[OWW-Discuss] Proposal to 'Wikify' GenBank Meets Stiff Resistance

[Mackenzie Cowell]

Why doesn't someone start mirroring ncbi and layering a lightweight
revisioning layer on top of the content?  It could live at ncbi2.org.  Or it
could be mirrored directly into freebase.com, which already provides those
tools.

Mac

On Mon, Mar 24, 2008 at 11:07 AM, Tom Knight <tk at csail.mit.edu> wrote:

> I think we all share this frustration.  An example of just how bad
> things are might be useful.
>
> About a year ago, I started working with yeast recombination, and
> wanted to use a pair of yeast artificial chromosome  vectors that had
> been developed in the early '90s.  The developer was kind and helpful,
> and provided the vectors, but there was no sequence information
> available (not unusual for early vectors, where sequencing was
> difficult and expensive).  One of the things I did was to fully
> sequence the vectors and to deposit the vector sequences into Genbank.
>
> I listed the original reference to the vectors as publication
> information.  Apparently, this is not allowed.  There was no way in
> which I could link the sequence I had just deposited with the source of
> the vector (or even to give credit for where it came from).  The only
> link is the name of the plasmid, which I suppose is unique enough.
>
> But this madness has to stop.
>
>
> On Mar 24, 2008, at 10:26 AM, Dan Bolser wrote:
>
> > "That we would wholesale start changing people's records goes against
> > our idea of an archive," says David Lipman, director of the National
> > Center for Biotechnology Information (NCBI), GenBank's home in
> > Bethesda, Maryland. "It would be chaos."
> >
> > I think that quote highlights the problem (ignorance) that we have to
> > overcome. People simply don't understand the nature of community
> > projects. Just take the open source software movement for example;
> > community + tools for basic collaboration = massively successful
> > projects.
> >
> > How many databases in the molecular biology community include even the
> > most basic of tools - a public bug tracker? If there is one out there,
> > I don't know it. I find this fact simultaneously infuriating and
> > dumbfounding, because it is simply unjustifiable. How about a public
> > database project with a publically archived mailing lists? I had to
> > start my own because the NCBI refused to do so;
> >
> > http://www.bioinformatics.org/mailman/listinfo/ssml-general
> >
> >
> > I am having a similar running battle with the PDB, who staunchly
> > refuse to alter (some of) their data, even though it contains clear
> > errors. The recent remediation has been a huge improvement, but it
> > doesn't go far enough.
> >
> > We simply need to build the kind of community annotation projects that
> > will show the way for others. I have given up on the above kind of
> > stupidity. There are only so many times that you can tell someone they
> > need to install a public bug tracker before you get too tired to care
> > that they won't install one any more.
> >
> >
> > With hope for the future,
> >
> > Dan.
> >
> >
> > ----
> >
> > http://BioDatabase.Org
> > http://PDBWiki.org
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>
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-- 
Mac Cowell
iGEM Coordinator
igem.org
231.313.9062
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