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From: Jones, A. <And...@li...> - 2008-06-27 13:37:55
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Hi all,
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't really want to add another attribute to this (it's less problematic cutting down FuGE than adding new things), so I'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:
<pf:Sequence isCircular="true" sequence="String" length="0" isApproximateLength="true" SequenceAnnotationSet_ref="String" start="0" end="0" identifier="String" name="String">
Several of these attributes were created to represent concepts that probably will never be required or implemented in AnalysisXML. How about the following:
<DBSequence identifier = "" name = "" isDecoy = "true">
<seq>MCTMG...</seq>
<pf:DatabaseReference Database_ref="" accession="Rev_IPI00013808.1"/>
</DBSequence>
Are any of the other attributes on Sequence actually required? I'll post a new version of the schema with other changes WRT to PeptideEvidence shortly,
Cheers
Andy
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From: David C. <dc...@ma...> - 2008-06-27 13:50:41
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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 -> id?)<br>
<br>
David<br>
<br>
Jones, Andy wrote:
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<p class="MsoNormal">Hi all,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </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’t really want to add another attribute to
this (it’s less problematic cutting down FuGE than adding new things),
so
I’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> </o:p></p>
<p class="MsoNormal"><span
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</span><span
style="background: white none repeat scroll 0%; font-size: 12pt; font-family: "Times New Roman","serif"; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;"><</span><span
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isCircular</span><span
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sequence</span><span
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style="background: white none repeat scroll 0%; font-size: 12pt; font-family: "Times New Roman","serif"; color: black; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">String</span><span
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length</span><span
style="background: white none repeat scroll 0%; font-size: 12pt; font-family: "Times New Roman","serif"; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">="</span><span
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isApproximateLength</span><span
style="background: white none repeat scroll 0%; font-size: 12pt; font-family: "Times New Roman","serif"; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">="</span><span
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SequenceAnnotationSet_ref</span><span
style="background: white none repeat scroll 0%; font-size: 12pt; font-family: "Times New Roman","serif"; 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: "Times New Roman","serif"; 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: "Times New Roman","serif"; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">"</span><span
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start</span><span
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style="background: white none repeat scroll 0%; font-size: 12pt; font-family: "Times New Roman","serif"; 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: "Times New Roman","serif"; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">"</span><span
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end</span><span
style="background: white none repeat scroll 0%; font-size: 12pt; font-family: "Times New Roman","serif"; 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: "Times New Roman","serif"; color: black; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">0</span><span
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style="background: white none repeat scroll 0%; font-size: 12pt; font-family: "Times New Roman","serif"; 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: "Times New Roman","serif"; 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: "Times New Roman","serif"; 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: "Times New Roman","serif"; 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: "Times New Roman","serif"; 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: "Times New Roman","serif"; 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: "Times New Roman","serif"; 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: "Times New Roman","serif"; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">"></span><span
style="font-size: 12pt; font-family: "Times New Roman","serif"; color: blue;"><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 12pt; font-family: "Times New Roman","serif"; color: blue;"><o:p> </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> </o:p></p>
<p class="MsoNormal"><DBSequence identifier = “” name = “”
isDecoy = “true”><o:p></o:p></p>
<p class="MsoNormal"> <seq>MCTMG...</seq><o:p></o:p></p>
<p class="MsoNormal"> <span
style="background: white none repeat scroll 0%; font-size: 12pt; font-family: "Times New Roman","serif"; 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: "Times New Roman","serif"; 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: "Times New Roman","serif"; 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: "Times New Roman","serif"; 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: "Times New Roman","serif"; 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: "Times New Roman","serif"; 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: "Times New Roman","serif"; 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: "Times New Roman","serif"; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">"/></span><span
style="font-size: 12pt; font-family: "Times New Roman","serif"; color: blue;"><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 12pt; font-family: "Times New Roman","serif"; color: blue;"></DBSequence><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 12pt; font-family: "Times New Roman","serif"; color: blue;"><o:p> </o:p></span></p>
<p class="MsoNormal">Are any of the other attributes on Sequence
actually
required? I’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> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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From: Phil J. @ E. <pj...@eb...> - 2008-06-27 13:58:09
