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From: David C. <dc...@ma...> - 2008-07-30 03:59:55
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Hi Andy,<br>
<br>
Thanks for the recent changes to the schema. You asked a question:<br>
<span style="font-size: 11pt; font-family: Calibri;" lang="EN-GB">Added</span><span
style="font-size: 12pt; font-family: "Times New Roman"; color: black;"
lang="EN-GB"><span style=""> </span></span><span
style="font-size: 12pt; font-family: "Times New Roman"; color: rgb(0, 0, 150);"
lang="EN-GB"><xsd:attribute</span><span
style="font-size: 12pt; font-family: "Times New Roman"; color: rgb(245, 132, 76);"
lang="EN-GB"> name</span><span
style="font-size: 12pt; font-family: "Times New Roman"; color: rgb(255, 128, 64);"
lang="EN-GB">=</span><span
style="font-size: 12pt; font-family: "Times New Roman"; color: rgb(153, 51, 0);"
lang="EN-GB">"SearchDatabase_ref"</span><span
style="font-size: 12pt; font-family: "Times New Roman"; color: rgb(245, 132, 76);"
lang="EN-GB"> type</span><span
style="font-size: 12pt; font-family: "Times New Roman"; color: rgb(255, 128, 64);"
lang="EN-GB">=</span><span
style="font-size: 12pt; font-family: "Times New Roman"; color: rgb(153, 51, 0);"
lang="EN-GB">"xsd:string"</span><span
style="font-size: 12pt; font-family: "Times New Roman"; color: rgb(0, 0, 150);"
lang="EN-GB">/> </span><span
style="font-size: 11pt; font-family: Calibri;" lang="EN-GB">to
DBSequence and </span><span
style="font-size: 12pt; font-family: "Times New Roman"; color: rgb(0, 0, 150);"
lang="EN-GB"><xsd:attribute</span><span
style="font-size: 12pt; font-family: "Times New Roman"; color: rgb(245, 132, 76);"
lang="EN-GB"> name</span><span
style="font-size: 12pt; font-family: "Times New Roman"; color: rgb(255, 128, 64);"
lang="EN-GB">=</span><span
style="font-size: 12pt; font-family: "Times New Roman"; color: rgb(153, 51, 0);"
lang="EN-GB">"accession"</span><span
style="font-size: 12pt; font-family: "Times New Roman"; color: rgb(245, 132, 76);"
lang="EN-GB"> type</span><span
style="font-size: 12pt; font-family: "Times New Roman"; color: rgb(255, 128, 64);"
lang="EN-GB">=</span><span
style="font-size: 12pt; font-family: "Times New Roman"; color: rgb(153, 51, 0);"
lang="EN-GB">"xsd:string"</span><span
style="font-size: 12pt; font-family: "Times New Roman"; color: rgb(0, 0, 150);"
lang="EN-GB">/> </span><span
style="font-size: 11pt; font-family: Calibri;" lang="EN-GB">should
either/both of these be set as required?<u><br>
<br>
</u>I think that the answer has to be yes. However, in the
MPC_use_case_working_temp.axml file, there is: SearchDatabase_ref="",
so maybe Martin could comment?<br>
<br>
</span><br>
And under<br>
<small><small><tt><big><big> <AnalysisCollection><br>
<SpectrumIdentification ... ><br>
</big></big><br>
</tt></small></small>you made the change from<br>
<small><small><tt><big><big> <SpectraData_ref id="SD_1"/><br>
<SearchDatabase_ref id="SDB_SwissProt"/><br>
</big></big></tt></small></small>to <br>
<small><small><tt><big><big> <SpectraData_ref ref="SD_1"/><br>
<SearchDatabase SearchDatabase_ref="SDB_SwissProt"/><br>
</big></big></tt><big><big><br>
which maybe isn't as consistent as you intended - or maybe I have
missed the point?<br>
There is also still a : <br>
<SpectrumIdentificationList_ref ref=...<br>
<br>
cvList is fine, except it can only be a list of exactly 1 item at the
moment... (I've not fixed the schema).<br>
<br>
I didn't notice it last time, but the schema doesn't validate with
xerces:<br>
Need to change (in 2 places):<br>
</big></big></small></small><small><small><big><big><xsd:pattern
value="[ABCDEFGHIJKLMNOPQRSTUVWXYZ?-]{1}"/><br>
</big></big></small></small>to<br>
<small><small><big><big><xsd:pattern
value="[ABCDEFGHIJKLMNOPQRSTUVWXYZ?\-]{1}"/><br>
</big></big></small></small><small><small><big><big>(I've not updated
the schema in svn - or checked to see if xerces is correct).<br>
<br>
Thanks,<br>
<br>
David<br>
<br>
</big></big></small></small>
<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>
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From: Jones, A. <And...@li...> - 2008-07-30 08:24:04
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Hi David,
There is also still a :
<SpectrumIdentificationList_ref ref=...
