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From: Jones, A. <And...@li...> - 2008-10-13 14:07:35
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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 |
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From: Jones, A. <And...@li...> - 2009-07-21 12:41:29
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Hi all, The draft of the specification document has been re-generated and is in the SVN and directly linked here: http://code.google.com/p/psi-pi/source/browse/trunk/specification_document/mzIdentML_releaseCandidate1.doc I'm hoping to submit this to the doc process by the end of Friday so can everyone review this carefully. I've picked up one or two things in the auto-generation process that need to be fixed (e.g. remove "pf:" throughout), but I think we can fix these with find and replace. I don't have much time to look at this for a couple of days but I thought I'd get it out now to give everyone as much time as possible for review. Please send minor fixes to me directly or issues for discussion can be posted in a new issue: http://code.google.com/p/psi-pi/issues/detail?id=51 Cheers Andy |
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From: Jones, A. <And...@li...> - 2009-07-22 15:11:18
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Hi all, We had scheduled a conference call for tomorrow afternoon. At the moment, the main outstanding task seems to be reviewing the spec document, so we may not need a call. If anyone would like to discuss any open issues, give me a mail and we’ll hold a brief call tomorrow, Cheers Andy From: Jones, Andy [mailto:And...@li...] Sent: 21 July 2009 13:41 To: 'psi...@li...' Subject: [Psidev-pi-dev] Spec doc Hi all, The draft of the specification document has been re-generated and is in the SVN and directly linked here: http://code.google.com/p/psi-pi/source/browse/trunk/specification_document/mzIdentML_releaseCandidate1.doc I’m hoping to submit this to the doc process by the end of Friday so can everyone review this carefully. I’ve picked up one or two things in the auto-generation process that need to be fixed (e.g. remove “pf:” throughout), but I think we can fix these with find and replace. I don’t have much time to look at this for a couple of days but I thought I’d get it out now to give everyone as much time as possible for review. Please send minor fixes to me directly or issues for discussion can be posted in a new issue: http://code.google.com/p/psi-pi/issues/detail?id=51 Cheers Andy |
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From: Jones, A. <And...@li...> - 2009-07-23 14:38:41
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Hi all, Just to confirm, there will not be a call today, Cheers Andy From: Jones, Andy [mailto:And...@li...] Sent: 22 July 2009 16:11 To: 'psi...@li...' Subject: Re: [Psidev-pi-dev] Spec doc Hi all, We had scheduled a conference call for tomorrow afternoon. At the moment, the main outstanding task seems to be reviewing the spec document, so we may not need a call. If anyone would like to discuss any open issues, give me a mail and we’ll hold a brief call tomorrow, Cheers Andy From: Jones, Andy [mailto:And...@li...] Sent: 21 July 2009 13:41 To: 'psi...@li...' Subject: [Psidev-pi-dev] Spec doc Hi all, The draft of the specification document has been re-generated and is in the SVN and directly linked here: http://code.google.com/p/psi-pi/source/browse/trunk/specification_document/mzIdentML_releaseCandidate1.doc I’m hoping to submit this to the doc process by the end of Friday so can everyone review this carefully. I’ve picked up one or two things in the auto-generation process that need to be fixed (e.g. remove “pf:” throughout), but I think we can fix these with find and replace. I don’t have much time to look at this for a couple of days but I thought I’d get it out now to give everyone as much time as possible for review. Please send minor fixes to me directly or issues for discussion can be posted in a new issue: http://code.google.com/p/psi-pi/issues/detail?id=51 Cheers Andy |
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From: Jones, A. <And...@li...> - 2009-07-24 12:25:02
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Hi all, Quick update on the spec document. Thanks to everyone who has commented so far. I won’t have time to go through it and submit till around Wed next week unfortunately, so if anyone else would like to proof read and comment before Tues, it would be much appreciated, Cheers Andy From: Jones, Andy [mailto:And...@li...] Sent: 23 July 2009 15:39 To: 'psi...@li...' Subject: Re: [Psidev-pi-dev] Spec doc Hi all, Just to confirm, there will not be a call today, Cheers Andy From: Jones, Andy [mailto:And...@li...] Sent: 22 July 2009 16:11 To: 'psi...@li...' Subject: Re: [Psidev-pi-dev] Spec doc Hi all, We had scheduled a conference call for tomorrow afternoon. At the moment, the main outstanding task seems to be reviewing the spec document, so we may not need a call. If anyone would like to discuss any open issues, give me a mail and we’ll hold a brief call tomorrow, Cheers Andy From: Jones, Andy [mailto:And...@li...] Sent: 21 July 2009 13:41 To: 'psi...@li...' Subject: [Psidev-pi-dev] Spec doc Hi all, The draft of the specification document has been re-generated and is in the SVN and directly linked here: http://code.google.com/p/psi-pi/source/browse/trunk/specification_document/mzIdentML_releaseCandidate1.doc I’m hoping to submit this to the doc process by the end of Friday so can everyone review this carefully. I’ve picked up one or two things in the auto-generation process that need to be fixed (e.g. remove “pf:” throughout), but I think we can fix these with find and replace. I don’t have much time to look at this for a couple of days but I thought I’d get it out now to give everyone as much time as possible for review. Please send minor fixes to me directly or issues for discussion can be posted in a new issue: http://code.google.com/p/psi-pi/issues/detail?id=51 Cheers Andy |
