Wikis for Genome Annotation (GenomeWiki) - Structured or Unstructured?
January 25, 2009
Wikis have been a popular tool for collaboration elsewhere, and have been very successful. The obvious question is why not then in Biology and Medicine ?
Recently a number of initiatives have come up to assimilate data taking inspiration from the Wikipedia. These includes annotation of Genes, pathways, etc based on Wiki.
It is evident right from the selection of software, that the concept of Wikipedia has heavily influenced these projects. Therefore the major issues both technical and conceptual, associated with Wikis stay.
Wikis are unstructured
The major issue with unstructured content (Biologists are already used to loads of text) is that while it is readable by a human, most often it is not readable by a machine (I just mean to say that machines will find it difficult to read the stuff and make sense out of it).
Recently there have been a lot of talk on the Semantic Web (dubbed the Web 3.0), which would enable computers to churn meaning out of truckloads of data (of course in a structured formats), and enable complex queries to be answered.
See: http://en.wikipedia.org/wiki/Semantic_Web
We at the Institute of Genomics and Integrative Biology(IGIB) have been using Structured Wikis for Genome Annotation.
The SysBorgTB
SysBorgTB was created as part of the Open Source Drug Discovery Initiative of CSIR and is a structured research Wiki based on the TWiki platform. It has sections for Genome Annotaion, Projects, LabNotebook etc, which is rather structured, and can be queried using a SQL like query language.
Zebrafish GenomeWiki
The Zebrafish GenomeWiki is alos a structured Wiki created on the TWiki platform for community annotation of the Zebrafish Genome. The Wiki is partitioned into different Webs and SubWebs for ease of organisation of data and ease of search. The database contains an enormous amount of data for more than 300,000 genomic identifiers, and is at the moment one of the most comprehensive resources available for the Zebrafish Genome.
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Comments
Wave of the Future
January 30, 2009 by Renaisauce, 42 weeks 2 days ago
Comment id: 34121
I know of some other groups that have considered using wikis and some google aps for collaborations. It would be very nice, however, to have a universal scientific collaboration system so that people don't have to keep making up their own. Scientists are busy dudes.
Collaboration System
January 31, 2009 by Anonymous, 42 weeks 2 days ago
Comment id: 34135
I agree with you, but only partly.
There cannot be something like a "Universal" collaboration system what will fit all pegs, because the field is so diverse, and the activities are equally diverse.
What could be a necessity is the tools to have data and resources interoperable. "Standards" for data and tools in Life Sciences is still a mirage !!
_V