Okay we should have a quick discussion about this on Thursday. The rule used in FuGE is that the element name is whatever you want, but the attribute that does the reference is called: objectBeingReferenced_ref – this way it is simple to write a parser to check that the correct element is referenced. I’m fairly sure we agreed to do this previously in a call, (although it’s less important if we have Key/KeyRefs), but I would have a slight preference to follow the rule.
I’ll make the other fixes later today,
Cheers
Andy
From: psi...@li... [mailto:psi...@li...] On Behalf Of David Creasy
Sent: 30 July 2008 05:00
To: psi...@li...
Subject: [Psidev-pi-dev] Changes to schema on 29th July 2008
Hi Andy,
Thanks for the recent changes to the schema. You asked a question:
Added <xsd:attribute name="SearchDatabase_ref" type="xsd:string"/> to DBSequence and <xsd:attribute name="accession" type="xsd:string"/> should either/both of these be set as required?
I think that the answer has to be yes. However, in the MPC_use_case_working_temp.axml file, there is: SearchDatabase_ref="", so maybe Martin could comment?
And under
<AnalysisCollection>
<SpectrumIdentification ... >
you made the change from
<SpectraData_ref id="SD_1"/>
<SearchDatabase_ref id="SDB_SwissProt"/>
to
<SpectraData_ref ref="SD_1"/>
<SearchDatabase SearchDatabase_ref="SDB_SwissProt"/>
which maybe isn't as consistent as you intended - or maybe I have missed the point?
There is also still a :
<SpectrumIdentificationList_ref ref=...
cvList is fine, except it can only be a list of exactly 1 item at the moment... (I've not fixed the schema).
I didn't notice it last time, but the schema doesn't validate with xerces:
Need to change (in 2 places):
<xsd:pattern value="[ABCDEFGHIJKLMNOPQRSTUVWXYZ?-]{1}"/>
to
<xsd:pattern value="[ABCDEFGHIJKLMNOPQRSTUVWXYZ?\-]{1}"/>
(I've not updated the schema in svn - or checked to see if xerces is correct).
Thanks,
David
--
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
dc...@ma...
http://www.matrixscience.com
Matrix Science Ltd. is registered in England and Wales
Company number 3533898
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From: Martin E. <mar...@ru...> - 2008-07-31 10:49:15
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Hi David, hi all!
Mh, I cannot find a MPC_use_case_working_temp.axml (where have you found it?);
the latest is MPC_use_case_working27June.axml and it has no empty SearchDatabase_ref.
But I think SearchDatabase_ref should be optional in the <Inputs> because of non-database searches.
Andy added SearchDatabase_ref and accession into <DBSequence> and there it
makes sense to make them mandatory (because it is “DB”sequence).
It would be more human-readable to have:
<SpectraData ref="SD_1"/>
<SearchDatabase ref="SDB_SwissProt"/>
but I agree with Andy it maybe more FuGe and more validatable to have
<SpectraData SpectraData_ref="SD_1"/>
<SearchDatabase SearchDatabase_ref="SDB_SwissProt"/>
(For some seconds I thought to move them to attributes but we have potentially more than one.)
Bye
Martin
Von: psi...@li... [mailto:psi...@li...] Im Auftrag von David Creasy
Gesendet: Wednesday, July 30, 2008 6:00 AM
An: psi...@li...
Betreff: [Psidev-pi-dev] Changes to schema on 29th July 2008
Hi Andy,
Thanks for the recent changes to the schema. You asked a question:
Added <xsd:attribute name="SearchDatabase_ref" type="xsd:string"/> to DBSequence and <xsd:attribute name="accession" type="xsd:string"/> should either/both of these be set as required?
