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From: Jennifer S. <jen...@ma...> - 2008-12-11 17:22:07
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Hi, Please find the minutes of todays teleconference here: http://www.psidev.info/index.php?q=node/400 Thanks, Jenny -- Dr. Jennifer Siepen Research Associate University of Manchester Faculty of Life Sciences Michael Smith Building Manchester M13 9PT Tel: 0161 275 1680 |
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From: Jones, A. <And...@li...> - 2008-12-11 17:32:27
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New schema uploaded by SVN: Made rank attribute mandatory. Added attribute passThreshold to SpectrumIdentificationItem and ProteinDetectionHypothesis. > -----Original Message----- > From: Jennifer Siepen [mailto:jen...@ma...] > Sent: 11 December 2008 17:22 > To: psi...@li... > Subject: [Psidev-pi-dev] Minutes of Telecon. 11th December > > Hi, > > Please find the minutes of todays teleconference here: > > http://www.psidev.info/index.php?q=node/400 > > Thanks, > > Jenny > > -- > > Dr. Jennifer Siepen > Research Associate > University of Manchester > Faculty of Life Sciences > Michael Smith Building > Manchester > M13 9PT > > Tel: 0161 275 1680 > > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > The future of the web can't happen without you. Join us at MIX09 to help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
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From: Eric D. <ede...@sy...> - 2008-12-11 18:30:06
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Hi everyone, I have just regenerated the docs based on the latest xsd, cv, mapping, examples in SVN: http://www.peptideatlas.org/tmp/AnalysisXML_working.html There is still a known issue that some definitions are not quite being pulled out of the xsd correctly, i.e. if a element has several definitions depending on its context, one of the definitions is presented, but not necessarily the correct one in that context. This will be fixed sometime. Note also that the embedded figures have not been updated in a while and might not be optimal. If someone sends me updates figures, I'll add. The version suitable for pasting into a Word doc is: http://www.peptideatlas.org/tmp/AnalysisXML_working_simple.html Regards, Eric > -----Original Message----- > From: Jones, Andy [mailto:And...@li...] > Sent: Thursday, December 11, 2008 9:32 AM > To: psi...@li... > Subject: Re: [Psidev-pi-dev] Minutes of Telecon. 11th December > > New schema uploaded by SVN: > > Made rank attribute mandatory. > > Added attribute passThreshold to SpectrumIdentificationItem and > ProteinDetectionHypothesis. > > > > > -----Original Message----- > > From: Jennifer Siepen [mailto:jen...@ma...] > > Sent: 11 December 2008 17:22 > > To: psi...@li... > > Subject: [Psidev-pi-dev] Minutes of Telecon. 11th December > > > > Hi, > > > > Please find the minutes of todays teleconference here: > > > > http://www.psidev.info/index.php?q=node/400 > > > > Thanks, > > > > Jenny > > > > -- > > > > Dr. Jennifer Siepen > > Research Associate > > University of Manchester > > Faculty of Life Sciences > > Michael Smith Building > > Manchester > > M13 9PT > > > > Tel: 0161 275 1680 > > > > > > ------------------------------------------------------------------------ > ------ > > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, > Nevada. > > The future of the web can't happen without you. Join us at MIX09 to > help > > pave the way to the Next Web now. Learn more and register at > > > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.co > m/ > > _______________________________________________ > > Psidev-pi-dev mailing list > > Psi...@li... > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > -------------------------------------------------------------------------- > ---- > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, > Nevada. > The future of the web can't happen without you. Join us at MIX09 to help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.co > m/ > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
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From: David C. <dc...@ma...> - 2008-12-14 22:39:06
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The Mascot examples have been updated and validate against the schema. Andreas, I'm not sure why, but I get this from the validator: Validation against the schema: Error at file Mascot_MSMS_example.axml, line 691, char 193 Message: attribute 'passThreshold' is not declared for element 'SpectrumIdentificationItem' But it is? I must be missing something subtle! Also, for PMF I get: Error: CV term used in invalid element: 'PI:00362 - number of unmatched peaks' at element '/AnalysisXML/DataCollection/AnalysisData/ProteinDetectionList/ProteinAmbiguityGroup/ProteinDetectionHypothesis' But I think I have put it in the correct place. Or maybe not... Thanks, David Jones, Andy wrote: > New schema uploaded by SVN: > > Made rank attribute mandatory. > > Added attribute passThreshold to SpectrumIdentificationItem and > ProteinDetectionHypothesis. > > > >> -----Original Message----- >> From: Jennifer Siepen [mailto:jen...@ma...] >> Sent: 11 December 2008 17:22 >> To: psi...@li... >> Subject: [Psidev-pi-dev] Minutes of Telecon. 11th December >> >> Hi, >> >> Please find the minutes of todays teleconference here: >> >> http://www.psidev.info/index.php?q=node/400 >> >> Thanks, >> >> Jenny >> >> -- >> >> Dr. Jennifer Siepen >> Research Associate >> University of Manchester >> Faculty of Life Sciences >> Michael Smith Building >> Manchester >> M13 9PT >> >> Tel: 0161 275 1680 >> >> >> ------------------------------------------------------------------------------ >> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. >> The future of the web can't happen without you. Join us at MIX09 to help >> pave the way to the Next Web now. Learn more and register at >> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ >> _______________________________________________ >> Psidev-pi-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > The future of the web can't happen without you. Join us at MIX09 to help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- 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: Andreas B. <be...@in...> - 2008-12-15 10:38:28
