Tag Archives: wikis

News bits: WikiGenes opportunity; HapMap data issue

Ok, I’m back from Thanksgiving and catching up on some emails and found a couple of news items I wanted to pass along.

WikiGenes invitation to edit a Nature Genetics paper

Here’s an interesting “experiment” I got notified about. You could potentially get authorship on this paper if you contribute to the development of this article.  Here’s the email I got from the WikiGenes mailing list–but click over for more details and you can see the article over there. I haven’t had time to check it all out yet, but as there is a deadline I wanted to mention it now.

Dear Mary,
The editor of Nature Genetics has commissioned a collaborative standards paper on Genome Wide Association Studies. An editable draft of this paper is now online at WikiGenes, http://www.wikigenes.org/GWAS.html?wpc=12

I hope this is an interesting opportunity for you, because significant contributions to this draft might get you a co-authorship on the final paper in Nature Genetics.

I would also like to use this occasion to ask you a favor.

If you like WikiGenes, please tell your friends about it. We do not have the budget of big publishers, so we depend fully on word-of-mouth publicity.

Or you could also help us by linking to WikiGenes from your website. Thank you!

Best of science,

Robert Hoffmann, PhD
Branco Weiss Fellow
WikiGenes – Evolutionary Knowledge

HapMap data in the HaploView tool

This came across from the HapMap mailing list. We tell people about using HapMap + HaploView all the time, so I wanted to mention this possible issue with some of the data:

Dear HapMap users,

Recently, there are several questions about Haploview data format errors when users tried to analyze HapMap release 28 data.  The current Haploview version (4.2) does not recognize the new individuals in release 28 and the software will generate an error similar to “Hapmap data format error: NA18876″ when trying to open the data.

Haploview is developed and maintained by an organization different from HapMap.  Please contact Haploview help desk (haploview@broadinstitute.org) for questions specific to this software.


Hua Zhang, Ph.D.
dbSNP Group

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.

Another Wiki, WikiPathways

ResearchBlogging.orgPLoS Biology reports today on WikiPathway. The paper entitled “WikiPathways: Pathway editing for the people,” announces a new wiki for the ‘public curation’ of pathway data. The authors argue that

 The exponential growth of diverse types of biological data presents the research community with an unprecedented challenge to keep the flood of biological data as accessible, up-to-date, and integrated as possible.

I agree with this. We’ve seen it here and mentioned it many times, the growth of data is exponential and difficult to keep track of. The proposed solution for pathway data, as there has been for other data types and curation that I’ve written about lately, is a wiki: WikiPathways to be exact. The authors have high hopes for this wiki, as they state:

WikiPathways will be a powerful resource for the research community and a vital forum for pathway curation, And we are hopeful that it will serve as an example for how the continuing flood of biological data can be managed and utilized by the community to irrigate future hypotheses and discoveries

I’ve already made known my “skeptical optimism” for wikis for biological data known in a previous post, reading this later paper, that would still apply here. But right now I’m not going to write beyond that, I’m just going to point you to this paper and wiki. Later (this week, next at the latest) I’ll be critiquing this paper more fully and more generally look at this trend currently to use wikis for community curation and documentation of biological data and databases.

Pico, A.R., Kelder, T., van Iersel, M.P., Hanspers, K., Conklin, B.R., Evelo, C. (2008). WikiPathways: Pathway Editing for the People. PLoS Biology, 6(7), e184. DOI: 10.1371/journal.pbio.0060184

Genomics resource blog roundup

Just thought I’d put down some things I’ve been reading for your enjoyment, edification or to pass the time.

Mike The Mad Biologist has a good overview of an interesting tool for analyzing 16S rRNA sequence data: STAP (described in a PLoS One paper here).

Omics! Omics! has a good technical review of a Wired article on “DIY Genomics” and all that is wrong with it.

Fungal Genomes Blog (yes, there is one!) blogs about the Oompa Loompa genome that is sure to come soon (now that the sequencing of the Theobroma cacao genome has been announced by Mars candy company (and others). I followed that link to two fungal wikis which somewhat goes to explain my reticence concerning wikis.

And A Blog Around the Clock reports on the Gene Wiki and another interesting paper just published in PLoS about the HealthMap project.

Lastly, want to battle it out with your colleague on who is the best? Try the Pubmedfight to see who has the most publications. Be careful though, middle initials can change the numbers :) and it didn’t seem to report everything (missed a huge majority of my publications). The fight is rigged I tell you! (hattip to ScienceRoll)