I think that the answer has to be yes. However, in the MPC_use_case_working_temp.axml file, there is: SearchDatabase_ref="", so maybe Martin could comment?
And under
<AnalysisCollection>
<SpectrumIdentification ... >
you made the change from
<SpectraData_ref id="SD_1"/>
<SearchDatabase_ref id="SDB_SwissProt"/>
to
<SpectraData_ref ref="SD_1"/>
<SearchDatabase SearchDatabase_ref="SDB_SwissProt"/>
which maybe isn't as consistent as you intended - or maybe I have missed the point?
There is also still a :
<SpectrumIdentificationList_ref ref=...
cvList is fine, except it can only be a list of exactly 1 item at the moment... (I've not fixed the schema).
I didn't notice it last time, but the schema doesn't validate with xerces:
Need to change (in 2 places):
<xsd:pattern value="[ABCDEFGHIJKLMNOPQRSTUVWXYZ?-]{1}"/>
to
<xsd:pattern value="[ABCDEFGHIJKLMNOPQRSTUVWXYZ?\-]{1}"/>
(I've not updated the schema in svn - or checked to see if xerces is correct).
Thanks,
David
--
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
dc...@ma...
http://www.matrixscience.com
Matrix Science Ltd. is registered in England and Wales
Company number 3533898
|
|
From: David C. <dc...@ma...> - 2008-07-31 12:14:32
|
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Hi Martin, Andy<br>
<br>
It's in schema_usecase_examples\working29July - probably added by Andy
actually.<br>
And yes, of course you are right about it being optional. (Could you
add a note to the documentation as to why it's optional)<br>
<br>
Sorry about that Andy, could you undo those changes.<br>
<br>
And while you are there, could you allow multiple TranslationTable
entries under DatabaseTranslationFrames?<br>
I've added a Mascot_NA_example.xml to
examples\schema_usecase_examples\working29July. <br>
I also think that we should change the name from
DatabaseTranslationFrames to DatabaseTranslation:<br>
<br>
<small><small><tt> <DatabaseTranslationFrames
frames="1,2,3,4,5,6"><br>
<TranslationTable id="0" name="Unspecified"><br>
<pf:cvParam accession="PI:00025" name="translation table"
cvRef="PSI-PI" value="" /><br>
</TranslationTable><br>
<TranslationTable id="1" name="Standard"><br>
<pf:cvParam accession="PI:00025" name="translation table"
cvRef="PSI-PI"
value="FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
" /><br>
</TranslationTable><br>
<TranslationTable id="2" name="Vertebrate Mitochondrial"><br>
<pf:cvParam accession="PI:00025" name="translation table"
cvRef="PSI-PI"
value="FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG
" /><br>
...<br>
</tt></small></small><br>
Since I've actually included the table, there is no need to reference
the NCBI ontology (which doesn't exist), and this then also copes with
the custom case? Can we also allow multiple cv items in the translation
table so the start codons can be specified?<br>
If anyone sees a problem, let me know otherwise I'll change the
example, add details to the wiki documentation and sign off issue #24<br>
<br>
Thanks,<br>
David<br>
<br>
Martin Eisenacher wrote:
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<p class="MsoNormal"><font color="black" face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB">Hi David, hi all!<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><span class="SpellE"><font color="black"
face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB">Mh</span></font></span><font face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB">, I cannot
find a <span class="SpellE">MPC_use_case_working_temp.axml</span>
(where have you
found it?); <o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB">the latest is MPC_use_case_working27June.axml
and it has no empty <span class="SpellE">SearchDatabase_ref</span>.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB">But I think <span class="SpellE">SearchDatabase_ref</span>
should be optional in the <Inputs> because of non-database
searches.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB">Andy added <span class="SpellE">SearchDatabase_ref</span>
and accession into <<span class="SpellE">DBSequence</span>> and
there it <o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB">makes sense to make them mandatory (because
it is “<span class="SpellE">DB”sequence</span>).<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB">It would be more human-readable to
have:<o:p></o:p></span></font></p>
<p class="MsoNormal"><tt><font color="black" face="Courier New"
size="4"><span style="font-size: 13.5pt;" lang="EN-US"><<span
class="SpellE">SpectraData</span> ref="SD_1"/></span></font></tt><font
