Menu
▾
▴
psidev-pi-dev — General Development List for Proteomics Informatics
You can subscribe to this list here.
| 2006 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
(1) |
Jul
(5) |
Aug
(4) |
Sep
(4) |
Oct
(10) |
Nov
(1) |
Dec
(1) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2007 |
Jan
|
Feb
|
Mar
(2) |
Apr
|
May
|
Jun
|
Jul
(4) |
Aug
|
Sep
|
Oct
(1) |
Nov
|
Dec
|
| 2008 |
Jan
|
Feb
(2) |
Mar
(2) |
Apr
(8) |
May
(40) |
Jun
(30) |
Jul
(61) |
Aug
(21) |
Sep
(12) |
Oct
(56) |
Nov
(99) |
Dec
(83) |
| 2009 |
Jan
(3) |
Feb
(9) |
Mar
(1) |
Apr
(5) |
May
(88) |
Jun
(43) |
Jul
(60) |
Aug
(54) |
Sep
(4) |
Oct
(18) |
Nov
(9) |
Dec
(5) |
| 2010 |
Jan
|
Feb
(3) |
Mar
(1) |
Apr
(8) |
May
(10) |
Jun
(8) |
Jul
(10) |
Aug
(18) |
Sep
(11) |
Oct
(19) |
Nov
(14) |
Dec
(26) |
| 2011 |
Jan
(27) |
Feb
(38) |
Mar
(50) |
Apr
(128) |
May
(54) |
Jun
(116) |
Jul
(79) |
Aug
(163) |
Sep
(21) |
Oct
(14) |
Nov
(19) |
Dec
(9) |
| 2012 |
Jan
(7) |
Feb
(34) |
Mar
(34) |
Apr
(50) |
May
(70) |
Jun
(23) |
Jul
(8) |
Aug
(24) |
Sep
(35) |
Oct
(40) |
Nov
(276) |
Dec
(34) |
| 2013 |
Jan
(25) |
Feb
(23) |
Mar
(12) |
Apr
(59) |
May
(31) |
Jun
(11) |
Jul
(21) |
Aug
(7) |
Sep
(18) |
Oct
(11) |
Nov
(12) |
Dec
(18) |
| 2014 |
Jan
(37) |
Feb
(22) |
Mar
(9) |
Apr
(10) |
May
(38) |
Jun
(20) |
Jul
(15) |
Aug
(4) |
Sep
(4) |
Oct
(3) |
Nov
(8) |
Dec
(5) |
| 2015 |
Jan
(13) |
Feb
(34) |
Mar
(27) |
Apr
(5) |
May
(12) |
Jun
(10) |
Jul
(12) |
Aug
(3) |
Sep
(1) |
Oct
(13) |
Nov
|
Dec
(6) |
| 2016 |
Jan
(1) |
Feb
(1) |
Mar
(17) |
Apr
(139) |
May
(120) |
Jun
(90) |
Jul
(10) |
Aug
|
Sep
|
Oct
(11) |
Nov
(6) |
Dec
(2) |
| 2017 |
Jan
(24) |
Feb
(8) |
Mar
(7) |
Apr
(2) |
May
(5) |
Jun
(11) |
Jul
(5) |
Aug
(9) |
Sep
(6) |
Oct
(4) |
Nov
(2) |
Dec
(4) |
| 2018 |
Jan
(7) |
Feb
|
Mar
(4) |
Apr
(6) |
May
(10) |
Jun
(6) |
Jul
(7) |
Aug
|
Sep
(7) |
Oct
(5) |
Nov
(3) |
Dec
(3) |
| 2019 |
Jan
(3) |
Feb
|
Mar
(4) |
Apr
(3) |
May
(2) |
Jun
(6) |
Jul
(3) |
Aug
(2) |
Sep
|
Oct
(2) |
Nov
(12) |
Dec
(1) |
| 2020 |
Jan
(3) |
Feb
(1) |
Mar
(2) |
Apr
|
May
|
Jun
|
Jul
|
Aug
(1) |
Sep
|
Oct
(1) |
Nov
|
Dec
|
| 2021 |
Jan
|
Feb
|
Mar
|
Apr
(3) |
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
|
From: <cod...@go...> - 2009-06-26 14:09:53
|
Comment #87 on issue 42 by eisenachM: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 The validator gives errors for the MPC example, because value types of some CV terms are set to 'boolean', although they should have: type string: 'MS:1001424 - ProteinExtractor:Methodname' type positiveInteger: 'MS:1001427 - ProteinExtractor:MaxNumberOfProteins' type double, unit Dalton: 'MS:1001428 - ProteinExtractor:MaxProteinMass' type positiveInteger: 'MS:1001429 - ProteinExtractor:MinNumberOfPeptides' -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-26 13:29:46
|
Comment #86 on issue 42 by eisenachM: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 When correcting the MPC example it became obvious that some CV terms are missing: [Term] id: MS:1001XXX name: ProteinScape:SearchResultId def: "The SearchResultId of this peptide as SearchResult in the ProteinScape database." xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score [Term] id: MS:1001XXX name: ProteinScape:SearchEventId def: "The SearchEventId of the SearchEvent in the ProteinScape database." xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score [Term] id: MS:1001XXX name: ProteinScape:ProfoundProbability def: "The Profound probability score stored by ProteinScape." xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score [Term] id: MS:1001XXX name: Profound:z value def: "The Profound z value." xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score [Term] id: MS:1001XXX name: Profound:Cluster def: "The Profound cluster score." xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score [Term] id: MS:1001XXX name: Profound:ClusterRank def: "The Profound cluster rank." xref: value-type:xsd\:positiveInteger "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score [Term] id: MS:1001XXX name: MSFit:Mowse score def: "The MSFit Mowse score." xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score [Term] id: MS:1001XXX name: Sonar:Score def: "The Sonar score." xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score [Term] id: MS:1001XXX name: ProteinScape:PFFSolverExp def: "The ProteinSolver exp value stored by ProteinScape." xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score [Term] id: