Menu
▾
▴
Re: [Psidev-pi-dev] AnalysisXML PMF Example
|
From: David C. <dc...@ma...> - 2008-10-17 15:10:22
|
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=windows-1252"
http-equiv="Content-Type">
<title></title>
</head>
<body bgcolor="#ffffff" text="#000000">
Ah yes... fixed now.<br>
(The examples don't contain real fragment masses yet - I'm just working
on this now).<br>
<br>
David<br>
<br>
Jones, Andy wrote:
<blockquote
cite="mid:08D...@EV..."
type="cite">
<meta http-equiv="Content-Type" content="text/html; ">
<meta name="Generator" content="Microsoft Word 12 (filtered medium)">
<style>
<!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:Consolas;
panose-1:2 11 6 9 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";
color:black;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
pre
{mso-style-priority:99;
mso-style-link:"HTML Preformatted Char";
margin:0cm;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";
color:black;}
p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
{mso-style-priority:34;
margin-top:0cm;
margin-right:0cm;
margin-bottom:0cm;
margin-left:36.0pt;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";
color:black;}
span.HTMLPreformattedChar
{mso-style-name:"HTML Preformatted Char";
mso-style-priority:99;
mso-style-link:"HTML Preformatted";
font-family:Consolas;
color:black;}
span.EmailStyle20
{mso-style-type:personal;
font-family:"Calibri","sans-serif";
color:#1F497D;}
span.EmailStyle21
{mso-style-type:personal;
font-family:"Calibri","sans-serif";
color:#1F497D;}
span.EmailStyle22
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page Section1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.Section1
{page:Section1;}
/* List Definitions */
@list l0
{mso-list-id:1008412603;
mso-list-type:hybrid;
mso-list-template-ids:1479431520 -1359946526 134807555 134807557 134807553 134807555 134807557 134807553 134807555 134807557;}
@list l0:level1
{mso-level-start-at:0;
mso-level-number-format:bullet;
mso-level-text:-;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:"Calibri","sans-serif";
mso-fareast-font-family:Calibri;
mso-bidi-font-family:"Times New Roman";}
@list l0:level2
{mso-level-tab-stop:72.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level3
{mso-level-tab-stop:108.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level4
{mso-level-tab-stop:144.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level5
{mso-level-tab-stop:180.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level6
{mso-level-tab-stop:216.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level7
{mso-level-tab-stop:252.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level8
{mso-level-tab-stop:288.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
@list l0:level9
{mso-level-tab-stop:324.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;}
ol
{margin-bottom:0cm;}
ul
{margin-bottom:0cm;}
-->
</style>
<!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<div class="Section1">
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Another
minor schema update: added Key KeyRef for Measures
within FragmentArray.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">The
FragmentationTable was missing from the Mascot example
(sorry David!). Here is what it should look like:<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">
<SpectrumIdentificationList id="SIL_1"
numSequencesSearched="71412"><br>
<FragmentationTable><br>
<Measure id="m_mz"><br>
<pf:cvParam cvRef="PSI-PI" accession="PI:00225"
name="product ion m/z"/><br>
</Measure><br>
<Measure id="m_intensity"><br>
<pf:cvParam cvRef="PSI-PI" accession="PI:00226"
name="product ion intensity"/><br>
</Measure> <br>
</FragmentationTable><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Also
made a few minor additions to the spec doc.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Cheers<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Andy<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></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: 0cm 0cm 0cm 4pt;">
<div>
<div
style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">
Jones, Andy [<a class="moz-txt-link-freetext" href="mailto:And...@li...">mailto:And...@li...</a>] <br>
<b>Sent:</b> 17 October 2008 13:17<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br>
<b>Subject:</b> Re: [Psidev-pi-dev] AnalysisXML PMF Example<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">A
few more minor schema changes – no changes to instance docs
needed:<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><span
style="">-<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></span></span><!--[endif]--><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Generally
added bits of documentation after reviewing the
autogenerated docs from Eric<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><span
style="">-<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></span></span><!--[endif]--><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Changed
the data type on MassTable-residue from xsd:string to a
single character A-Z, seem reasonable?<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><span