face="Courier New" size="4"><span
style="font-size: 13.5pt; font-family: "Courier New";" lang="EN-US"><br>
<tt><font face="Courier New"><span style=""><<span class="SpellE">SearchDatabase</span>
ref="<span class="SpellE">SDB_SwissProt</span>"/><o:p></o:p></span></font></tt></span></font></p>
<p class="MsoNormal"><font color="black" face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB">but I agree with Andy it maybe more <span class="SpellE">FuGe</span>
and more <span class="SpellE">validatable</span> to have<br>
<<span class="SpellE">SpectraData</span> <span class="SpellE">SpectraData_ref</span>="SD_1"/><br>
<<span class="SpellE">SearchDatabase</span> <span
class="SpellE">SearchDatabase_ref</span>="<span class="SpellE">SDB_SwissProt</span>"/><br
style="">
<!--[if !supportLineBreakNewLine]--><br style="">
<!--[endif]--><o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB">(For some seconds I thought to move
them to attributes but we have potentially more than one.)<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB"><span style=""> </span>Bye<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB"><span style="">
</span>Martin<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB"><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: 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><font color="black" face="Tahoma" size="2"><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext; font-weight: bold;">Von:</span></font></b><font
color="black" face="Tahoma" size="2"><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;">
<a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a>
[<a class="moz-txt-link-freetext" href="mailto:psi...@li...">mailto:psi...@li...</a>] <b><span
style="font-weight: bold;">Im Auftrag von </span></b>David Creasy<br>
<b><span style="font-weight: bold;">Gesendet:</span></b> Wednesday,
July 30, 2008
6:00 AM<br>
<b><span style="font-weight: bold;">An:</span></b>
<a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br>
<b><span style="font-weight: bold;">Betreff:</span></b>
[Psidev-pi-dev] Changes
to schema on 29th July 2008<o:p></o:p></span></font></p>
</div>
</div>
<p class="MsoNormal"><font color="black" face="Times New Roman"
size="3"><span style="font-size: 12pt;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Times New Roman"
size="3"><span style="font-size: 12pt;">Hi Andy,<br>
<br>
Thanks for the recent changes to the schema. You asked a question:<br>
</span></font><font face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB">Added</span></font><span style="" lang="EN-GB">
</span><font color="#000096"><span style="color: rgb(0, 0, 150);"
lang="EN-GB"><xsd:attribute</span></font><font color="#f5844c"><span
style="color: rgb(245, 132, 76);" lang="EN-GB"> name</span></font><font
color="#ff8040"><span style="color: rgb(255, 128, 64);" lang="EN-GB">=</span></font><font
color="#993300"><span style="color: rgb(153, 51, 0);" lang="EN-GB">"SearchDatabase_ref"</span></font><font
color="#f5844c"><span style="color: rgb(245, 132, 76);" lang="EN-GB">
type</span></font><font color="#ff8040"><span
style="color: rgb(255, 128, 64);" lang="EN-GB">=</span></font><font
color="#993300"><span style="color: rgb(153, 51, 0);" lang="EN-GB">"xsd:string"</span></font><font
color="#000096"><span style="color: rgb(0, 0, 150);" lang="EN-GB">/>
</span></font><font face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB">to
DBSequence and </span></font><font color="#000096"><span
style="color: rgb(0, 0, 150);" lang="EN-GB"><xsd:attribute</span></font><font
color="#f5844c"><span style="color: rgb(245, 132, 76);" lang="EN-GB">
name</span></font><font color="#ff8040"><span
style="color: rgb(255, 128, 64);" lang="EN-GB">=</span></font><font
color="#993300"><span style="color: rgb(153, 51, 0);" lang="EN-GB">"accession"</span></font><font
color="#f5844c"><span style="color: rgb(245, 132, 76);" lang="EN-GB">
type</span></font><font color="#ff8040"><span
style="color: rgb(255, 128, 64);" lang="EN-GB">=</span></font><font
color="#993300"><span style="color: rgb(153, 51, 0);" lang="EN-GB">"xsd:string"</span></font><font
color="#000096"><span style="color: rgb(0, 0, 150);" lang="EN-GB">/>
</span></font><font face="Calibri" size="2"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif";"
lang="EN-GB">should either/both
of these be set as required?<u><br>
<br>
</u>I think that the answer has to be yes. However, in the
MPC_use_case_working_temp.axml file, there is: SearchDatabase_ref="",
so maybe Martin could comment?<br>
<br>