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From: Jones, A. <And...@li...> - 2011-06-07 07:36:07
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Hi all, I'm planning to submit the specifications tomorrow afternoon, can anyone who would like to comment please do so by the end of the day if possible. cheers Andy |
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From: Juan A. V. <ju...@eb...> - 2011-06-08 08:29:26
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Hi Andy, Some comments about the spec document. 1. I agree completety with Matt in this point. It seems contradictory: "A PMF search and an MS-MS search of the same sample can be saved in the same instance document as long as the result is one combined protein list." seems to contradict the earlier statement about aggregating evidence between different MS levels. If we can combine multiple MS levels in one protein list, why can't we do it for MS2 and MS3 as well as we can for MS1 and MS2?" 2. Neutral losses. In Heidelberg, Eric and Pierre-Alain suggested to separate the ion type from the neutral loss, e.g. having CV terms "y ion" and "neutral loss H2O" and be able to combine them freely. In the multiple search engines example (at least), the neutral losses are encoded in the way it has been done so far. There are two choices then: leave the examples the way they are today (and change then later) or remove neutral losses from the example files. I am aware that the new CV terms have not been created yet and that the CV is really a mess, so the example files cannot be modified today. In any case, this is quite an important change that will need to be added/ documented properly in the future. 3. I think it would be a good idea to provide with the example files (where possible), the corresponding spectra files that the mzIdentML examples are linking to. For some cases it is quite obvious how the link is done but in other cases it is not so straightforward (for instance .mgf) since it is based in the index in the file. 4. Add the specific accession number for the 'unknown modification' in the MS CV (MS:1001460). 5. As a suggestion, add a diagram explaining the relationships between the key elements in the schema, before the model in XML schema. It would be similar to the figures included in the first version of the mzIdentML publication. I know this is a spec document and not a tutorial, but I think it would be useful. Cheers, Juan On 7 Jun 2011, at 08:35, Jones, Andy wrote: > Hi all, > > I'm planning to submit the specifications tomorrow afternoon, can > anyone who would like to comment please do so by the end of the day > if possible. > cheers > Andy > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
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From: Jones, A. <And...@li...> - 2011-06-08 08:50:40
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Hi all, Thanks for all your comments, I will assemble them today and see if I can get it submitted, or at worst tomorrow, Cheers Andy > -----Original Message----- > From: Juan Antonio Vizcaíno [mailto:ju...@eb...] > Sent: 08 June 2011 09:29 > To: Jones, Andy > Cc: psi...@li... > Subject: Re: [Psidev-pi-dev] Spec doc > > Hi Andy, > > Some comments about the spec document. > > 1. I agree completety with Matt in this point. It seems contradictory: > > "A PMF search and an MS-MS search of the same sample can be saved in > the same instance document > as long as the result is one combined protein list." seems to > contradict the earlier statement about > aggregating evidence between different MS levels. If we can combine > multiple MS levels in one > protein list, why can't we do it for MS2 and MS3 as well as we can for > MS1 and MS2?" > > 2. Neutral losses. In Heidelberg, Eric and Pierre-Alain suggested to > separate the ion type from the neutral loss, e.g. having CV terms "y > ion" and "neutral loss H2O" and be able to combine them freely. In the > multiple search engines example (at least), the neutral losses are > encoded in the way it has been done so far. There are two choices > then: leave the examples the way they are today (and change then > later) or remove neutral losses from the example files. > > I am aware that the new CV terms have not been created yet and that > the CV is really a mess, so the example files cannot be modified today. > > In any case, this is quite an important change that will need to be > added/ documented properly in the future. > > 3. I think it would be a good idea to provide with the example files > (where possible), the corresponding spectra files that the mzIdentML > examples are linking to. For some cases it is quite obvious how the > link is done but in other cases it is not so straightforward (for > instance .mgf) since it is based in the index in the file. > > 4. Add the specific accession number for the 'unknown modification' in > the MS CV (MS:1001460). > > 5. As a suggestion, add a diagram explaining the relationships between > the key elements in the schema, before the model in XML schema. It > would be similar to the figures included in the first version of the > mzIdentML publication. I know this is a spec document and not a > tutorial, but I think it would be useful. > > Cheers, > > Juan > > > > On 7 Jun 2011, at 08:35, Jones, Andy wrote: > > > Hi all, > > > > I'm planning to submit the specifications tomorrow afternoon, can > > anyone who would like to comment please do so by the end of the day > > if possible. > > cheers > > Andy > > ------------------------------------------------------------------------------ > > EditLive Enterprise is the world's most technically advanced content > > authoring tool. Experience the power of Track Changes, Inline Image > > Editing and ensure content is compliant with Accessibility Checking. > > http://p.sf.net/sfu/ephox-dev2dev > > _______________________________________________ > > Psidev-pi-dev mailing list > > Psi...@li... > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > > > > > |
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From: Jones, A. <And...@li...> - 2011-06-08 12:35:34
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Thanks Juan, comments below and I've now updated the altered spec doc, schema and example files. Too all - any further comments by tomorrow please, then I'll submit. Cheers Andy > -----Original Message----- > From: Juan Antonio Vizcaíno [mailto:ju...@eb...] > Sent: 08 June 2011 09:29 > To: Jones, Andy > Cc: psi...@li... > Subject: Re: [Psidev-pi-dev] Spec doc > > Hi Andy, > > Some comments about the spec document. > > 1. I agree completety with Matt in this point. It seems contradictory: > > "A PMF search and an MS-MS search of the same sample can be saved in > the same instance document > as long as the result is one combined protein list." seems to > contradict the earlier statement about > aggregating evidence between different MS levels. If we can combine > multiple MS levels in one > protein list, why can't we do it for MS2 and MS3 as well as we can for > MS1 and MS2?" Yes I removed this part for PMF. > > 2. Neutral losses. In Heidelberg, Eric and Pierre-Alain suggested to > separate the ion type from the neutral loss, e.g. having CV terms "y > ion" and "neutral loss H2O" and be able to combine them freely. In the > multiple search engines example (at least), the neutral losses are > encoded in the way it has been done so far. There are two choices > then: leave the examples the way they are today (and change then > later) or remove neutral losses from the example files. I only see neutral losses in the Mascot file, which doesn't contain fragmentation info in this version, so in which example files is this a problem? > > I am aware that the new CV terms have not been created yet and that > the CV is really a mess, so the example files cannot be modified today. > > In any case, this is quite an important change that will need to be > added/ documented properly in the future. > > 3. I think it would be a good idea to provide with the example files > (where possible), the corresponding spectra files that the mzIdentML > examples are linking to. For some cases it is quite obvious how the > link is done but in other cases it is not so straightforward (for > instance .mgf) since it is based in the index in the file. I have added one MGF file that was used to generate the Mascot, Omssa and Tandem examples. > > 4. Add the specific accession number for the 'unknown modification' in > the MS CV (MS:1001460). Done > > 5. As a suggestion, add a diagram explaining the relationships between > the key elements in the schema, before the model in XML schema. It > would be similar to the figures included in the first version of the > mzIdentML publication. I know this is a spec document and not a > tutorial, but I think it would be useful. Good suggestion, added in section 6 > > Cheers, > > Juan > > > > On 7 Jun 2011, at 08:35, Jones, Andy wrote: > > > Hi all, > > > > I'm planning to submit the specifications tomorrow afternoon, can > > anyone who would like to comment please do so by the end of the day > > if possible. > > cheers > > Andy > > ------------------------------------------------------------------------------ > > EditLive Enterprise is the world's most technically advanced content > > authoring tool. Experience the power of Track Changes, Inline Image > > Editing and ensure content is compliant with Accessibility Checking. > > http://p.sf.net/sfu/ephox-dev2dev > > _______________________________________________ > > Psidev-pi-dev mailing list > > Psi...@li... > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > > > > > |
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From: Matthew C. <mat...@gm...> - 2011-06-08 16:23:58
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Hi Andy, I assume you saw Eric's post that he would change the order of the elements in his automated script and other fixes? Any comments on the type attribute on UserParam? I'd be quite frustrated to have to separate the mzML/traML and mzIdentML param types in pwiz because of a single attribute. -Matt On 6/8/2011 3:50 AM, Jones, Andy wrote: > Hi all, > Thanks for all your comments, I will assemble them today and see if I can get it submitted, or at worst tomorrow, > Cheers > Andy |
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From: Eric D. <ede...@sy...> - 2011-06-08 16:37:45
