[Pdbwiki-devel] Uniprot mapping & error reports question

Henning Stehr stehr at molgen.mpg.de
Tue Jul 28 06:20:09 EDT 2009

Hi Dan,

Jose and I went through the Uniprot mappings.

In fact, out of 83455 polymeric chains (which could potentially
contain mappings to Uniprot),
60316 are correct,
14158 have no Uniprot cross reference in the CIF file
8981 have a broken link, because there was a Uniprot cross reference,
but the value was NULL, which we didn't check for (see e.g. 2cad)
1 had garbage in the Uniprot reference field in the cif file, so we
wrote a comment in the Wiki about it (3g6d H)

So the broken links do exist in about 11% of the chains (or ~12% of
the entries). We have fixed the script such that this should not
happen for future entries. If time permits, Jose
will also update the old entries with the search-and-replace-script.

I have another general question:

Shall we compile a list with "errors collected by the PDBWiki
community" and send it to the PDB?

At the same time we could ask the PDB to link to our site.

Anyways, this is not the highest priority, so we should probably
finish the other stuff first.


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