers anymore. It’s in these databases and it’s up to you and me to find and deal with it.  But how will the data providers offer it to you? These folks are thinking about this–and it may alter the way you interact with the data.  Again, I’m not giving it away: go read the report.

Thanks for the GMOD community for doing these reports. They are nice to have, and for those of us who can’t be there they offer a really helpful look inside.

Quick links to the reports:

Community Annotation Satellite Meeting Report

Post Reference Genome Tools Satellite Meeting Report

GBrowse: http://gmod.org/wiki/Gbrowse

Tip of the Week: UCSC wiki annotations


In the continuing effort to get scientists and researchers to annotate and curate data and to capture the huge amount of knowledge available, UCSC Genome Browser has added a wiki annotation track to the browser. It’s not the first effort of course, GeneWiki is an effort, with mixed results so far, to annotate gene function information as a community exercise using Wikipedia. Some journals are requiring wiki entries, and several databases have opened wikis for curation. Wikis could be a solution for capturing the exponentially increasing amount of data,

or they could be just another place for adding confusion… or both. I suspect out of the plethora the wikis coming available for annotation and curation of genomic data, something will stick and find that Goldilocks balance of a dedicated community, ease of use, usability, and other aspects that will be needed for this to work.

Perhaps UCSC Genome Browser has that balance. It will remain to be seen, but let’s get started. Today’s tip is introducing the new wiki track in the UCSC Genome Browser.

Required Wiki updates?

In the push to ‘communitize’ annotation and curation, one journal, RNA Biology, is requiring submitters to add or update their RNA sequences on wikipedia. This article suggests that it’s working so far (update, link to the article added),

The first examples of this program in action are already online. The journal is hosting an open access paper that describes a family of RNA molecules found in nematode worms; a corresponding Wikipedia page is already in place. In good Wikipedia form, the phylogenetic analysis of these RNAs is dinged for not providing citations, while the article as a whole is flagged as having excess jargon. (The talk page hosts an interesting discussion of how much jargon can possibly be eliminated from a highly technical description like this.)

So far, everyone is happy with the results. A few scientists have started updating the scientific content of the RNA entries, while the usual Wikipedia denizens have helped out in terms of catching typos and improving the formatting. The people backing the project expect that it will be immune to some of the issues that plague other Wikipedia entries; Nature quotes one of the biologists as saying, “”We don’t think vandalism will ever be as much of a problem for a Wikipedia page on transfer RNAs as it is for a page on George Bush.”

And looking at that one entry, it does seem to. But I have a question, if researchers are soon required not only to submit and/or annotate in a database and to wikis and curate and annotate if they wish to publish, doesn’t this start to place an undue burden on researchers who already have grant writing, teaching, and more in addition to actual research? There does need to be a solution to the growing need for curation and annotation of data, it will be interesting to see if this is one solution that will hold.

Gene Wiki?

ResearchBlogging.org PLoS Biology has an article out today entitled “A Gene Wiki for Community Annotation of Gene Function.” The article describes the authors attempts to create a comprehensive gene wiki of gene functions by ‘seeding’ Wikipedia with a foundation of ‘stub’ articles with information from existing databases (such as Entrez Gene). This foundation would then be built upon in Wikipedia fashion by community editing.

Continue reading

Wikification of Genbank

Speaking of Genbank’s 25th, a few weeks ago Science had a news piece “Proposal to ‘Wikify’ Genbank Meets Stiff Resistance.” Apparently, those in the Mycology research community have found many inaccuracies in the Genbank records and wish to see a change that would allow annotations to be made by the community:

a scheme like those used in herbaria and museums, where specimens often have multiple annotations: listing original and new entries side by side. It would be a community operation, like Wikipedia, in which the users themselves update and add information, but not anonymously.

But the idea is meeting resistance from Genbank’s Managers:

Continue reading

Web strolling finds

ScienceRoll links to a search engine for Radiology, links to a post about a “Gene Wiki” project, from which I re-find the excellent blog by Deepak Singh. From there I find this interesting resource: FreeBase, which is different that Wikipedia (it doesn’t have ‘articles’, it has stats), which reminds me of that Google project I mentioned earlier and leads me to GoogleBase.

It’s all about finding that info!