MS:1001XXX name: ProteinScape:PFFSolverScore def: "The ProteinSolver score stored by ProteinScape." xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score [Term] id: MS:1001XXX name: ProteinScape:IntensityCoverage def: "The intensity coverage of the identified peaks in the spectrum calculated by ProteinScape." xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score [Term] id: MS:1001XXX name: ProteinScape:SequestMetaScore def: "The Sequest meta score calculated by ProteinScape from the original Sequest scores." xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score [Term] id: MS:1001XXX name: ProteinExtractor:Score def: "The score calculated by ProteinExtractor." xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001116 ! single protein result details is_a: MS:1001153 ! search engine specific score -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-26 10:37:06
|
Comment #15 on issue 49 by andrewrobertjones: Issues / schema updates prior to version 1 release http://code.google.com/p/psi-pi/issues/detail?id=49 schema updates: Schema update: - Added in Sample and Sample_ref - Added corresponding keys and keyrefs - experimentalMassToCharge use="required" - chargeState use="required" Some updates to the mapping file for taxonomy for Sample and DBFilter type,exclude and include -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-26 10:33:02
|
Comment #85 on issue 42 by andrewrobertjones: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Fixing the mapping for taxonomy, a similar mapping is required for 3 parts of the schema: - Sample (previously called GenericMaterial) - DBSequence - Filter Include/Exclude Filter currently maps to "database filtering" which has a child term: DB filter taxonomy. This term should be depracated. I have added a mapping for all three to the child terms of MS:1001089 "molecule taxonomy" I have also added a mapping from FilterType to the exact term (no child terms) "molecule taxonomy" "molecule taxonomy" is currently a child of "database sequence details" so we should move it up the hierarchy so it covers samples as well. Andreas, can you give me a mail offline to check through these changes? -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: Juan A. V. <ju...@eb...> - 2009-06-26 09:28:33
|
Hi all, Minutes from yesterday's phone conference can be found here: http://www.psidev.info/index.php?q=node/427 Cheers, Juan Antonio Juan Antonio Vizcaíno, Ph.D. EMBL European Bioinformatics Institute Proteomics Services Team, PANDA Group Wellcome Trust Genome Campus Hinxton, Cambridge, UK CB10 1SD Tel: +44 (0) 1223 492 686 Fax: +44 (0) 1223 494 468 Skype: javizca |
|
From: <cod...@go...> - 2009-06-25 15:52:01
|
Comment #84 on issue 42 by andrewrobertjones: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Decided to allow the following two terms only: [Term] id: UO:0000186 name: dimensionless unit def: "A derived unit which is a standard measure of physical quantity consisting of only a numerical number without any units." [Wikipedia:Wikipedia "http://www.wikipedia.org/"] is_a: UO:0000046 ! derived unit [Term] id: UO:0000187 name: percent def: "A dimensionless ratio unit which denotes numbers as fractions of 100." [Wikipedia:Wikipedia "http://www.wikipedia.org/"] synonym: "%" EXACT [] is_a: UO:0000190 ! ratio we need examples of these i.e. "5" "percent" and "0.05" "dimensionless unit" -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-25 15:03:00
|
Comment #14 on issue 49 by andrewrobertjones: Issues / schema updates prior to version 1 release http://code.google.com/p/psi-pi/issues/detail?id=49 Comment from Patrick @ Matrix: Why is the experimentalMassToCharge attribute of SpectrumIdentificationType optional? If it isn't set you could potentially have real trouble matching back to the source spectrum (for example in a PMF search there could be no reference at all to the entered mass, and if there isn't a handy reference to e.g. the dta file name you could have the same problem with MS/MS datasets). The example XTandem file doesn't have the experimentalMassToCharge set, although all the others do. Thanks, Patrick We should review the other cardinalities of SpectrumIdentificationItem as well -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-25 07:35:38
|