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Hi David, hi all, > The Mascot examples have been updated and validate against the schema. > > Andreas, I'm not sure why, but I get this from the validator: > > Validation against the schema: > Error at file Mascot_MSMS_example.axml, line 691, char 193 Message: > attribute 'passThreshold' is not declared for element > 'SpectrumIdentificationItem' > But it is? I must be missing something subtle! Sorry, the schema for validation was not up-to-date. > Also, for PMF I get: > > Error: CV term used in invalid element: 'PI:00362 - number of unmatched > peaks' at element > '/AnalysisXML/DataCollection/AnalysisData/ProteinDetectionList/ProteinAmbig >uityGroup/ProteinDetectionHypothesis' But I think I have put it in the > correct place. Or maybe not... You're right. I've updated the cv and added the parent PI:00116 "single protein result details". All allowed terms for a specific location in the schema can be found at "http://www-bs2.informatik.uni- tuebingen.de/services/OpenMS/analysisXML/mapping_and_cv.html" everything which is not listed here, will probably not validate! Best, A. -- Div. for Simulation of Biological Systems, WSI, University of Tuebingen Room C322, Sand 14, 72076 Tuebingen, Germany phone: +49-7071-29-70461 fax: +49-7071-29-5152 http://www-bs.informatik.uni-tuebingen.de |
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From: Jones, A. <And...@li...> - 2008-12-15 14:03:15
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Hi Andreas, I've just looked through the mapping file and I think we have some errors in how it's being implemented at the moment. Each mapping has the requirementLevel set as "MAY", which means that the terms are optional and should not throw an error if they are not provided. I think most of these should be set as "MUST" with a few exceptions e.g. GenericMaterial (where descriptive terms could come from anywhere), which should be set as "MAY"? Also, throughout we have the attribute cvTermsCombinationLogic set as "OR". This means that only one of the terms listed can be provided. Some of these should definitely be "AND" e.g. AdditionalSearchParams. I would guess that they should all be set to "AND" by default. If only one term should be provided, this is almost certainly checked in the schema anyway e.g. SearchType. I can't think of any other examples where we want to use an OR for restricting the terms that can be selected. I think this attribute was added to the mapping file XSD in essence to encode some ontology logic for mzML that couldn't be done in OBO. Each term has the attribute isRepeatable set to true at the moment. By default, I think all of these should be set to false (Documentation: "Value is 'True' when a term can be repeated in the same instance of the associated XML element.") Cheers Andy > -----Original Message----- > From: Andreas Bertsch [mailto:be...@in...] > Sent: 15 December 2008 10:40 > To: psi...@li... > Subject: Re: [Psidev-pi-dev] Minutes of Telecon. 11th December > > Hi David, hi all, > > > The Mascot examples have been updated and validate against the schema. > > > > Andreas, I'm not sure why, but I get this from the validator: > > > > Validation against the schema: > > Error at file Mascot_MSMS_example.axml, line 691, char 193 Message: > > attribute 'passThreshold' is not declared for element > > 'SpectrumIdentificationItem' > > But it is? I must be missing something subtle! > Sorry, the schema for validation was not up-to-date. > > > Also, for PMF I get: > > > > Error: CV term used in invalid element: 'PI:00362 - number of unmatched > > peaks' at element > > '/AnalysisXML/DataCollection/AnalysisData/ProteinDetectionList/ProteinAmbig > >uityGroup/ProteinDetectionHypothesis' But I think I have put it in the > > correct place. Or maybe not... > You're right. I've updated the cv and added the parent PI:00116 "single > protein result details". > > All allowed terms for a specific location in the schema can be found at > "http://www-bs2.informatik.uni- > tuebingen.de/services/OpenMS/analysisXML/mapping_and_cv.html" everything > which > is not listed here, will probably not validate! > > Best, > A. > > > > -- > Div. for Simulation of Biological Systems, WSI, University of Tuebingen > Room C322, Sand 14, 72076 Tuebingen, Germany > phone: +49-7071-29-70461 fax: +49-7071-29-5152 > http://www-bs.informatik.uni-tuebingen.de > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > The future of the web can't happen without you. Join us at MIX09 to help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
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From: Jones, A. <And...@li...> - 2008-12-15 14:11:12