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Hi Andy, I posted that I have completely refreshed the HTML (and pastable) autogen docs. I hope you saw that. I think that should address all your issues. I also noted a few issues that probably should be fixed and then I can refresh the docs if you like. I agree with Matt on the UserParam issue. Regards, Eric -----Original Message----- From: Matthew Chambers [mailto:mat...@gm...] Sent: Wednesday, June 08, 2011 9:24 AM To: psi...@li... Subject: Re: [Psidev-pi-dev] Spec doc Hi Andy, I assume you saw Eric's post that he would change the order of the elements in his automated script and other fixes? Any comments on the type attribute on UserParam? I'd be quite frustrated to have to separate the mzML/traML and mzIdentML param types in pwiz because of a single attribute. -Matt On 6/8/2011 3:50 AM, Jones, Andy wrote: > Hi all, > Thanks for all your comments, I will assemble them today and see if I can get it submitted, or at worst tomorrow, > Cheers > Andy -------------------------------------------------------------------------- ---- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
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From: Eric D. <ede...@sy...> - 2008-10-17 06:44:06
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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 |
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From: David C. <dc...@ma...> - 2008-10-17 08:43:30
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Hi Eric, <br>
<br>
Eric Deutsch wrote:
<blockquote cite="mid:1FA6C1F2633447F4BED00987D6AF412E@fozzie"
type="cite">
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<div class="Section1">
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;">Hi everyone,
I updated the current draft
of the on-line autogenerated schema docs to the latest svn. The result
is at:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><a moz-do-not-send="true"
href="http://www.peptideatlas.org/tmp/AnalysisXML_working.html">http://www.peptideatlas.org/tmp/AnalysisXML_working.html</a></span></font></p>
</div>
</blockquote>
That's looking great, thanks. I'll be starting to use it rather than
trawling through the schema...<br>
<br>
<blockquote cite="mid:1FA6C1F2633447F4BED00987D6AF412E@fozzie"
type="cite">
<div class="Section1">
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<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">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:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><a moz-do-not-send="true"
href="http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType">http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType</a></span></font></p>
</div>
</blockquote>
Looks like it's going to be a very useful tool once the mapping file is
more complete.<br>
<blockquote cite="mid:1FA6C1F2633447F4BED00987D6AF412E@fozzie"
type="cite">
<div class="Section1">
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">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?</span></font></p>
</div>
</blockquote>
The X Tandem and Omssa examples will be rather similar to the Mascot
ones Since a simple ms-ms search result probably demonstrates the most
common 'use case' it may be the best example for the time being.
Presumably it takes the first occurrence of each element that it sees.
Maybe we should also try and make a 'search engine neutral' example.<br>
<br>
Cheers,<br>
<br>
David<br>
<br>
<blockquote cite="mid:1FA6C1F2633447F4BED00987D6AF412E@fozzie"
type="cite">
<div class="Section1">
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">Regards,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">Eric<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<div
style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0in 0in 0in 4pt;">
<div>
<div class="MsoNormal" style="text-align: center;" align="center"><font
face="Times New Roman" size="3"><span
style="font-size: 12pt; font-family: "Times New Roman";">
<hr tabindex="-1" align="center" size="2" width="100%"></span></font></div>
<p class="MsoNormal"><b><font face="Tahoma" size="2"><span
style="font-size: 10pt; font-family: Tahoma; font-weight: bold;">From:</span></font></b><font
face="Tahoma" size="2"><span
style="font-size: 10pt; font-family: Tahoma;"> Jones, Andy
[<a class="moz-txt-link-freetext" href="mailto:And...@li...">mailto:And...@li...</a>] <br>
<b><span style="font-weight: bold;">Sent:</span></b> Monday, October
13, 2008
7:07 AM<br>
<b><span style="font-weight: bold;">To:</span></b>
<a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br>
<b><span style="font-weight: bold;">Subject:</span></b>
[Psidev-pi-dev] Spec doc</span></font><font face="Times New Roman"
size="3"><span style="font-size: 12pt; font-family: "Times New Roman";"><o:p></o:p></span></font></p>
</div>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">Hi all,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">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... <o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">Main tasks still to do:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="msolistparagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><font
face="Calibri" size="2"><span style="font-size: 11pt;" lang="EN-GB"><span
style="">-<font face="Times New Roman" size="1"><span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></font></span></span></font><!--[endif]--><span lang="EN-GB">Finish