style="">-<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></span></span><!--[endif]--><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Added
some docs to FuGElight<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">There
is another change I want to make which won’t affect any
current instances but does place an extra restriction.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Currently
AnalysisCollection references pf:ProtocolApplication
and AnalysisProtocolCollection references pf:Protocol, so any
subclasses of
these can be used – including FuGE GenericProtocol and
GenericProtocolApplication (which we don’t want to support in version
1). <o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">We
also have an abstract AnalysisProtocol and
AnalysisProtocolApplication in the schema which we aren’t using. I
would like
to remove all the attributes from AnalysisProtocol and
AnalysisProtocolApplication, just leaving documentation explaining that
this is
an extension point from which new Protocols or ProtocolApplications
will be
added in later versions.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">AnalysisCollection
would then reference
AnalysisProtocolApplication, of which the only available subclasses are
SpectrumIdentification and ProteinDetection (new analyses may be added
in v 2) and
AnalysisProtocolCollection would reference AnalysisProtocol.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">This
won’t affect current instances but is a reasonable
structural change so I wanted to circulate it to the list before I make
this
change – if I don’t hear any dissent I’ll change this.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Cheers<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Andy<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></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: 0cm 0cm 0cm 4pt;">
<div>
<div
style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">
Jones, Andy [<a class="moz-txt-link-freetext" href="mailto:And...@li...">mailto:And...@li...</a>] <br>
<b>Sent:</b> 16 October 2008 17:26<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br>
<b>Subject:</b> Re: [Psidev-pi-dev] AnalysisXML PMF Example<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">New
schema uploaded by SVN with changes agreed on the call:<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">-
Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to
handle PMF data)<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">-
Altered documentation for SpectrumIdentificationItem to
clarify that this is a single peptide-spectrum identification<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">-
Altered documentation for SpectrumIdentificationResult – one
SpectrumIdentificationResult for one spectrum<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">-
Moved spectrumID and SpectraData_ref as attributes of
SpectrumIdentificationResult, and made these composite unique, removed
SpectrumElement<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Andy<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></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: 0cm 0cm 0cm 4pt;">
<div>
<div
style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">
Pierre-Alain Binz [<a class="moz-txt-link-freetext" href="mailto:pie...@is...">mailto:pie...@is...</a>] <br>
<b>Sent:</b> 16 October 2008 14:26<br>
<b>To:</b> Jones, Andy<br>
<b>Cc:</b> <a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br>
<b>Subject:</b> Re: [Psidev-pi-dev] AnalysisXML PMF Example<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Actually, there might be a score associated with
each
peptide - peak couple, similar to "weights" that coulld be attributed
to a specific fragment ion match in a MS/MS spectrum. But at the end,
even if a
software goes through this, and maybe scores the peptides in an
intermediary
process, it will at the end always link a spectrum with one or more
molecule(s)
(in the case of PMF the molecule(s) is(are) proteins). It can annotate
the
spectrum, either with potential peptides of fragments, respectively.
Anyway, we
have not encoded any scores to the interpretation of fragment ions in
MS/MS
spectra. Similarly, we wouldn't do it for PMF. Annotation is the sole
point of
discussion, which I think we want to postone for v2, right?<br>
<br>
<br>
Pierre-Alain<br>
<br>
Jones, Andy wrote: <o:p></o:p></p>
<pre>Ah, I was getting confused, I was thinking that there would be one<o:p></o:p></pre>
<pre>SpectrumIdentificationItem for one Spectrum, in fact there is one for each<o:p></o:p></pre>
<pre>peptide.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>The problem with the way it's encoded (probably the only way possible without a<o:p></o:p></pre>
<pre>schema change) is that it's not obvious how to tie together all the results from<o:p></o:p></pre>
<pre>a single spectrum-protein identification. Even querying for the same spectrumID<o:p></o:p></pre>
<pre>will not resolve it, since there may be multiple ranked spectrum-protein<o:p></o:p></pre>
<pre>identifications from the same spectrum.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>I suggest we look at this in the call, I think we might need an alteration to<o:p></o:p></pre>
