Do You Use Any Of The Wiki-Resources For Biology/Genomics?

Question

[Nathan Harmston]

Hi everyone,

I'm currently thinking about starting doing some work building a wiki and a knowledge base for metagenomics. I was wondering do people here actually use any of the existing wikis ( http://www.snpedia.com/ , http://www.wikigenes.org/ etc ) and do they find them useful?

I know with these kind of things it is very important to get/build community contribution/usage so what would it take to get you to actively contribute to such a resource. I was considering a kudos system such as the one at stackexchange.

Many thanks

Nathan

PS. I am not expecting that if I build a resource, that people would definitely use it ... just that I would like to try as much as possible to have a chance of getting people to use it and assess its feasibility.

PPS. I know this isn't really a question that can't be answered....but I'm not really sure where else to ask it.

Answer 1

[Pierre Lindenbaum]

First, do you really need to create another wiki ? See this document.

My experience with MediaWiki:

I worked with Andrew Su to add the protein-protein interaction data for records of GeneWiki. I also played with the Mediawiki API to extract some informations from wikipedia: e.g. see

• Extracting Scientists &SF writers from Wikipedia.
• French Scientists executed by decapitation

If you plan to extract some structured data from mediawiki, you should also have a look at the DBPedia.org project which has designed some nice tools to parse the mediawiki infoboxes and generate a RDF database.

You must also have a look at Freebase . It is a social semi-structured database with a powerful API.

[Neilfws]

what Pierre said :-)

[Samuel Lampa]

If looking for adding structured data to MediaWiki, with RDF and SPARQL support, one could not omit Semantic MediaWiki (which is used on SNPedia and others)

[Nathan Harmston]

I agree ...freebase is awesome and my current plans are to create an RDF triplestore as the knowledge base. Thanks for the links.

[Pierre Lindenbaum]

thanks Neil, ... +1 for you comment #!*$?!!% .... :-)

Answer 2

[biobot 0.0.77.a.1099]

To add another data point to your survey; yes, I'm aware of a number of wikis in my field and no, I don't use or contribute to any of them. The main reason for non-use is that wikis generally have very weak query and data extraction interfaces, so I can't find what I'm looking for, or save it once I've got it. The data are at best semi-structured, so even with the query APIs some wikis provide, it's hit and miss (and you never know how much you've missed by). I'm disinclined to contribute to a resource that I can't use effectively. E.g. wikigenes is a particularly unhappy experience for me.

By the way, to end on a positive note, Rfam are heavy contributors to Wikipedia, so by their example it may not be necessary to set up your own wiki. As you say, it's the contributors who are key. Find a core of enthusiastic individuals who need the resource first and you have a good chance of success.

[Nathan Harmston]

my current plan/idea is to make the knowledge base available as RDF so people can query/export using its associated toolset. Would this make using a wiki better for you?

[biobot 0.0.77.a.1099]

Yes, that would be a point in favour.

[Khader Shameer]

Keith : You mean Rfam? AFAIK, there is no official contribution from Pfam to Wikipedia. Please let me know if I am missing something. Thanks.

[biobot 0.0.77.a.1099]

Oops, yes. I mean Rfam. I'm not sure they'll thank me for that slip... we're in the same building!

Answer 3

[Fred Fleche]

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[Mndoci]

I have a question. When you say tables, are you looking for a csv file or SQL tables you can query? Given the download bit, I presume the former

Answer 4

[Andrewjgrimm]

I occasionally use Wikipedia, but I remember to take it with a pinch of salt. Apart from that, I don't use any wikis. I wouldn't mind if our work group set up an internal wiki to help with day-to-day stuff, eg "How to install that printer under Windows XP".