section on use cases when we have finally agreed the list
online and made all the example files.<o:p></o:p></span></p>
<p class="msolistparagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><font
face="Calibri" size="2"><span style="font-size: 11pt;" lang="EN-GB"><span
style="">-<font face="Times New Roman" size="1"><span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></font></span></span></font><!--[endif]--><span lang="EN-GB">Import
some parts of the example files to demonstrate a few specific
points<o:p></o:p></span></p>
<p class="msolistparagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><font
face="Calibri" size="2"><span style="font-size: 11pt;" lang="EN-GB"><span
style="">-<font face="Times New Roman" size="1"><span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></font></span></span></font><!--[endif]--><span lang="EN-GB">Import
the autogenerated documentation<o:p></o:p></span></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">Before we can submit, the main
outstanding issues are:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="msolistparagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><font
face="Calibri" size="2"><span style="font-size: 11pt;" lang="EN-GB"><span
style="">-<font face="Times New Roman" size="1"><span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></font></span></span></font><!--[endif]--><span lang="EN-GB">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<o:p></o:p></span></p>
<p class="msolistparagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><font
face="Calibri" size="2"><span style="font-size: 11pt;" lang="EN-GB"><span
style="">-<font face="Times New Roman" size="1"><span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></font></span></span></font><!--[endif]--><span lang="EN-GB">Mapping
file<o:p></o:p></span></p>
<p class="msolistparagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><font
face="Calibri" size="2"><span style="font-size: 11pt;" lang="EN-GB"><span
style="">-<font face="Times New Roman" size="1"><span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></font></span></span></font><!--[endif]--><span lang="EN-GB">Finish
example files.<o:p></o:p></span></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">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...<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">Also new schema uploaded with a
few bits of improved documentation.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">Cheers<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">Andy<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="margin-left: 0.25in;"><font face="Calibri"
size="2"><span style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
</div>
</div>
<pre wrap="">
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_______________________________________________
Psidev-pi-dev mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Psi...@li...">Psi...@li...</a>
<a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev">https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev</a>
</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
<a class="moz-txt-link-abbreviated" href="mailto:dc...@ma...">dc...@ma...</a>
<a class="moz-txt-link-freetext" href="http://www.matrixscience.com">http://www.matrixscience.com</a>
Matrix Science Ltd. is registered in England and Wales
Company number 3533898</pre>
</body>
</html>
|
|
From: Jones, A. <And...@li...> - 2008-10-17 10:33:57
|
Hi Eric, This looks really good, thanks v much! Not wanting to give you more work... but there’s a few minor things to fix if you get a chance, should be fairly simple I think: - Attributes – if required/optional is unspecified, currently “-“ is shown. XSD default is optional – so replace “-“ with “optional”. - The attributes and documentation for FuGE elements is not being extracted e.g. Organization. If this is a big headache you could always generate a separate document for FuGElight and I’ll manually compile them? - Documentation missing where elements have been referenced as sub-elements e.g. AnalysisSoftwareList à AnalysisSoftware and all references to FuGE elements of this type say “?!?” 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 |
|
From: Martin E. <mar...@ru...> - 2008-11-05 14:29:45
|
Hi all! I made minor changes and medium-sized additions to the spec doc (with "Track Changes"). I hope, my svn commit does not conflict with someone's local copy (then tell me for merging). Bye Martin Von: Jones, Andy [mailto:And...@li...] Gesendet: Friday, October 17, 2008 12:34 PM An: psi...@li... Betreff: Re: [Psidev-pi-dev] Spec doc Hi Eric, This looks really good, thanks v much! Not wanting to give you more work... but there's a few minor things to fix if you get a chance, should be fairly simple I think: - Attributes - if required/optional is unspecified, currently "-" is shown. XSD default is optional - so replace "-" with "optional". - The attributes and documentation for FuGE elements is not being extracted e.g. Organization. If this is a big headache you could always generate a separate document for FuGElight and I'll manually compile them? - Documentation missing where elements have been referenced as sub-elements e.g. AnalysisSoftwareList --> AnalysisSoftware and all references to FuGE elements of this type say "?!?" 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 |
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