</span></font><span style=""><br>
And under<br>
</span><tt><font face="Courier New" size="4"><span
style="font-size: 13.5pt;">
<AnalysisCollection></span></font></tt><font face="Courier New"
size="4"><span style="font-size: 13.5pt; font-family: "Courier New";"><br>
<tt><font face="Courier New"><span style="">
<SpectrumIdentification ... ></span></font></tt><br>
</span></font><font face="Courier New" size="2"><span
style="font-size: 10pt; font-family: "Courier New";"><br>
</span></font><span style="">you made
the change from<br>
</span><tt><font face="Courier New" size="4"><span
style="font-size: 13.5pt;">
<SpectraData_ref id="SD_1"/></span></font></tt><font
face="Courier New" size="4"><span
style="font-size: 13.5pt; font-family: "Courier New";"><br>
<tt><font face="Courier New"><span style="">
<SearchDatabase_ref
id="SDB_SwissProt"/></span></font></tt><br>
</span></font><span style="">to <br>
</span><tt><font face="Courier New" size="4"><span
style="font-size: 13.5pt;">
<SpectraData_ref ref="SD_1"/></span></font></tt><font
face="Courier New" size="4"><span
style="font-size: 13.5pt; font-family: "Courier New";"><br>
<tt><font face="Courier New"><span style=""> <SearchDatabase
SearchDatabase_ref="SDB_SwissProt"/></span></font></tt><br>
</span></font><span style=""><br>
which maybe isn't as consistent as you intended - or maybe I have
missed the
point?<br>
There is also still a : <br>
<SpectrumIdentificationList_ref ref=...<br>
<br>
cvList is fine, except it can only be a list of exactly 1 item at the
moment...
(I've not fixed the schema).<br>
<br>
I didn't notice it last time, but the schema doesn't validate with
xerces:<br>
Need to change (in 2 places):<br>
<xsd:pattern value="[ABCDEFGHIJKLMNOPQRSTUVWXYZ?-]{1}"/><br>
to<br>
<xsd:pattern value="[ABCDEFGHIJKLMNOPQRSTUVWXYZ?\-]{1}"/><br>
(I've not updated the schema in svn - or checked to see if xerces is
correct).<br>
<br>
Thanks,<br>
<br>
David<br>
<br style="">
<!--[if !supportLineBreakNewLine]--><br style="">
<!--[endif]--><o:p></o:p></span></p>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">-- <o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">David Creasy<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">Matrix Science<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">64 Baker Street<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">London W1U 7GB, UK<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">Tel: +44 (0)20 7486 1050<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">Fax: +44 (0)20 7224 1344<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;"><o:p> </o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;"><a moz-do-not-send="true"
href="mailto:dc...@ma...">dc...@ma...</a><o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;"><a moz-do-not-send="true"
href="http://www.matrixscience.com">http://www.matrixscience.com</a><o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;"><o:p> </o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span
style="font-size: 10pt;">Matrix Science Ltd. is registered in England and Wales<o:p></o:p></span></font></pre>
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style="font-size: 10pt;">Company number 3533898<o:p></o:p></span></font></pre>
</div>
</div>
</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>
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From: Jones, A. <And...@li...> - 2008-07-31 12:31:54
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Hi all,
I only made SearchDatabase mandatory on DBSequence, so I think this is okay?
And while you are there, could you allow multiple TranslationTable entries under DatabaseTranslationFrames?
I've added a Mascot_NA_example.xml to examples\schema_usecase_examples\working29July.
I also think that we should change the name from DatabaseTranslationFrames to DatabaseTranslation:
Done.
I also think that we should change the name from DatabaseTranslationFrames to DatabaseTranslation
Done.
Since I've actually included the table, there is no need to reference the NCBI ontology (which doesn't exist), and this then also copes with the custom case? Can we also allow multiple cv items in the translation table so the start codons can be specified?
If anyone sees a problem, let me know otherwise I'll change the example, add details to the wiki documentation and sign off issue #24
i.e. Make the reference to CVParam 0..*? Done.
Speak at 4, cheers
Andy
From: psi...@li... [mailto:psi...@li...] On Behalf Of David Creasy
Sent: 31 July 2008 13:15
To: Martin Eisenacher
Cc: psi...@li...
