Christine, The new versions are now in place, thanks for bringing it to our attention. By the way, the latest version of pepXML is 117.
As to the validation -- I recently ran into the same issue and will take a look at it. I noticed it with xmlint, and I've also encountered errors using SAX2Count. -Joe On Fri, Dec 10, 2010 at 8:49 AM, Christine <[email protected]>wrote: > Dear all, > > We would like to create pepXML and protXML exports for our inhouse > search engine. I notice that schemas available from the website: > http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v114.xsd > http://sashimi.sourceforge.net/schema_revision/protXML/protXML_v5.xsd > > are not the ones distributed in the TPP zip file: > pepXML_v115.xsd > protXML_v6.xsd > > Would it be possible to have the new versions on the website, so that > we can reference them in the xml header ? > > Some comments and documentation are copy-pasted for different > elements, example: raw_data and raw_data_type: > <xs:attribute name="raw_data_type" type="xs:string" use="required"> > <xs:annotation> > <xs:documentation>raw data type extension (e.g. .mzXML)</ > xs:documentation> > </xs:annotation> > </xs:attribute> > <xs:attribute name="raw_data" type="xs:string" use="required"> > <xs:annotation> > <xs:documentation>raw data type extension (e.g. .mzXML)</ > xs:documentation> > </xs:annotation> > </xs:attribute> > > Concerning modification at the peptide terminus (search_database), > should it be: > <aminoacid_modification description="TMTsixplex_Nterm" aminoacid="." > peptide_terminus="n" massdiff="+229.162932" mass="357.25789199999997" > variable="N"/> > or > <terminal_modification description="TMTsixplex_Nterm" terminus="n" > massdiff="+229.162932" mass="229.162932" variable="N"/> > > Finally trying to validate the produced files with xmllint definitely > don't pass! Example of errors: > > line 5: element search_summary: Schemas validity error : Element > '{http://regis-web.systemsbiology.net/pepXML}search_summary<http://regis-web.systemsbiology.net/pepXML%7Dsearch_summary>': > This > element is not expected. Expected is ( {http://regis- > web.systemsbiology.net/pepXML}sample_enzyme<http://web.systemsbiology.net/pepXML%7Dsample_enzyme>). > > despite the fact that sample_enzyme is not specified as required in > the schema. > > Another example with this line: > <search_summary search_engine="Phenyx" > precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" > base_name="/home/hoogland/projects/easyprot/trunk/easyprot/data/users/ > chh/phenyx/jobs/2010/09/1283330051656" search_id="1283330051656"> > > line 6: element search_summary: Schemas validity error : Element > '{http://regis-web.systemsbiology.net/pepXML}search_summary<http://regis-web.systemsbiology.net/pepXML%7Dsearch_summary> > ', > attribute 'search_id': '1283330051656' is not a valid value of the > atomic type > '{http://regis-web.systemsbiology.net/pepXML}positiveInt<http://regis-web.systemsbiology.net/pepXML%7DpositiveInt> > '. > line 6: element search_summary: Schemas validity error : Element > '{http://regis-web.systemsbiology.net/pepXML}search_summary<http://regis-web.systemsbiology.net/pepXML%7Dsearch_summary> > ', > attribute 'search_id': Warning: No precomputed value available, the > value was either invalid or something strange happend. > line 6: element search_summary: Schemas validity error : Element > '{http://regis-web.systemsbiology.net/pepXML}search_summary<http://regis-web.systemsbiology.net/pepXML%7Dsearch_summary>': > Not all > fields of key identity-constraint '{http://regis- > web.systemsbiology.net/pepXML}search_summary_id<http://web.systemsbiology.net/pepXML%7Dsearch_summary_id>' > evaluate to a node. > > > What would you recommend to validate those xml files? > > Another remark: I am not able to extract the files in > XML_sample_files.tgz (from TPP_4-4-1-src.zip), are they available from > elsewhere? > > Thanks for your help, > Best regards, > Christine > > -- > > ------------------------------------------------------ > Christine Hoogland > Biomedical Proteomics Research Group (BPRG) - 9056 > Department of Structural Biology and Bioinformatics > University Medical Center (CMU), University of Geneva > 1 rue Michel Servet, 1211 Geneva 4, Switzerland > Phone: +41 (0)22 379 41 69 > Fax: +41 (0)22 379 55 02 > Email: [email protected] > ------------------------------------------------------ > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]<spctools-discuss%[email protected]> > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- Joe Slagel Institute for Systems Biology [email protected] (206) 732-1362 -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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