Why doesn't someone start mirroring ncbi and layering a lightweight revisioning layer on top of the content? It could live at <a href="http://ncbi2.org">ncbi2.org</a>. Or it could be mirrored directly into <a href="http://freebase.com">freebase.com</a>, which already provides those tools.<br>
<br>Mac<br><br><div class="gmail_quote">On Mon, Mar 24, 2008 at 11:07 AM, Tom Knight <<a href="mailto:tk@csail.mit.edu">tk@csail.mit.edu</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I think we all share this frustration. An example of just how bad<br>
things are might be useful.<br>
<br>
About a year ago, I started working with yeast recombination, and<br>
wanted to use a pair of yeast artificial chromosome vectors that had<br>
been developed in the early '90s. The developer was kind and helpful,<br>
and provided the vectors, but there was no sequence information<br>
available (not unusual for early vectors, where sequencing was<br>
difficult and expensive). One of the things I did was to fully<br>
sequence the vectors and to deposit the vector sequences into Genbank.<br>
<br>
I listed the original reference to the vectors as publication<br>
information. Apparently, this is not allowed. There was no way in<br>
which I could link the sequence I had just deposited with the source of<br>
the vector (or even to give credit for where it came from). The only<br>
link is the name of the plasmid, which I suppose is unique enough.<br>
<br>
But this madness has to stop.<br>
<div><div></div><div class="Wj3C7c"><br>
<br>
On Mar 24, 2008, at 10:26 AM, Dan Bolser wrote:<br>
<br>
> "That we would wholesale start changing people's records goes against<br>
> our idea of an archive," says David Lipman, director of the National<br>
> Center for Biotechnology Information (NCBI), GenBank's home in<br>
> Bethesda, Maryland. "It would be chaos."<br>
><br>
> I think that quote highlights the problem (ignorance) that we have to<br>
> overcome. People simply don't understand the nature of community<br>
> projects. Just take the open source software movement for example;<br>
> community + tools for basic collaboration = massively successful<br>
> projects.<br>
><br>
> How many databases in the molecular biology community include even the<br>
> most basic of tools - a public bug tracker? If there is one out there,<br>
> I don't know it. I find this fact simultaneously infuriating and<br>
> dumbfounding, because it is simply unjustifiable. How about a public<br>
> database project with a publically archived mailing lists? I had to<br>
> start my own because the NCBI refused to do so;<br>
><br>
> <a href="http://www.bioinformatics.org/mailman/listinfo/ssml-general" target="_blank">http://www.bioinformatics.org/mailman/listinfo/ssml-general</a><br>
><br>
><br>
> I am having a similar running battle with the PDB, who staunchly<br>
> refuse to alter (some of) their data, even though it contains clear<br>
> errors. The recent remediation has been a huge improvement, but it<br>
> doesn't go far enough.<br>
><br>
> We simply need to build the kind of community annotation projects that<br>
> will show the way for others. I have given up on the above kind of<br>
> stupidity. There are only so many times that you can tell someone they<br>
> need to install a public bug tracker before you get too tired to care<br>
> that they won't install one any more.<br>
><br>
><br>
> With hope for the future,<br>
><br>
> Dan.<br>
><br>
><br>
> ----<br>
><br>
> <a href="http://BioDatabase.Org" target="_blank">http://BioDatabase.Org</a><br>
> <a href="http://PDBWiki.org" target="_blank">http://PDBWiki.org</a><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Mac Cowell<br>iGEM Coordinator<br><a href="http://igem.org">igem.org</a><br>231.313.9062