Subject: Re: [Psidev-pi-dev] Changes to schema on 29th July 2008
Hi Martin, Andy
It's in schema_usecase_examples\working29July - probably added by Andy actually.
And yes, of course you are right about it being optional. (Could you add a note to the documentation as to why it's optional)
Sorry about that Andy, could you undo those changes.
And while you are there, could you allow multiple TranslationTable entries under DatabaseTranslationFrames?
I've added a Mascot_NA_example.xml to examples\schema_usecase_examples\working29July.
I also think that we should change the name from DatabaseTranslationFrames to DatabaseTranslation:
<DatabaseTranslationFrames frames="1,2,3,4,5,6">
<TranslationTable id="0" name="Unspecified">
<pf:cvParam accession="PI:00025" name="translation table" cvRef="PSI-PI" value="" />
</TranslationTable>
<TranslationTable id="1" name="Standard">
<pf:cvParam accession="PI:00025" name="translation table" cvRef="PSI-PI" value="FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG " />
</TranslationTable>
<TranslationTable id="2" name="Vertebrate Mitochondrial">
<pf:cvParam accession="PI:00025" name="translation table" cvRef="PSI-PI" value="FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG " />
...
Since I've actually included the table, there is no need to reference the NCBI ontology (which doesn't exist), and this then also copes with the custom case? Can we also allow multiple cv items in the translation table so the start codons can be specified?
If anyone sees a problem, let me know otherwise I'll change the example, add details to the wiki documentation and sign off issue #24
Thanks,
David
Martin Eisenacher wrote:
Hi David, hi all!
Mh, I cannot find a MPC_use_case_working_temp.axml (where have you found it?);
the latest is MPC_use_case_working27June.axml and it has no empty SearchDatabase_ref.
But I think SearchDatabase_ref should be optional in the <Inputs> because of non-database searches.
Andy added SearchDatabase_ref and accession into <DBSequence> and there it
makes sense to make them mandatory (because it is “DB”sequence).
It would be more human-readable to have:
<SpectraData ref="SD_1"/>
<SearchDatabase ref="SDB_SwissProt"/>
but I agree with Andy it maybe more FuGe and more validatable to have
<SpectraData SpectraData_ref="SD_1"/>
<SearchDatabase SearchDatabase_ref="SDB_SwissProt"/>
(For some seconds I thought to move them to attributes but we have potentially more than one.)
Bye
Martin
Von: psi...@li... [mailto:psi...@li...] Im Auftrag von David Creasy
Gesendet: Wednesday, July 30, 2008 6:00 AM
An: psi...@li...
Betreff: [Psidev-pi-dev] Changes to schema on 29th July 2008
Hi Andy,
Thanks for the recent changes to the schema. You asked a question:
Added <xsd:attribute name="SearchDatabase_ref" type="xsd:string"/> to DBSequence and <xsd:attribute name="accession" type="xsd:string"/> should either/both of these be set as required?
I think that the answer has to be yes. However, in the MPC_use_case_working_temp.axml file, there is: SearchDatabase_ref="", so maybe Martin could comment?
And under
<AnalysisCollection>
<SpectrumIdentification ... >
you made the change from
<SpectraData_ref id="SD_1"/>
<SearchDatabase_ref id="SDB_SwissProt"/>
to
<SpectraData_ref ref="SD_1"/>
<SearchDatabase SearchDatabase_ref="SDB_SwissProt"/>
which maybe isn't as consistent as you intended - or maybe I have missed the point?
There is also still a :
<SpectrumIdentificationList_ref ref=...
cvList is fine, except it can only be a list of exactly 1 item at the moment... (I've not fixed the schema).
I didn't notice it last time, but the schema doesn't validate with xerces:
Need to change (in 2 places):
<xsd:pattern value="[ABCDEFGHIJKLMNOPQRSTUVWXYZ?-]{1}"/>
to
<xsd:pattern value="[ABCDEFGHIJKLMNOPQRSTUVWXYZ?\-]{1}"/>
(I've not updated the schema in svn - or checked to see if xerces is correct).
Thanks,
David
--
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
dc...@ma...
http://www.matrixscience.com
Matrix Science Ltd. is registered in England and Wales
Company number 3533898
--
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
dc...@ma...
http://www.matrixscience.com
Matrix Science Ltd. is registered in England and Wales
Company number 3533898
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