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': This
element is not expected. Expected is ( {http://regis-
web.systemsbiology.net/pepXML}sample_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',
attribute 'search_id': '1283330051656' is not a valid value of the
atomic type '{http://regis-web.systemsbiology.net/pepXML}positiveInt'.
line 6: element search_summary: Schemas validity error : Element
'{http://regis-web.systemsbiology.net/pepXML}search_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': Not all
fields of key identity-constraint '{http://regis-
web.systemsbiology.net/pepXML}search_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].
For more options, visit this group at
http://groups.google.com/group/spctools-discuss?hl=en.