Comment #5 on issue 45 by pierrealainbinz: Number of peptides / proteins to be reported http://code.google.com/p/psi-pi/issues/detail?id=45 for Phenyx we probably already have something: a) representation of peptide scores: id: MS:1001395 name: Phenyx:Pepzscore and id: MS:1001396 name: Phenyx:PepPvalue both are is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score id: MS:1001384 name: Phenyx:MinPepzscore and id: MS:1001385 name: Phenyx:MaxPepPvalue both is_a: MS:1001302 ! search engine specific input parameter 2) and we also have 2 binary values for a "valid" or "accepted" peptide status, corresponding to automatic selection (unedited search result) and user-defined selection (that has gone through manual selection), respectively: id: MS:1001393 name: Phenyx:Auto and id: MS:1001394 name: Phenyx:User both defined is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score As the thresholding we talk about about is a "post processing" event (something we apply to the "raw" result), which one would you consider? I'm just wondering which one could fit best for a passThreshold criterium. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-24 18:01:47
|
Comment #4 on issue 45 by andrewrobertjones: Number of peptides / proteins to be reported http://code.google.com/p/psi-pi/issues/detail?id=45 Agreed, we need a few different terms here, not sure if they exist in the CV or just not in the mapping at present e.g. p-value, mascot:SigThreshold, some terms for Sequest etc. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-24 17:45:28
|
Comment #17 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 None of the examples include a BibliographicReference - added to the PMF_example.mzid -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: Patrick E. <pat...@ma...> - 2009-06-24 16:00:09
|
Hi All, Why is the experimentalMassToCharge attribute of SpectrumIdentificationType optional? If it isn't set you could potentially have real trouble matching back to the source spectrum (for example in a PMF search there could be no reference at all to the entered mass, and if there isn't a handy reference to e.g. the dta file name you could have the same problem with MS/MS datasets). The example XTandem file doesn't have the experimentalMassToCharge set, although all the others do. Thanks, Patrick -- Patrick Emery Matrix Science Ltd 64 Baker Street London W1U 7GB Tel +44 (0)20 7486 1050 Fax +44 (0)20 7224 1344 pat...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 |
|
From: Jones, A. <And...@li...> - 2009-06-24 13:00:27
|
Hi all, There will be an mzIdentML conference call tomorrow (25th June) at 4pm UK time: http://www.timeanddate.com/worldclock/fixedtime.html?day=25&month=6&year=2009&hour=16&min=0&sec=0&p1=136 Agenda: 1. Review minutes from last week: http://www.psidev.info/index.php?q=node/425 2. Review issues list: http://code.google.com/p/psi-pi/issues/list 3. Plan for resubmission to the process 4. AOB Please send me any other agenda items. It would be great if we could have all instance documents validating in time for the call, then we have very few outstanding issues before re-generating the documentation and submitting. Cheers, Andy Dial in details: + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 |
|
From: <cod...@go...> - 2009-06-24 08:29:35
|
Comment #83 on issue 42 by eisenachM: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 We use percent, but both should be allowed -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-23 17:06:46
|
Updates: Status: Accepted Comment #3 on issue 45 by dcreasy: Number of peptides / proteins to be reported http://code.google.com/p/psi-pi/issues/detail?id=45 I've re-opened this issue rather than add the problem to the end of the CV issue because it seems more relevant here. We (or maybe just me) may have lost the plot here... Comment 2 says what we added to the schema. The structure for specifying which items "PassThreshold" is described here: http://code.google.com/p/psi-pi/issues/detail?id=49#c3 Currently, the only CV items allowed in the 'Threshold' are: MS:1001448: pep:FDR threshold MS:1001447: prot:FDR threshold MS:1001494: no threshold However, using an FDR is not the only way to do this. For example, if you've only got a few spectra, then FDR is definitely is not an option. I think we need other terms to be allowed here. For example, you might want to specify that the threshold is "ZYXScore > 23.4" In the Mascot example, there is for example: <ProteinDetectionProtocol id="PDP_MascotParser... <AnalysisParams> <cvParam accession="MS:1001316" name="mascot:SigThreshold" cvRef="PSI-MS" value="0.05"/> And I guess in this case I would like to specify MS:1001316 in AnalysisProtocolCollection/SpectrumIdentificationProtocol/Threshold/ -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-23 15:49:05
