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Re: [Psidev-pi-dev] FW: Spec doc
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From: Pierre-Alain B. <pie...@is...> - 2008-12-02 11:17:37
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Hi, David Creasy wrote: > Hi Andy, > > Some minor changes: > From: > <pf:Person id="PERSON_DOC_OWNER" firstName="" lastName="Some Person" email="so...@so..."> > to: > <pf:Person id="PERSON_DOC_OWNER" firstName="Some" lastName="Person" email="so...@so..."> > > > Example Context: > <pf:cv id="PSI-PI" fullName="PSI-PI" URI=*MailScanner has detected a possible fraud attempt from "www.psidev.info" claiming to be* "http://www.psidev.info/not_sure_of_url_to_cv.obo"></pf:cv> > We only want the cv psidev.info when we finally release. Guess it's OK to leave this as it is at the moment. > > > Element <AnalysisSoftware> > Definition: A data set containing spectra data (consisting of one or more spectra). > Definition looks like a copy and paste of something quite different! > > > Element <pf:ContactRole> > Definition: The Contact that provided the document instance. > We use the contact role in several different places. Definition needs to be a bit more general? > In the example it is for a software vendor. > > > > Element <pf:Person> > Example needs filling out a bit with some fictitious person. > > > Element <Peptide> > sequenceMass xsd:double - The sum of the unmodified (poly)peptide sequence residues, exclusive of the termini masses in Daltons. > > Oh dear. Some of the examples are inclusive of the termini masses and > any modifications, others are not. In theory, it's possible to > calculate the mass given the modification delta and the CTermGain="OH" > NTermGain="H" from the enzyme. However, that's not trivial in a case > of multiple enzymes. I'd suggest we change the definition to include > the termini and mods. Martin (whose examples followed the > documentation) may think differently? I aggree: with termini and mods. Calculated neutral mass in Da (not m/z), monoisotopic, 6digits after unit? > > > Element <Inputs> > Definition: The inputs to the analyses including the databases > searched and the spectral data > The example shows the input file to the process that created the > analysisXML document (the Mascot .dat file) > The global definition needs changing. Also, need to add a definition > for SpectraData. > > > Element <DatabaseTranslation> > Could take examples from Mascot_NA_example.axml > > > Element <Enzyme> > missedCleavages xsd:int optional URI of the analysis software > e.g. manufacturer's website > semiSpecific - shouldn't this be a boolean? > > > Element <PlusValue> > unitName xsd:string - The name of the unit. > Shame that it doesn't pull out the allowed CV from the mapping file: > > <CvTerm termAccession="UO:0000221" useTermName="false" useTerm="true" > termName="dalton" cvIdentifierRef="UO" /> > <CvTerm termAccession="UO:0000166" useTermName="false" useTerm="false" > termName="parts per notation" cvIdentifierRef="UO" /> > > Element <SpectrumIdentificationItem> > Has an attribute of rank and also a CV item. From the minutes here: > http://psidev.info/index.php?q=node/380 > Looks as though we agreed it should be an attribute and removed from > the CV > > Cheers, > David > > Jones, Andy wrote: >> >> Hi all, >> >> Eric has re-generated the schema documentation for us. This is >> getting fairly close to a version I can cut and paste into the spec >> doc. Let me know if you have any comments, >> >> Cheers >> >> Andy >> >> >> >> >> >> *From:* Eric Deutsch [mailto:ede...@sy...] >> *Sent:* 01 December 2008 09:23 >> *To:* Jones, Andy >> *Cc:* 'Eric Deutsch' >> *Subject:* RE: [Psidev-pi-dev] Spec doc >> >> >> >> Hi Andy, sorry for the delay, US holiday over here. You will find >> updated HTML documentation at: >> >> >> >> http://www.peptideatlas.org/tmp/AnalysisXML_working.html >> >> >> >> A version that is suitable for cut-n-paste into a word doc is at: >> >> >> >> http://www.peptideatlas.org/tmp/AnalysisXML_working_simple.html >> >> >> >> I fixed some of the problems. The main problem I still know about is >> that in the subelement listing, any subelements that are double-tall >> nested substitution grouped elements do not have their definition >> visible. If one clicks on the subelement, the main element does have >> a definition. So it’s there, but my program is stymied by the various >> levels. This is fixable, but probably not before submission. >> >> >> >> If you send me screen-capture images to embed in some elements, that >> can be done if you like. >> >> >> >> If there are still other outstanding issues, please let me know >> >> >> >> Regards, >> >> Eric >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------ >> >> *From:* Jones, Andy [mailto:And...@li...] >> *Sent:* Thursday, November 27, 2008 4:56 AM >> *To:* Eric Deutsch >> *Subject:* RE: [Psidev-pi-dev] Spec doc >> >> >> >> Hi Eric, >> >> >> >> Any chance you could look at the generated documentation this week? >> We’re aiming to submit the specs to the document process by Monday... >> >> Thanks >> >> Andy >> >> >> >> *From:* Eric Deutsch [mailto:ede...