Missing NCBI DTD in Bio.Entrez
Created by: mutalyzerbot
Original ticket: https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/27 Original date: 2011/02/09 Original reporter: m DOT vermaat DOT hg AND lumc DOT nl
Reported by Ivar. With UD_12972395149, getTranscriptsAndInfo fails on retriever.loadrecord, because eLink_101123.dtd is not present. I cannot find this DTD anywhere.
Ivar also tried our local Mutalyzer installations.
Unable to load DTD file eLink_101123.dtd
Bio.Entrez uses NCBI's DTD files to parse XML files returned by NCBI Entrez. Though most of NCBI's DTD files are included in the Biopython distribution, sometimes you may find that a particular DTD file is missing. In such a case, you can download the DTD file from NCBI and install it manually.
Usually, you can find missing DTD files at either http://www.ncbi.nlm.nih.gov/dtd/ or http://eutils.ncbi.nlm.nih.gov/entrez/query/DTD/
If you cannot find eLink_101123.dtd there, you may also try to search for it with a search engine such as Google.
Please save eLink_101123.dtd in the directory /usr/lib/pymodules/python2.6/Bio/Entrez/DTDs in order for Bio.Entrez to find it.
Alternatively, you can save eLink_101123.dtd in the directory Bio/Entrez/DTDs in the Biopython distribution, and reinstall Biopython.