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> Also, throughout we have the attribute cvTermsCombinationLogic set as "OR". > This > means that only one of the terms listed can be provided. Some of these should > definitely be "AND" e.g. AdditionalSearchParams. I would guess that they should > all be set to "AND" by default. If only one term should be provided, this is > almost certainly checked in the schema anyway e.g. SearchType. I can't think of > any other examples where we want to use an OR for restricting the terms that can > be selected. I think this attribute was added to the mapping file XSD in essence > to encode some ontology logic for mzML that couldn't be done in OBO. Hmm, maybe I'm wrong about the purpose of AND and OR here, since there is also an XOR option. > -----Original Message----- > From: Jones, Andy [mailto:And...@li...] > Sent: 15 December 2008 14:03 > To: Andreas Bertsch; psi...@li... > Subject: Re: [Psidev-pi-dev] Minutes of Telecon. 11th December > > Hi Andreas, > > I've just looked through the mapping file and I think we have some errors in how > it's being implemented at the moment. Each mapping has the requirementLevel set > as "MAY", which means that the terms are optional and should not throw an error > if they are not provided. > > I think most of these should be set as "MUST" with a few exceptions e.g. > GenericMaterial (where descriptive terms could come from anywhere), which > should > be set as "MAY"? > > Also, throughout we have the attribute cvTermsCombinationLogic set as "OR". > This > means that only one of the terms listed can be provided. Some of these should > definitely be "AND" e.g. AdditionalSearchParams. I would guess that they should > all be set to "AND" by default. If only one term should be provided, this is > almost certainly checked in the schema anyway e.g. SearchType. I can't think of > any other examples where we want to use an OR for restricting the terms that can > be selected. I think this attribute was added to the mapping file XSD in essence > to encode some ontology logic for mzML that couldn't be done in OBO. > > Each term has the attribute isRepeatable set to true at the moment. By default, > I think all of these should be set to false (Documentation: "Value is 'True' > when a term can be repeated in the same instance of the associated XML > element.") > > > Cheers > Andy > > > > > > > > > > > > > > > > -----Original Message----- > > From: Andreas Bertsch [mailto:be...@in...] > > Sent: 15 December 2008 10:40 > > To: psi...@li... > > Subject: Re: [Psidev-pi-dev] Minutes of Telecon. 11th December > > > > Hi David, hi all, > > > > > The Mascot examples have been updated and validate against the schema. > > > > > > Andreas, I'm not sure why, but I get this from the validator: > > > > > > Validation against the schema: > > > Error at file Mascot_MSMS_example.axml, line 691, char 193 Message: > > > attribute 'passThreshold' is not declared for element > > > 'SpectrumIdentificationItem' > > > But it is? I must be missing something subtle! > > Sorry, the schema for validation was not up-to-date. > > > > > Also, for PMF I get: > > > > > > Error: CV term used in invalid element: 'PI:00362 - number of unmatched > > > peaks' at element > > > '/AnalysisXML/DataCollection/AnalysisData/ProteinDetectionList/ProteinAmbig > > >uityGroup/ProteinDetectionHypothesis' But I think I have put it in the > > > correct place. Or maybe not... > > You're right. I've updated the cv and added the parent PI:00116 "single > > protein result details". > > > > All allowed terms for a specific location in the schema can be found at > > "http://www-bs2.informatik.uni- > > tuebingen.de/services/OpenMS/analysisXML/mapping_and_cv.html" everything > > which > > is not listed here, will probably not validate! > > > > Best, > > A. > > > > > > > > -- > > Div. for Simulation of Biological Systems, WSI, University of Tuebingen > > Room C322, Sand 14, 72076 Tuebingen, Germany > > phone: +49-7071-29-70461 fax: +49-7071-29-5152 > > http://www-bs.informatik.uni-tuebingen.de > > > > ------------------------------------------------------------------------------ > > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > > The future of the web can't happen without you. Join us at MIX09 to help > > pave the way to the Next Web now. Learn more and register at > > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > > _______________________________________________ > > Psidev-pi-dev mailing list > > Psi...@li... > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > The future of the web can't happen without you. Join us at MIX09 to help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
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From: Jones, A. <And...@li...> - 2008-12-15 14:03:25
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Hi all,
I want to insert the following text into the spec document but the first example
probably will not validate, since this would not be counted as a valid mapping
for AdditionalSearchParams:
<pf:cvParam accession="PI:00364" name="pep:global FDR" cvRef="PSI-PI" value =
"0.01"/>
Can we update this mapping or someone suggest a suitable example CV term for
setting a threshold for peptide-spectrum matches.
Also, feel free to suggest any amendments to this text.
Cheers
Andy
7.1.4 Reporting peptide and protein identifications passing a significance
threshold
The elements <SpectrumIdentificationItem> and <ProteinDetectionHypothesis> have
a mandatory Boolean attribute passThreshold that allows a file producer to
indicate that an identification has passed a given threshold or that it has been
manually validated. Depending on the intended purpose of the file, the file
producer MAY wish to report a number of identifications that fall below the
given significance threshold, for example to allow global statistics to be
performed which is not possible if only identifications passing the threshold
are reported. If the file producer does not want to indicate that a threshold
has been set, all identifications MUST have passThreshold = “true”. Thresholds
for peptide-spectrum matches or for protein identification can be encoded as
instances of <cvParam> within <SpectrumDetectionProtocol> or
<ProteinDetectionProtocol> for example as follows:
<SpectrumIdentificationProtocol id="SEQUEST_proto"
AnalysisSoftware_ref="SEQUEST_SW">
<SearchType>
<pf:cvParam accession="PI:00083" name="ms-ms search"
cvRef="PSI-PI"/>
</SearchType>
<AdditionalSearchParams>
<pf:cvParam accession="PI:00364" name="pep:global FDR"
cvRef="PSI-PI" value = "0.01"/>
...