@sy...] >> *Sent:* 21 November 2008 17:44 >> *To:* Jones, Andy >> *Cc:* 'Eric Deutsch' >> *Subject:* RE: [Psidev-pi-dev] Spec doc >> >> >> >> Hi Andy, yes, I will fix the bugs and regenerate the docs from the >> latest schema and files early next week. >> >> >> >> I will also have a look at TPP related materials for AnalysisXML and >> get back to you. >> >> >> >> Sorry I’ve missed the calls. That time is very awkward for me and >> I’ve occasionally been confused by Wednesday/Thursday switches. >> >> >> >> Regards, >> >> Eric >> >> >> >> >> >> ------------------------------------------------------------------------ >> >> *From:* Jones, Andy [mailto:And...@li...] >> *Sent:* Friday, November 21, 2008 2:09 AM >> *To:* Eric Deutsch >> *Subject:* RE: [Psidev-pi-dev] Spec doc >> >> >> >> Hi Eric, >> >> >> >> Would you be able to do a couple of updates to the auto-generated >> docs? There’s a couple of errors to fix. >> >> >> >> When there is an instance of: <xsd:element ref="pf:DatabaseReference" >> minOccurs="0">, would you be able to retrieve the documentation in >> the table from the referenced element. >> >> >> >> Also, when an element is inherited from, documentation for inherited >> attributes does not appear in the table (e.g. see Specificity rule, >> no docs for cvRef, unitName etc.) – unless we were missing >> documentation for these attributes when it was last generated?. >> >> >> >> There are also a few instances of elements imported from the >> FuGE-light schema which are completely empty, no attributes or >> documentation e.g. Organization or Person. >> >> >> >> We’re aiming to submit the specs to the PSI process by the end of >> month (i.e. a week on Monday), so if you would be able to look at >> this fairly soon it would be very much appreciated! Also, any chance >> that you can get someone to generate the TPP and SpectraST examples >> at your end. It’s no disaster if we submit to the process without >> these but it would be beneficial. >> >> >> >> Cheers >> >> Andy >> >> >> >> >> >> >> >> >> >> >> >> >> >> *From:* Eric Deutsch [mailto:ede...@sy...] >> *Sent:* 17 October 2008 07:43 >> *To:* psi...@li... >> *Subject:* Re: [Psidev-pi-dev] Spec doc >> >> >> >> Hi everyone, I updated the current draft of the on-line autogenerated >> schema docs to the latest svn. The result is at: >> >> >> >> http://www.peptideatlas.org/tmp/AnalysisXML_working.html >> >> >> >> It looks like the current mapping file is just a template without any >> term mappings themselves. Just as a test, I wrote into the >> axml-mapping.xml file the mapping information for SearchType and it >> seemed to pull it out of the CV nicely: >> >> >> >> http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType >> >> >> >> The autogeneration pulls examples out of one file. I randomly chose >> Mascot_MSMS_example.axml. Is there a better instance document to >> automatically pull examples out of? >> >> >> >> Regards, >> >> Eric >> >> >> >> >> >> >> >> ------------------------------------------------------------------------ >> >> *From:* Jones, Andy [mailto:And...@li...] >> *Sent:* Monday, October 13, 2008 7:07 AM >> *To:* psi...@li... >> *Subject:* [Psidev-pi-dev] Spec doc >> >> >> >> Hi all, >> >> >> >> A new version of the spec document has been uploaded by SVN (in the >> specification_document directory), and previous versions have been >> put in a subfolder. I think the document is getting there... >> >> >> >> Main tasks still to do: >> >> >> >> - Finish section on use cases when we have finally agreed >> the list online and made all the example files. >> >> - Import some parts of the example files to demonstrate a >> few specific points >> >> - Import the autogenerated documentation >> >> >> >> Before we can submit, the main outstanding issues are: >> >> >> >> - CV - looking through the CV there is still a fair bit of >> work to do, there’s quite a few terms with missing or incorrect >> documentation >> >> - Mapping file >> >> - Finish example files. >> >> >> >> Prior to the call on Thurs, can we have a think about how we plan to >> get the CV into shape and discuss it as a main agenda item... >> >> >> >> Also new schema uploaded with a few bits of improved documentation. >> >> Cheers >> >> Andy >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge >> Build the coolest Linux based applications with Moblin SDK & win great prizes >> Grand prize is a trip for two to an Open Source event anywhere in the world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Psidev-pi-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev >> > > -- > David Creasy > Matrix Science > 64 Baker Street > London W1U 7GB, UK > Tel: +44 (0)20 7486 1050 > Fax: +44 (0)20 7224 1344 > > dc...@ma... > http://www.matrixscience.com > > Matrix Science Ltd. is registered in England and Wales > Company number 3533898 > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ------------------------------------------------------------------------ > > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > |
