GeneWiki – overadventurous or unambitious

28 07 2008

Doesn’t it annoying you when you think “I thought of that first” when something is brought out in the spotlight. But then you realise, that hey, that’s probably been in the pipeline for some time, maybe they did think of it first.

That’s what I’m feeling about GeneWiki.

Last year as part of my comparative genomics project, I went through a very rough self guided crash course in bioinformatics. Having to navigate through competing and partially overlapping databases that use different sequence formats was a big frustration.

There is a whole lot of freely accessible genetic sequence data out there. And the best thing is that you do not need a heavy duty wet lab to do any work with it. It’s all bits and bytes. All you need is a computer. You might need a heavy duty supercomputer to do complex high throughput similarity screening – but to do simple analysis and comparisons – a standard desktop should be plenty – as free online access to supercomputers that do the hard processing for you is also readily available.

The worst thing is it is very clogged up. Over catalogued and under-connected. For a web-savvy post-Y-gen-er like me – it is very annoying to find linkable content unlinked.

Wiki-technology to me seems and obvious way to bring everything together

The simple nature of wiki does make it easy for anyone to create links without any real programming language. If you can write an email, you can write a wiki.

The nature of multi-user editing also facilitates the creation of a wide network by allowing new links to be inserted or old links to be updated – and even future links can be  predicted, suggested or even demanded.

Content can also be layered and catalogued. Forums are in-built. Best of all external software can be developed to aggregate and process information contained in the wiki.

My biggest concern here isn’t so much accuracy. One would expect GeneWiki to have at least the same level of peer review that Wikipedia does (which works rather well) if not more – such as verifying registration, or non-immediate publishing. I’d be more concerned about maintaining user interest and capacity to create cooperation to release what might otherwise be sensitive data in a free-to-access form.

Another part of me also cries that so much more is feasible with online technology. Why limit to just human genes? A database that provides referencing to homologues and orthologues in non-human species would be great. And are we also going to limit ourselves to outmodable concepts like “gene” and “species”. Summary data on mammalian, reptilian or avian gene groups, their transcription factors, chromosomes, and even whole genomes now – the information is all there – a lot of it already online – it just needs to get connected.

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2 responses

29 07 2008
Computers

[…] midgetgems wrote an interesting post today Here […]

3 08 2008
zayzayem

My name is not “midgetgems”. I do not even know how your autocomplete/spellcheck managed to mangle my handle that badly.

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