<pre>the schema to model PMF more intuitively, unless I've misunderstood something.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Cheers<o:p></o:p></pre>
<pre>Andy<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre> <o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre> <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>-----Original Message-----<o:p></o:p></pre>
<pre>From: David Creasy [<a moz-do-not-send="true"
href="mailto:dc...@ma...">mailto:dc...@ma...</a>]<o:p></o:p></pre>
<pre>Sent: 16 October 2008 13:54<o:p></o:p></pre>
<pre>To: <a moz-do-not-send="true"
href="mailto:psi...@li...">psi...@li...</a><o:p></o:p></pre>
<pre>Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Hi Andy,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>For PMF, with Mascot, (and all other search engines as far as I know),<o:p></o:p></pre>
<pre>there is no score assigned to matching a single peak to an individual<o:p></o:p></pre>
<pre>peptide. A score for one peak in isolation would have little meaning -<o:p></o:p></pre>
<pre>you can only really score the match of the complete spectrum.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>David<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Jones, Andy wrote:<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>Hi David,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>You may be right that the parameter should be optionally anyway, but in this<o:p></o:p></pre>
<pre>particular example is there not some score assigned to the peptide-spectrum<o:p></o:p></pre>
<pre>identification?<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>In the equivalent MS/MS example, we have:<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre> <pf:cvParam accession="PI:00171" name="mascot:score"<o:p></o:p></pre>
<pre>cvRef="PSI-PI" value="62.72" /><o:p></o:p></pre>
<pre> <pf:cvParam accession="PI:00172" name="mascot:expectation value"<o:p></o:p></pre>
<pre>cvRef="PSI-PI" value="0.000863428353297988" /><o:p></o:p></pre>
<pre> <pf:cvParam accession="PI:99999" name="mascot_rank"<o:p></o:p></pre>
<pre>cvRef="PSI-PI" value="1" /><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Are the same sort of scores not valid for PMF as well...?<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Cheers<o:p></o:p></pre>
<pre>Andy<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre> <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>-----Original Message-----<o:p></o:p></pre>
<pre>From: David Creasy [<a moz-do-not-send="true"
href="mailto:dc...@ma...">mailto:dc...@ma...</a>]<o:p></o:p></pre>
<pre>Sent: 16 October 2008 12:29<o:p></o:p></pre>
<pre>To: <a moz-do-not-send="true"
href="mailto:psi...@li...">psi...@li...</a><o:p></o:p></pre>
<pre>Subject: [Psidev-pi-dev] AnalysisXML PMF Example<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Hi All,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>There's an example PMF file here:<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><a moz-do-not-send="true"
href="http://code.google.com/p/psi">http://code.google.com/p/psi</a>-<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
</blockquote>
</blockquote>
<pre>pi/source/browse/trunk/examples/PMF_example.axml<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>The only small problem that I can see is that for<o:p></o:p></pre>
<pre> <SpectrumIdentificationItem><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>the schema has:<o:p></o:p></pre>
<pre> <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0"<o:p></o:p></pre>
<pre>maxOccurs="unbounded"/><o:p></o:p></pre>
<pre> <xsd:element ref="pf:Param" maxOccurs="unbounded"/><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>and I can't think of any required CV here<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>To find it, search for<o:p></o:p></pre>
<pre><pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt<o:p></o:p></pre>
<pre>to say here here"<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>I suggest that we have minOccurs=0 for pfParam here unless anyone<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
</blockquote>
</blockquote>
<pre>disagrees?<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>David<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>--<o:p></o:p></pre>
<pre>David Creasy<o:p></o:p></pre>
<pre>Matrix Science<o:p></o:p></pre>
<pre>64 Baker Street<o:p></o:p></pre>
<pre>London W1U 7GB, UK<o:p></o:p></pre>
<pre>Tel: +44 (0)20 7486 1050<o:p></o:p></pre>
<pre>Fax: +44 (0)20 7224 1344<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><a moz-do-not-send="true"
href="mailto:dc...@ma...">dc...@ma...</a><o:p></o:p></pre>
<pre><a moz-do-not-send="true"
href="http://www.matrixscience.com">http://www.matrixscience.com</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Matrix Science Ltd. is registered in England and Wales<o:p></o:p></pre>
<pre>Company number 3533898<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>-------------------------------------------------------------------------<o:p></o:p></pre>
<pre>This SF.Net email is sponsored by the Moblin Your Move Developer's<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
</blockquote>
</blockquote>
