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Re: [Psidev-pi-dev] FW: Spec doc
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From: Jones, A. <And...@li...> - 2008-12-03 12:05:10
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Hi all, Jenny has pointed out that the images are missing from the uploaded version, they seem to be hyperlinked to images stored locally on my machine (which happened during the conversion from html to word). If anyone knows how to get around this problem (without manually inserting each image), let me know. Cheers Andy From: Jones, Andy [mailto:And...@li...] Sent: 03 December 2008 10:13 To: psi...@li... Subject: Re: [Psidev-pi-dev] FW: Spec doc Hi all, I’ve uploaded a new version of the spec doc, in which I’ve inserted the auto-generated documentation. There’s still a few things to fix with this (the schema updates from yesterday have not been incorporated yet) but at this stage it would be really useful if everyone could take a look and provide feedback (http://code.google.com/p/psi-pi/source/browse/#svn/trunk/specification_document ). Main questions: - Are we generally happy with this format? - Are there any major omissions? I think we all agree that we want to the this submitted ASAP to the PSI document process, so if you could get feedback to me this week it would be much appreciated, Cheers Andy From: Jones, Andy [mailto:And...@li...] Sent: 02 December 2008 17:36 To: psi...@li... Subject: Re: [Psidev-pi-dev] FW: Spec doc Hi all, New schema uploaded: Various documentation changes, as discussed below. PlusValue / MinusValue now encoded as CVParams Made a change to AnalysisProtocolCollection and AnalysisCollection that prevented GenericProtocol and GenericProtocolApplication being used – I’ve been meaning to fix this for a while. It also means the files are now restricted to containing at most one ProteinDetection and one ProteinDetectionApplication. In the schema, we have some fairly pointless abstract classes AnalysisProtocol and AnalysisProtocolApplication. They were put in the schema at one stage to demonstrate how the format should be extended in the future, following this design pattern (or something like this...). I vote we get rid of them, and write in the spec document about future extension strategies. Cheers Andy From: Jones, Andy [mailto:And...@li...] Sent: 02 December 2008 12:23 To: psi...@li... Subject: Re: [Psidev-pi-dev] FW: Spec doc Hi David, The changes relating the instance docs are coming from the Mascot MS/MS example so these are for you to fix ;-) Eric, are you able to import certain parts of the instance docs from other examples. Element <DatabaseTranslation> could take examples from Mascot_NA_example.axml? I’ll make the other recommended changes to the XSD documentation (some of these require a fix to the generating script, which I’ve flagged to Eric separately). Martin, are you happy for us to make the change relating to peptide mass documentation (see below). >semiSpecific - shouldn't this be a boolean? Agreed, I’ll make this change. ><PlusValue> Eric is right to query this part of the schema. In fact, we’ve used the PropertyValue element only for PlusValue and MinusValue in the entire schema. Let’s make these CV terms: <pf:cvParam accession="PI:00999" name="search tolerance plus value" value=”0.5” cvRef="PSI-PI" unitAccession="UO:0000221" name="dalton" cvRef="UO" /> Andreas can you add: “search tolerance plus value” and “search tolerance minus value” to the CV and mapping file and I’ll change the schema, does this seem reasonable to everyone…? Getting there… Cheers Andy From: Pierre-Alain Binz [mailto:pie...@is...] Sent: 02 December 2008 11:17 To: David Creasy Cc: psi...@li... Subject: Re: [Psidev-pi-dev] FW: Spec doc Hi, David Creasy wrote: Hi Andy, Some minor changes: From: <pf:Person id="PERSON_DOC_OWNER" firstName="" lastName="Some Person" email="so...@so..." <mailto:so...@so...> > to: <pf:Person id="PERSON_DOC_OWNER" firstName="Some" lastName="Person" email="so...@so..." <mailto: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" <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 |