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Hi, The suggested solution looks good. The main issue will be the need for some very clear and accessible documentation of how to use the format in this context. I know this is self evident, however the identification of proteins is particularly prone to misuse. For example, for a UniProt protein entry there is: a protein accession (e.g. Q12345) ... which may have a version number (e.g. Q12345.1) ... and / or a splice variant number (e.g. Q12345-1 a protein ID (e.g. A4_HUMAN) a human-readable description line. So it needs to be clear, probably with examples for all the major protein sequence databases, how this should be encoded using the suggested format. The 'name' attribute is potentially most open to abuse, as this could reasonably be interpreted as being either the protein ID or the description line (in the UniProt example). best regards, Phil. 2008/6/27 Jones, Andy <And...@li...>: > Hi all, > > > > 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't really want to add another attribute to this (it's less > problematic cutting down FuGE than adding new things), so I'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: > > > > <pf:Sequence isCircular="true" sequence="String"length > ="0" isApproximateLength="true" SequenceAnnotationSet_ref="String" start=" > 0" end="0" identifier="String" name="String"> > > > > Several of these attributes were created to represent concepts that > probably will never be required or implemented in AnalysisXML. How about the > following: > > > > <DBSequence identifier = "" name = "" isDecoy = "true"> > > <seq>MCTMG...</seq> > > <pf:DatabaseReference Database_ref="" accession="Rev_ > IPI00013808.1"/> > > </DBSequence> > > > > Are any of the other attributes on Sequence actually required? I'll post a > new version of the schema with other changes WRT to PeptideEvidence shortly, > > Cheers > > Andy > > > > > > > > > > > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://sourceforge.net/services/buy/index.php > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > -- Phil Jones Senior Software Engineer PRIDE Project Team PANDA Group, EMBL-EBI Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SD UK. Work phone: +44 1223 492610 Skype: philip-jones |
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From: Pierre-Alain B. <pie...@is...> - 2008-06-27 15:15:35
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format-version: 1.0 date: 23:04:2008 10:40 saved-by: pab auto-generated-by: OBO-Edit 1.101 default-namespace: PSI-DB remark: When appropriate the definition and synonyms of a term are reported exactly as in the chapter 12 of IUPAC orange book. See http://www.iupac.org/projects/2003/2003-056-2-500.html. [Term] id: DB:0000001 name: Common Sequence Database Format Controlled Vocabulary def: "Common Sequence Database Format Controlled Vocabulary." [PSI:DB] [Term] id: DB:0000002 name: File Header Section def: "Common Sequence Database Format File Header Section." [PSI:DB] is_a: DB:0000001 ! CV root term [Term] id: DB:0000003 name: Individual Sequence Entry Section def: "Common Sequence Database Format Individual Entry Section." [PSI:DB] is_a: DB:0000001 ! CV root term [Term] id: DB:0000004 name: DbName def: "Sequence Database Name." [PSI:DB] is_a: DB:0000002 ! File Header Section term [Term] id: DB:0000005 name: Prefix def: "Sequence Database Prefix." [PSI:DB] is_a: DB:0000002 ! File Header Section term [Term] id: DB:0000006 name: DbDescription def: "Sequence Database Short description." [PSI:DB] is_a: DB:0000002 ! File Header Section term [Term] id: DB:0000007 name: Decoy def: "Speciofies whether the Sequence Database is a Decoy." [PSI:DB] is_a: DB:0000002 ! File Header Section term [Term] id: DB:0000008 name: DbSource def: "Source of the database file." [PSI:DB] is_a: DB:0000002 ! File Header Section term [Term] id: DB:0000009 name: DbVersion def: "Database version (release date) according to database provider." [PSI:DB] is_a: DB:0000002 ! File Header Section term [Term] id: DB:0000010 name: DbDate def: "Database date (release or file date of the source) according to database provider." [PSI:DB] is_a: DB:0000002 ! File Header Section term is: obsolete [Term] id: DB:0000011 name: NumberOfEntries def: "Number of sequence entries in the database." [PSI:DB] is_a: DB:0000002 ! File Header Section term [Term] id: DB:0000012 name: Conversion def: "Description of the conversion from original format to this current one." [PSI:DB] is_a: DB:0000002 ! File Header Section term [Term] id: DB:0000013 name: SequenceType def: "Molecular type of the sequences." [PSI:DB] is_a: DB:0000002 ! File Header Section term [Term] id: DB:0000014 name: SpecificKey def: "Db specific information (not included in the current list of allowed keys)." [PSI:DB] is_a: DB:0000002 ! File Header Section term [Term] id: DB:0000015 name: SpecificValue def: "DB specific values for a defined key." [PSI:DB] is_a: DB:0000002 ! File Header Section term [Term] id: DB:0001001 name: DbUniqueId def: "Sequence Database unique indentifier." [PSI:DB] is_a: DB:0000003 ! Individual Entry Section term [Term] id: DB:0001002 name: PName def: "Protein Name, description." [PSI:DB] is_a: DB:0000003 ! Individual Entry Section term [Term] id: DB:0001003 name: NcbiTaxId def: "NCBI taxonomy identifier." [PSI:DB] is_a: DB:0000003 ! Individual Entry Section term [Term] id: DB:0001004 name: TaxName def: "Taxonomy name (latin or common name)." [PSI:DB] is_a: DB:0000003 ! Individual Entry Section term [Term] id: DB:0001005 name: GName def: "Gene name." [PSI:DB] is_a: DB:0000003 ! Individual Entry Section term [Term] id: DB:0001006 name: Length def: "Sequence length." [PSI:DB] is_a: DB:0000003 ! Individual Entry Section term [Term] id: DB:0001007 name: SV def: "Sequence version." [PSI:DB] is_a: DB:0000003 ! Individual Entry Section term [Term] id: DB:0001008 name: EV def: "Entry version." [PSI:DB] is_a: DB:0000003 ! Individual Entry Section term [Term] id: DB:0001009 name: PE def: "Protein Evidence; A UniprotKB code." [PSI:DB] is_a: DB:0000003 ! Individual Entry Section term [Term] id: DB:0001010 name: Processed def: "Processed Molecule." [PSI:DB] is_a: DB:0000003 ! Individual Entry Section term [Term] id: DB:0001011 name: Variant def: "Sequence variation (substitution, insertion, deletion)." [PSI:DB] is_a: DB:0000003 ! Individual Entry Section term [Term] id: DB:0001012 name: ModResPsi def: "Modified residue with PSI-MOD identifier." [PSI:DB] is_a: DB:0000003 ! Individual Entry Section term [Term] id: DB:0001013 name: ModRes def: "Modified residue without PSI-MOD identifier." [PSI:DB] is_a: DB:0000003 ! Individual Entry Section term [Term] id: DB:0001014 name: AltAC def: "Alternative Accession Code." [PSI:DB] is_a: DB:0000003 ! Individual Entry Section term |
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