<pre>challenge<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>Build the coolest Linux based applications with Moblin SDK & win great<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
</blockquote>
</blockquote>
</blockquote>
<pre>prizes<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>Grand prize is a trip for two to an Open Source event anywhere in the world<o:p></o:p></pre>
<pre><a moz-do-not-send="true"
href="http://moblin-contest.org/redirect.php?banner_id=100&url=/">http://moblin-contest.org/redirect.php?banner_id=100&url=/</a><o:p></o:p></pre>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Psidev-pi-dev mailing list<o:p></o:p></pre>
<pre><a moz-do-not-send="true"
href="mailto:Psi...@li...">Psi...@li...</a><o:p></o:p></pre>
<pre><a moz-do-not-send="true"
href="https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev">https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev</a><o:p></o:p></pre>
<pre> <o:p></o:p></pre>
</blockquote>
<pre>-------------------------------------------------------------------------<o:p></o:p></pre>
<pre>This SF.Net email is sponsored by the Moblin Your Move Developer's challenge<o:p></o:p></pre>
<pre>Build the coolest Linux based applications with Moblin SDK & win great<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
</blockquote>
</blockquote>
<pre>prizes<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>Grand prize is a trip for two to an Open Source event anywhere in the world<o:p></o:p></pre>
<pre><a moz-do-not-send="true"
href="http://moblin-contest.org/redirect.php?banner_id=100&url=/">http://moblin-contest.org/redirect.php?banner_id=100&url=/</a><o:p></o:p></pre>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Psidev-pi-dev mailing list<o:p></o:p></pre>
<pre><a moz-do-not-send="true"
href="mailto:Psi...@li...">Psi...@li...</a><o:p></o:p></pre>
<pre><a moz-do-not-send="true"
href="https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev">https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev</a><o:p></o:p></pre>
<pre> <o:p></o:p></pre>
</blockquote>
<pre>--<o:p></o:p></pre>
<pre>David Creasy<o:p></o:p></pre>
<pre>Matrix Science<o:p></o:p></pre>
<pre>64 Baker Street<o:p></o:p></pre>
<pre>London W1U 7GB, UK<o:p></o:p></pre>
<pre>Tel: +44 (0)20 7486 1050<o:p></o:p></pre>
<pre>Fax: +44 (0)20 7224 1344<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><a moz-do-not-send="true"
href="mailto:dc...@ma...">dc...@ma...</a><o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="http://www.matrixscience.com">http://www.matrixscience.com</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Matrix Science Ltd. is registered in England and Wales<o:p></o:p></pre>
<pre>Company number 3533898<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>-------------------------------------------------------------------------<o:p></o:p></pre>
<pre>This SF.Net email is sponsored by the Moblin Your Move Developer's challenge<o:p></o:p></pre>
<pre>Build the coolest Linux based applications with Moblin SDK & win great prizes<o:p></o:p></pre>
<pre>Grand prize is a trip for two to an Open Source event anywhere in the world<o:p></o:p></pre>
<pre><a moz-do-not-send="true"
href="http://moblin-contest.org/redirect.php?banner_id=100&url=/">http://moblin-contest.org/redirect.php?banner_id=100&url=/</a><o:p></o:p></pre>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Psidev-pi-dev mailing list<o:p></o:p></pre>
<pre><a moz-do-not-send="true"
href="mailto:Psi...@li...">Psi...@li...</a><o:p></o:p></pre>
<pre><a moz-do-not-send="true"
href="https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev">https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev</a><o:p></o:p></pre>
<pre> <o:p></o:p></pre>
</blockquote>
<pre><o:p> </o:p></pre>
<pre>-------------------------------------------------------------------------<o:p></o:p></pre>
<pre>This SF.Net email is sponsored by the Moblin Your Move Developer's challenge<o:p></o:p></pre>
<pre>Build the coolest Linux based applications with Moblin SDK & win great prizes<o:p></o:p></pre>
<pre>Grand prize is a trip for two to an Open Source event anywhere in the world<o:p></o:p></pre>
<pre><a moz-do-not-send="true"
href="http://moblin-contest.org/redirect.php?banner_id=100&url=/">http://moblin-contest.org/redirect.php?banner_id=100&url=/</a><o:p></o:p></pre>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Psidev-pi-dev mailing list<o:p></o:p></pre>
<pre><a moz-do-not-send="true"
href="mailto:Psi...@li...">Psi...@li...</a><o:p></o:p></pre>
<pre><a moz-do-not-send="true"
href="https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev">https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre> <o:p></o:p></pre>
</div>
</div>
</div>
</div>
<pre wrap="">
<hr size="4" width="90%">
-------------------------------------------------------------------------
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
<a class="moz-txt-link-freetext" href="http://moblin-contest.org/redirect.php?banner_id=100&url=/">http://moblin-contest.org/redirect.php?banner_id=100&url=/</a></pre>
<pre wrap="">
<hr size="4" width="90%">
_______________________________________________
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>
|