<ProteinDetectionProtocol id="PDP_MascotParser_1"
AnalysisSoftware_ref="AS_mascot_parser">
<AnalysisParams>
<pf:cvParam accession="PI:00316" name="mascot:SigThreshold" cvRef="PSI-PI"
value="0.05"/>
…
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From: David C. <dc...@ma...> - 2008-12-15 16:03:00
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Hi, Text looks fine to me. Having PI:00364 under SpectrumIdentificationItem really looks wrong to me - it's a global value, so we shouldn't have to report it for each spectrum... (Not to be confused with "PI:00250" name="local FDR" which is also under SpectrumIdentificationItem) However, there are arguments for putting it in two separate places: a) <AdditionalSearchParams> You choose a FDR and the search/analysis software only creates a list of peptides within that FDR - therefore it is a 'search' parameter. b) <SpectrumIdentificationList> You do the search against a forward and decoy database. From the results you calculate the global FDR. In this case, I suppose it's part of the results. As far as I'm aware, the net effect for the consumer of the AnalysisXML document is the same. We don't want to allow the same cv term in two places, so I'd vote for having it under <AdditionalSearchParams> Any other thoughts? David Jones, Andy wrote: > Hi all, > > I want to insert the following text into the spec document but the first example > probably will not validate, since this would not be counted as a valid mapping > for AdditionalSearchParams: > > <pf:cvParam accession="PI:00364" name="pep:global FDR" cvRef="PSI-PI" value = > "0.01"/> > > Can we update this mapping or someone suggest a suitable example CV term for > setting a threshold for peptide-spectrum matches. > > Also, feel free to suggest any amendments to this text. > > Cheers > Andy > > > > 7.1.4 Reporting peptide and protein identifications passing a significance > threshold > > The elements <SpectrumIdentificationItem> and <ProteinDetectionHypothesis> have > a mandatory Boolean attribute passThreshold that allows a file producer to > indicate that an identification has passed a given threshold or that it has been > manually validated. Depending on the intended purpose of the file, the file > producer MAY wish to report a number of identifications that fall below the > given significance threshold, for example to allow global statistics to be > performed which is not possible if only identifications passing the threshold > are reported. If the file producer does not want to indicate that a threshold > has been set, all identifications MUST have passThreshold = “true”. Thresholds > for peptide-spectrum matches or for protein identification can be encoded as > instances of <cvParam> within <SpectrumDetectionProtocol> or > <ProteinDetectionProtocol> for example as follows: > > <SpectrumIdentificationProtocol id="SEQUEST_proto" > AnalysisSoftware_ref="SEQUEST_SW"> > <SearchType> > <pf:cvParam accession="PI:00083" name="ms-ms search" > cvRef="PSI-PI"/> > </SearchType> > <AdditionalSearchParams> > <pf:cvParam accession="PI:00364" name="pep:global FDR" > cvRef="PSI-PI" value = "0.01"/> > ... > > > <ProteinDetectionProtocol id="PDP_MascotParser_1" > AnalysisSoftware_ref="AS_mascot_parser"> > <AnalysisParams> > <pf:cvParam accession="PI:00316" name="mascot:SigThreshold" cvRef="PSI-PI" > value="0.05"/> > … > > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > The future of the web can't happen without you. Join us at MIX09 to help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- 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: Jones, A. <And...@li...> - 2008-12-15 16:16:21
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Hi David, > Text looks fine to me. Having PI:00364 under SpectrumIdentificationItem > really looks wrong to me - it's a global value, so we shouldn't have to > report it for each spectrum... (Not to be confused with "PI:00250" > name="local FDR" which is also under SpectrumIdentificationItem) Agreed but I wasn't suggesting this ;-) I put it under SpectrumIdentificationProtocol. Currently, PI:00364 is set as a child term of: [Term] id: PI:00213 name: search result details def: "Scores and global result characteristics So I guess it would be fine to map to this from either AdditionalSearchParams or from SpectrumIdentificationList. Just to be clear, I was suggesting the term be used for a very specific purpose though - documenting which identifications are flagged with passThreshold = "true". It shouldn't impact how many results are actually output by the search engine. I would also vote for putting this as AdditionalSearchParams. Cheers, Andy > -----Original Message----- > From: David Creasy [mailto:dc...@ma...] > Sent: 15 December 2008 16:03 > To: psi...