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 -~----------~----~----~----~------~----~------~--~---
