Sorry, got pulled into other things. Here is my two cents. Specifically, I'd like a value "PepArML" to support my peptide identification meta-search engine and combiner infrastructure.
I have users of my infrastructure for which pepXML is the desired output format, as it is already supported by downstream non-TPP tools as a peptide identification import format. There is generally a small amount of specific configuration necessary per search engine (extraction of the primary ranking "score", for example) but otherwise the effort to import results from any given search engine (or search engine like tool) is relatively small. I'm also working on various X!Tandem pluggable scores, all of which would technically require their own value here - k-score is indicated with the value "X!Tandem (K-score)" for example. While pepXML is clearly not designed as a universal format for peptide identification results and is very much tied to the specifics of TPP, a number of tools do use it as a universal import format. Perhaps they should just turn off validation. :-) A pragmatic solution that would permit validating parsers might be to designate a value, say "Other" for non-mainstream tools to use, and allow developers to adopt a convention to use the free-form "parameter" entity of the search_summary entity to specify an unconstrained search_engine name: <search_summary search_engine="Other"...> <parameter name="OtherSearchEngine" value="PepArML"> </search_summary> Thanks, - n On Jun 24, 12:53 pm, Jesse J <[email protected]> wrote: > Out of curiosity, what search engines did you have in mind? > > On Jun 24, 9:41 am, Nathan Edwards <[email protected]> wrote: > > > The wiki says to send this request to the spctools-dev mailing list, > > but I can't find out where this list is, or how to send to it. > > > I'd like to request the addition of a (few) search engine names to the > > pepXML search_summary entity, search_engine attribute enumeration. > > > How do I go about this? > > > Thanks, > > > - n -- 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.