@li... > Subject: Re: [Psidev-pi-dev] Reporting identifications passing threshold > > Hi, > > Text looks fine to me. Having PI:00364 under SpectrumIdentificationItem > really looks wrong to me - it's a global value, so we shouldn't have to > report it for each spectrum... (Not to be confused with "PI:00250" > name="local FDR" which is also under SpectrumIdentificationItem) > > However, there are arguments for putting it in two separate places: > a) <AdditionalSearchParams> > You choose a FDR and the search/analysis software only creates a list of > peptides within that FDR - therefore it is a 'search' parameter. > > b) <SpectrumIdentificationList> > You do the search against a forward and decoy database. From the results > you calculate the global FDR. In this case, I suppose it's part of the > results. > > As far as I'm aware, the net effect for the consumer of the AnalysisXML > document is the same. > > We don't want to allow the same cv term in two places, so I'd vote for > having it under <AdditionalSearchParams> > > Any other thoughts? > > David > > > Jones, Andy wrote: > > Hi all, > > > > I want to insert the following text into the spec document but the first example > > probably will not validate, since this would not be counted as a valid mapping > > for AdditionalSearchParams: > > > > <pf:cvParam accession="PI:00364" name="pep:global FDR" cvRef="PSI-PI" > value = > > "0.01"/> > > > > Can we update this mapping or someone suggest a suitable example CV term for > > setting a threshold for peptide-spectrum matches. > > > > Also, feel free to suggest any amendments to this text. > > > > Cheers > > Andy > > > > > > > > 7.1.4 Reporting peptide and protein identifications passing a significance > > threshold > > > > The elements <SpectrumIdentificationItem> and <ProteinDetectionHypothesis> > have > > a mandatory Boolean attribute passThreshold that allows a file producer to > > indicate that an identification has passed a given threshold or that it has been > > manually validated. Depending on the intended purpose of the file, the file > > producer MAY wish to report a number of identifications that fall below the > > given significance threshold, for example to allow global statistics to be > > performed which is not possible if only identifications passing the threshold > > are reported. If the file producer does not want to indicate that a threshold > > has been set, all identifications MUST have passThreshold = “true”. Thresholds > > for peptide-spectrum matches or for protein identification can be encoded as > > instances of <cvParam> within <SpectrumDetectionProtocol> or > > <ProteinDetectionProtocol> for example as follows: > > > > <SpectrumIdentificationProtocol id="SEQUEST_proto" > > AnalysisSoftware_ref="SEQUEST_SW"> > > <SearchType> > > <pf:cvParam accession="PI:00083" name="ms-ms search" > > cvRef="PSI-PI"/> > > </SearchType> > > <AdditionalSearchParams> > > <pf:cvParam accession="PI:00364" name="pep:global FDR" > > cvRef="PSI-PI" value = "0.01"/> > > ... > > > > > > <ProteinDetectionProtocol id="PDP_MascotParser_1" > > AnalysisSoftware_ref="AS_mascot_parser"> > > <AnalysisParams> > > <pf:cvParam accession="PI:00316" name="mascot:SigThreshold" > cvRef="PSI-PI" > > value="0.05"/> > > … > > > > > > ------------------------------------------------------------------------------ > > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > > The future of the web can't happen without you. Join us at MIX09 to help > > pave the way to the Next Web now. Learn more and register at > > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > > _______________________________________________ > > Psidev-pi-dev mailing list > > Psi...@li... > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > -- > 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 > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > The future of the web can't happen without you. Join us at MIX09 to help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
|
From: Martin E. <mar...@ru...> - 2008-12-22 14:59:20
|
Hi!
I added "prot:FDR threshold" and "pep:FDR threshold"
as child terms of "search input details / quality estimation details".
Does that solve this issue?
Jenny encountered a similar problem with "OMSSA e-value threshold", which I added to
"search-engine specific input parameter".
Bye
Martin
> -----Ursprüngliche Nachricht-----
> Von: Jones, Andy [mailto:And...@li...]
> Gesendet: Monday, December 15, 2008 5:16 PM
> An: psi...@li...
> Betreff: Re: [Psidev-pi-dev] Reporting identifications passing threshold
>
> Hi David,
>
> > Text looks fine to me. Having PI:00364 under SpectrumIdentificationItem
> > really looks wrong to me - it's a global value, so we shouldn't have to
> > report it for each spectrum... (Not to be confused with "PI:00250"
> > name="local FDR" which is also under SpectrumIdentificationItem)
>
> Agreed but I wasn't suggesting this ;-) I put it under
> SpectrumIdentificationProtocol.
>
> Currently, PI:00364 is set as a child term of:
>
> [Term]
> id: PI:00213
> name: search result details
> def: "Scores and global result characteristics
>
> So I guess it would be fine to map to this from either AdditionalSearchParams or
> from SpectrumIdentificationList. Just to be clear, I was suggesting the term be
> used for a very specific purpose though - documenting which identifications are
> flagged with passThreshold = "true". It shouldn't impact how many results are
> actually output by the search engine. I would also vote for putting this as
> AdditionalSearchParams.
>
> Cheers,
> Andy
>
>
>
>
> > -----Original Message-----
> > From: David Creasy [mailto:dc...@ma...]
> > Sent: 15 December 2008 16:03
> > To: psi...@li...
> > Subject: Re: [Psidev-pi-dev] Reporting identifications passing threshold
> >
> > Hi,
> >
> > Text looks fine to me. Having PI:00364 under SpectrumIdentificationItem
> > really looks wrong to me - it's a global value, so we shouldn't have to
> > report it for each spectrum... (Not to be confused with "PI:00250"
> > name="local FDR" which is also under SpectrumIdentificationItem)
> >
> > However, there are arguments for putting it in two separate places:
> > a) <AdditionalSearchParams>
> > You choose a FDR and the search/analysis software only creates a list of
> > peptides within that FDR - therefore it is a 'search' parameter.
