Hi Hendrik, I think we need to get an authoritative answer from David on this one. And he is currently traveling in the Land of the Finns. We will let/ask him to answer when he is next able.
Regards, Eric > From: [email protected] [mailto:spctools- > [email protected]] On Behalf Of Hendrik Weisser > > Hi! > > I'm working on the pepXML parser in OpenMS. I've been confronted with > a type of pepXML file I hadn't seen before, where search results from > different search engines - but for the same experiment - were > collected in one file (with one "msms_run_summary" per search engine). > I've added (maybe prematurely) support for this to the OpenMS parser, > and then wanted to construct a simple pepXML file for testing > purposes. > > In doing so, I've now come across a constraint in the pepXML schema > (at least from v1.8 on) that says values of the "base_name" attribute > (supposed to contain the full path to the searched mzXML file) in the > "search_summary" element have to be unique within the document. > What is the rationale behind this constraint? Is it supposed to > prevent the above case, where different searches of the same > experiment end up in one file? Why would that be desirable/necessary? > (Also note that I can construct a valid and parseable pepXML file from > two different search runs of the same file if I change the path in > "base_name"...) > > In an earlier discussion (http://groups.google.com/group/spctools- > discuss/msg/7760dcda02877922?hl=en), it was mentioned that > "base_name"s in "msms_run_summary" elements had to be unique in the > document - however, as per the schema, that's not true. Also, the > "base_name" of an "msms_run_summary" is not tied to the "base_name" in > subordinate "search_summary"s. If there were such a constraint, it > would be impossible to have more than one "search_summary" under an > "msms_run_summary" - however, this is allowed in the schema. > When does it make sense to have different "base_name"s in an > "msms_run_summary" and its subordinate "search_summary"(s)? Judging > from the schema documentation and the files I've seen, it seems that > the values should be the same. On the other hand, why have the > attribute in both elements then? > > All this adds to my confusion about the appropriate use of > "base_name"... > > I would be happy if someone could clear things up for me. > > > Best regards > > Hendrik > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
