Re: [Psidev-pi-dev] Representing Sequences

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Hi Andy,<br>
<br>
length may be useful, because some people won't want to output the
actual sequence for space reasons. The other things we wanted to add
before were pI and mass. <br>
Why do we want name? Is this for, say, a description line?<br>
(Also, identifier -&gt; id?)<br>
<br>
David<br>
<br>
Jones, Andy wrote:
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  <div class="Section1">
  <p class="MsoNormal">Hi all,<o:p></o:p></p>
  <p class="MsoNormal"><o:p>&nbsp;</o:p></p>
  <p class="MsoNormal">It was decided on the call that we would like to
flag that
Sequences in the ConceptualMoleculeCollection should have a Boolean
attribute to
capture if they are decoy sequences. At the moment we are using the
FuGE:Sequence element. I don&#8217;t really want to add another attribute to
this (it&#8217;s less problematic cutting down FuGE than adding new things),
so
I&#8217;m wondering if we should define our own Sequence type in AnalysisXML.
This would also allow us to choose exactly the relevant attributes. At
the
moment, Sequence can have all of the following:<o:p></o:p></p>
  <p class="MsoNormal"><o:p>&nbsp;</o:p></p>
  <p class="MsoNormal"><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: black; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
  </span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">&lt;</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: maroon; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">pf:Sequence</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: red; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">
isCircular</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">="</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: black; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">true</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">"</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: red; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">
sequence</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">="</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: black; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">String</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">"</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: red; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">
length</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">="</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: black; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">0</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">"</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: red; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">
isApproximateLength</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">="</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: black; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">true</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">"</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: red; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">
SequenceAnnotationSet_ref</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">="</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: black; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">String</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">"</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: red; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">
start</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">="</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: black; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">0</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">"</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: red; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">
end</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">="</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: black; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">0</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">"</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: red; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">
identifier</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">="</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: black; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">String</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">"</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: red; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">
name</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">="</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: black; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">String</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">"&gt;</span><span
 style="font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue;"><o:p></o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue;"><o:p>&nbsp;</o:p></span></p>
  <p class="MsoNormal">Several of these attributes were created to
represent
concepts that probably will never be required or implemented in
AnalysisXML. How
about the following:<o:p></o:p></p>
  <p class="MsoNormal"><o:p>&nbsp;</o:p></p>
  <p class="MsoNormal">&lt;DBSequence identifier = &#8220;&#8221; name = &#8220;&#8221;
isDecoy = &#8220;true&#8221;&gt;<o:p></o:p></p>
  <p class="MsoNormal">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;seq&gt;MCTMG...&lt;/seq&gt;<o:p></o:p></p>
  <p class="MsoNormal">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">&lt;</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: maroon; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">pf:DatabaseReference</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: red; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">
Database_ref</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">=""</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: red; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">
accession</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">="Rev_</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: black; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">IPI00013808.1</span><span
 style="background: white none repeat scroll 0%; font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">"/&gt;</span><span
 style="font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue;"><o:p></o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue;">&lt;/DBSequence&gt;<o:p></o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;; color: blue;"><o:p>&nbsp;</o:p></span></p>
  <p class="MsoNormal">Are any of the other attributes on Sequence
actually
required? I&#8217;ll post a new version of the schema with other changes WRT
to
PeptideEvidence shortly,<o:p></o:p></p>
  <p class="MsoNormal">Cheers<o:p></o:p></p>
  <p class="MsoNormal">Andy<o:p></o:p></p>
  <p class="MsoNormal"><o:p>&nbsp;</o:p></p>
  <p class="MsoNormal"><o:p>&nbsp;</o:p></p>
  <p class="MsoNormal"><o:p>&nbsp;</o:p></p>
  <p class="MsoNormal"><o:p>&nbsp;</o:p></p>
  <p class="MsoNormal"><o:p>&nbsp;</o:p></p>
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