> >
> > b) <SpectrumIdentificationList>
> > You do the search against a forward and decoy database. From the results
> > you calculate the global FDR. In this case, I suppose it's part of the
> > results.
> >
> > As far as I'm aware, the net effect for the consumer of the AnalysisXML
> > document is the same.
> >
> > We don't want to allow the same cv term in two places, so I'd vote for
> > having it under <AdditionalSearchParams>
> >
> > Any other thoughts?
> >
> > David
> >
> >
> > Jones, Andy wrote:
> > > Hi all,
> > >
> > > I want to insert the following text into the spec document but the first
> example
> > > probably will not validate, since this would not be counted as a valid
> mapping
> > > for AdditionalSearchParams:
> > >
> > > <pf:cvParam accession="PI:00364" name="pep:global FDR" cvRef="PSI-PI"
> > value =
> > > "0.01"/>
> > >
> > > Can we update this mapping or someone suggest a suitable example CV term for
> > > setting a threshold for peptide-spectrum matches.
> > >
> > > Also, feel free to suggest any amendments to this text.
> > >
> > > Cheers
> > > Andy
> > >
> > >
> > >
> > > 7.1.4 Reporting peptide and protein identifications passing a
> significance
> > > threshold
> > >
> > > The elements <SpectrumIdentificationItem> and <ProteinDetectionHypothesis>
> > have
> > > a mandatory Boolean attribute passThreshold that allows a file producer to
> > > indicate that an identification has passed a given threshold or that it has
> been
> > > manually validated. Depending on the intended purpose of the file, the file
> > > producer MAY wish to report a number of identifications that fall below the
> > > given significance threshold, for example to allow global statistics to be
> > > performed which is not possible if only identifications passing the
> threshold
> > > are reported. If the file producer does not want to indicate that a
> threshold
> > > has been set, all identifications MUST have passThreshold = true.
> Thresholds
> > > for peptide-spectrum matches or for protein identification can be encoded as
> > > instances of <cvParam> within <SpectrumDetectionProtocol> or
> > > <ProteinDetectionProtocol> for example as follows:
> > >
> > > <SpectrumIdentificationProtocol id="SEQUEST_proto"
> > > AnalysisSoftware_ref="SEQUEST_SW">
> > > <SearchType>
> > > <pf:cvParam accession="PI:00083" name="ms-ms search"
> > > cvRef="PSI-PI"/>
> > > </SearchType>
> > > <AdditionalSearchParams>
> > > <pf:cvParam accession="PI:00364" name="pep:global FDR"
> > > cvRef="PSI-PI" value = "0.01"/>
> > > ...
> > >
> > >
> > > <ProteinDetectionProtocol id="PDP_MascotParser_1"
> > > AnalysisSoftware_ref="AS_mascot_parser">
> > > <AnalysisParams>
> > > <pf:cvParam accession="PI:00316" name="mascot:SigThreshold"
> > cvRef="PSI-PI"
> > > value="0.05"/>
> > >
> > >
> > >
> > >
> ------------------------------------------------------------------------------
> > > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
> > > The future of the web can't happen without you. Join us at MIX09 to help
> > > pave the way to the Next Web now. Learn more and register at
> > > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/
> > > _______________________________________________
> > > Psidev-pi-dev mailing list
> > > Psi...@li...
> > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
> >
> > --
> > 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
> >
> > ------------------------------------------------------------------------------
> > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
> > The future of the web can't happen without you. Join us at MIX09 to help
> > pave the way to the Next Web now. Learn more and register at
> > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/
> > _______________________________________________
> > Psidev-pi-dev mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
>
> ------------------------------------------------------------------------------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
> The future of the web can't happen without you. Join us at MIX09 to help
> pave the way to the Next Web now. Learn more and register at
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
|
|
From: Martin E. <mar...@ru...> - 2008-12-22 15:16:49
|
I added and changed some CV terms according to the discussion in the last TeleCon
(mainly thresholds and decoy terms).
Changed:
"quality estimation method" -> "quality estimation details"
"forward+reverse decoy DB" -> "DB composition forward+decoy"
"reverse decoy DB" -> "decoy DB type reverse"
"randomized decoy DB" -> "decoy DB type randomized"
Added:
data stored in database
prot:FDR threshold
pep:FDR threshold
OMSSA e-value threshold
ProteinExtractor input parameters
decoy DB details
decoy DB generation algorithm
decoy DB type shuffle
DB composition only decoy
quality estimation with implicite decoy sequences
Only MPC_example became non-valid as it used "forward+decoy DB", so I commented
out this line, until Andreas updated the obo used for validation.
Bye
Martin
> -----Ursprüngliche Nachricht-----
> Von: Martin Eisenacher [mailto:mar...@ru...]
> Gesendet: Monday, December 22, 2008 3:59 PM
> An: 'Jones, Andy'; psi...@li...
> Betreff: Re: [Psidev-pi-dev] Reporting identifications passing threshold
>
> Hi!
>
> I added "prot:FDR threshold" and "pep:FDR threshold"
> as child terms of "search input details / quality estimation details".
>
> Does that solve this issue?
> Jenny encountered a similar problem with "OMSSA e-value threshold", which I added to
> "search-engine specific input parameter".
>
> Bye
> Martin
>
>
> > -----Ursprüngliche Nachricht-----
> > Von: Jones, Andy [mailto:And...@li...]
> > Gesendet: Monday, December 15, 2008 5:16 PM
> > An: psi...@li...
> > Betreff: Re: [Psidev-pi-dev] Reporting identifications passing threshold
> >
> > Hi David,
> >
> > > Text looks fine to me. Having PI:00364 under SpectrumIdentificationItem
> > > really looks wrong to me - it's a global value, so we shouldn't have to
> > > report it for each spectrum... (Not to be confused with "PI:00250"
> > > name="local FDR" which is also under SpectrumIdentificationItem)
> >
> > Agreed but I wasn't suggesting this ;-) I put it under
> > SpectrumIdentificationProtocol.
> >
> > Currently, PI:00364 is set as a child term of:
> >
> > [Term]
> > id: PI:00213
> > name: search result details
> > def: "Scores and global result characteristics
> >
> > So I guess it would be fine to map to this from either AdditionalSearchParams or
> > from SpectrumIdentificationList. Just to be clear, I was suggesting the term be
> > used for a very specific purpose though - documenting which identifications are
> > flagged with passThreshold = "true". It shouldn't impact how many results are
> > actually output by the search engine. I would also vote for putting this as
> > AdditionalSearchParams.
> >
> > Cheers,
> > Andy
> >
> >
> >
> >
> > > -----Original Message-----
> > > From: David Creasy [mailto:dc...@ma...]
> > > Sent: 15 December 2008 16:03
> > > To: psi...@li...
> > > Subject: Re: [Psidev-pi-dev] Reporting identifications passing threshold
> > >
> > > Hi,
> > >
> > > Text looks fine to me. Having PI:00364 under SpectrumIdentificationItem
> > > really looks wrong to me - it's a global value, so we shouldn't have to
> > > report it for each spectrum... (Not to be confused with "PI:00250"
> > > name="local FDR" which is also under SpectrumIdentificationItem)
> > >
> > > However, there are arguments for putting it in two separate places:
> > > a) <AdditionalSearchParams>
> > > You choose a FDR and the search/analysis software only creates a list of
> > > peptides within that FDR - therefore it is a 'search' parameter.
> > >
> > > b) <SpectrumIdentificationList>
> > > You do the search against a forward and decoy database. From the results
> > > you calculate the global FDR. In this case, I suppose it's part of the
> > > results.
> > >
> > > As far as I'm aware, the net effect for the consumer of the AnalysisXML
> > > document is the same.
> > >
> > > We don't want to allow the same cv term in two places, so I'd vote for
> > > having it under <AdditionalSearchParams>
> > >
> > > Any other thoughts?
> > >
> > > David
> > >
> > >
> > > Jones, Andy wrote:
> > > > Hi all,
> > > >
> > > > I want to insert the following text into the spec document but the first
> > example
> > > > probably will not validate, since this would not be counted as a valid
> > mapping
> > > > for AdditionalSearchParams:
> > > >
> > > > <pf:cvParam accession="PI:00364" name="pep:global FDR" cvRef="PSI-PI"
> > > value =
> > > > "0.01"/>
> > > >
> > > > Can we update this mapping or someone suggest a suitable example CV term for
> > > > setting a threshold for peptide-spectrum matches.
> > > >
> > > > Also, feel free to suggest any amendments to this text.
> > > >
> > > > Cheers
> > > > Andy
> > > >
> > > >
> > > >
> > > > 7.1.4 Reporting peptide and protein identifications passing a
> > significance
> > > > threshold
> > > >
> > > > The elements <SpectrumIdentificationItem> and <ProteinDetectionHypothesis>
> > > have
> > > > a mandatory Boolean attribute passThreshold that allows a file producer to
> > > > indicate that an identification has passed a given threshold or that it has
> > been
> > > > manually validated. Depending on the intended purpose of the file, the file
> > > > producer MAY wish to report a number of identifications that fall below the
> > > > given significance threshold, for example to allow global statistics to be
> > > > performed which is not possible if only identifications passing the
> > threshold
> > > > are reported. If the file producer does not want to indicate that a
> > threshold
> > > > has been set, all identifications MUST have passThreshold = true.
> > Thresholds
> > > > for peptide-spectrum matches or for protein identification can be encoded as
> > > > instances of <cvParam> within <SpectrumDetectionProtocol> or
> > > > <ProteinDetectionProtocol> for example as follows:
> > > >
> > > > <SpectrumIdentificationProtocol id="SEQUEST_proto"
> > > > AnalysisSoftware_ref="SEQUEST_SW">
> > > > <SearchType>
> > > > <pf:cvParam accession="PI:00083" name="ms-ms search"
> > > > cvRef="PSI-PI"/>
> > > > </SearchType>
> > > > <AdditionalSearchParams>
> > > > <pf:cvParam accession="PI:00364" name="pep:global FDR"
> > > > cvRef="PSI-PI" value = "0.01"/>
> > > > ...
> > > >
> > > >
> > > > <ProteinDetectionProtocol id="PDP_MascotParser_1"
> > > > AnalysisSoftware_ref="AS_mascot_parser">
> > > > <AnalysisParams>
> > > > <pf:cvParam accession="PI:00316" name="mascot:SigThreshold"
> > > cvRef="PSI-PI"
> > > > value="0.05"/>
> > > >
> > > >
> > > >
> > > >
> > ------------------------------------------------------------------------------
> > > > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
> > > > The future of the web can't happen without you. Join us at MIX09 to help
> > > > pave the way to the Next Web now. Learn more and register at
> > > > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/
> > > > _______________________________________________
> > > > Psidev-pi-dev mailing list
> > > > Psi...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
> > >
> > > --
> > > 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
> > >
> > > ------------------------------------------------------------------------------
> > > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
> > > The future of the web can't happen without you. Join us at MIX09 to help
> > > pave the way to the Next Web now. Learn more and register at
> > > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/
> > > _______________________________________________
> > > Psidev-pi-dev mailing list
> > > Psi...@li...
> > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
> >
> > ------------------------------------------------------------------------------
> > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
> > The future of the web can't happen without you. Join us at MIX09 to help
> > pave the way to the Next Web now. Learn more and register at
> > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/
> > _______________________________________________
> > Psidev-pi-dev mailing list
> > Psi...@li...
> > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
|
|
From: David C. <dc...@ma...> - 2008-12-15 14:39:20
|
Hi everyone, From the minutes: > Encoding NCBI translational tables, I'm not sure about the current > encoding in the instance doc - id numbers match NCBI accession numbers > - just in document references. David to change to make simpler. Add in > a translation table source location.. The change isn't so much to make it simpler, but to make it clearer. <TranslationTable id="1" name="Standard"> . . . <PeptideEvidence ... TranslationTable_ref="1"> Will become: <TranslationTable id="TT_1" name="Standard"> . . . <PeptideEvidence ... TranslationTable_ref="TT_1"> The aim is to try and avoid any confusion with the '1' being an NCBI id value - it is just an internal reference value. Now google is back up and running (thought the world would end if google went down...), I can check in the changed example file. > David to look over and propose a > CV term so it is known where the > value has come from. How about another CV term: [Term] id: PI:xxxxx name: translation table description def: "A URL that describes the translation table used to translate the nucleotides to amino acids." [PSI:PI] xref_analog: value-type:xsd\:anyURI "The allowed value-type for this CV term." is_a: PI:00011 ! search database details <pf:cvParam accession="PI:00xxx" name="translation table description" cvRef="PSI-PI" value="http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG1" Does this look reasonable, or can someone think of a better way of doing it? David Jennifer Siepen wrote: > Hi, > > Please find the minutes of todays teleconference here: > > http://www.psidev.info/index.php?q=node/400 > > Thanks, > > Jenny > -- 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: Jones, A. <And...@li...> - 2008-12-15 15:17:39
|
Hi David, I think that CV term looks fine to me as long as its use is optional. I guess we may need to add some other options later in case other translation tables are used that don't have a URL to identify them, Cheers Andy > -----Original Message----- > From: David Creasy [mailto:dc...@ma...] > Sent: 15 December 2008 14:39 > To: psi...@li... > Subject: Re: [Psidev-pi-dev] Minutes of Telecon. 11th December > > Hi everyone, > > From the minutes: > > Encoding NCBI translational tables, I'm not sure about the current > > encoding in the instance doc - id numbers match NCBI accession numbers > > - just in document references. David to change to make simpler. Add in > > a translation table source location.. > > The change isn't so much to make it simpler, but to make it clearer. > > <TranslationTable id="1" name="Standard"> > . . . > <PeptideEvidence ... TranslationTable_ref="1"> > > > Will become: > <TranslationTable id="TT_1" name="Standard"> > . . . > <PeptideEvidence ... TranslationTable_ref="TT_1"> > > The aim is to try and avoid any confusion with the '1' being an NCBI id > value - it is just an internal reference value. > > > Now google is back up and running (thought the world would end if google > went down...), I can check in the changed example file. > > > > David to look over and propose a > CV term so it is known where the > > value has come from. > > How about another CV term: > > [Term] > id: PI:xxxxx > name: translation table description > def: "A URL that describes the translation table used to translate the > nucleotides to amino acids." [PSI:PI] > xref_analog: value-type:xsd\:anyURI "The allowed value-type for this CV > term." > is_a: PI:00011 ! search database details > > > <pf:cvParam accession="PI:00xxx" name="translation table description" > cvRef="PSI-PI" > value="http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapt > er=cgencodes#SG1" > > > > Does this look reasonable, or can someone think of a better way of doing it? > > > David > > Jennifer Siepen wrote: > > Hi, > > > > Please find the minutes of todays teleconference here: > > > > http://www.psidev.info/index.php?q=node/400 > > > > Thanks, > > > > Jenny > > > > -- > 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 > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. > The future of the web can't happen without you. Join us at MIX09 to help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
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