|
Comment #82 on issue 42 by a.bertsch0815: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Should the FDR threshold terms be allowed to have units? i.e. "MS:1001447 - prot:FDR threshold" and the respective pep term. per cent? parts per notation? -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-23 10:45:01
|
Comment #81 on issue 42 by dcreasy: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 We seem to have two different ways of specifying taxonomy: <SequenceCollection> <DBSequence id="DBSeq_HSP7D_MANSE" length="652" SearchDatabase_ref="SDB_SwissProt" accession="HSP7D_MANSE" > <seq>MAKAPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTDRLIGDAAKNQVAMNP...</seq> <cvParam accession="MS:1001088" name="protein description" cvRef="PSI-MS" value="Heat shock 70 kDa protein cognate... - Manduca sexta ..." /> <cvParam accession="MS:1001469" name="taxonomy: scientific name" cvRef="PSI-MS" value="Manduca sexta"/> <cvParam accession="MS:1001467" name="taxonomy: NCBI TaxID" cvRef="PSI-MS" value="7130"/> </DBSequence> and <cv id="NCBI-TAXONOMY" fullName="NCBI-TAXONOMY" URI="ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz"></cv> . . . <DatabaseFilters> <Filter> <FilterType> <cvParam accession="MS:1001020" name="DB filter taxonomy" cvRef="PSI-MS" /> </FilterType> <Include> <cvParam accession="NCBI:33208" name="Metazoa" cvRef="NCBI-TAXONOMY" /> </Include> </Filter> </DatabaseFilters> Obviously we should be consistent and get rid of one of the methods. The other CV that could be used in the first example is: id: MS:1001470 name: taxonomy: Swiss-Prot ID id: MS:1001468 name: taxonomy: common name I suggest that we ditch the second method and allow: MS:1001467 - taxonomy: NCBI TaxID MS:1001468 - taxonomy: common name MS:1001469 - taxonomy: scientific name MS:1001470 - taxonomy: Swiss-Prot ID to be included in DatabaseFilters/Filter/Include For MS:1001468, MS:1001469, MS:1001470, I would like to see something like this added to the def: Recommend using MS:1001467 where possible For MS:1001467, the type should be an unsigned 32 bit integer -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-23 10:24:37
|
Comment #15 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Regarding comment #7: Add an example of how <components> are used. Fixed in Mascot_N15_example.mzid -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-23 10:23:42
|
Comment #16 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 None of the examples seem to include missedCleavages in <PeptideEvidence>. Added to Mascot examples. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: Jones, A. <And...@li...> - 2009-06-18 10:30:29
|
Hi all, A couple of minor schema updates. - There were some old keys/keyrefs that were removed and some new ones added - shouldn't change any instance docs. - Some minor documentation changes that had been requested in the past - Changed the data type of DBSequence from xsd:string to "sequence" - which specific they must be an unbroken string of uppercase letters. This had been discussed at Turku but never fixed. I can't see any reason to have non uppercase chars in a protein sequence? Cheers Andy |
|
From: Juan A. V. <ju...@eb...> - 2009-06-18 09:37:47
|
Hi all, Minutes from yesterday's phone conference can be found here: http://www.psidev.info/index.php?q=node/425 Cheers, Juan Antonio Juan Antonio Vizcaíno, Ph.D. EMBL European Bioinformatics Institute Proteomics Services Team, PANDA Group Wellcome Trust Genome Campus Hinxton, Cambridge, UK CB10 1SD Tel: +44 (0) 1223 492 686 Fax: +44 (0) 1223 494 468 Skype: javizca |
|
From: <cod...@go...> - 2009-06-17 19:52:41
|
Comment #80 on issue 42 by dcreasy: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 I think that the passThreshold="true" or passThreshold="false" attributes should still apply? It's just that it is the user's own threshold in this case. In which case, adding a string value to the comments would be fine. Um... looks like it can take a string already: [Term] id: MS:1001125 name: manual validation def: "Result of quality estimation: decision of a manual validation." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." Perhaps we just need to add this to one of the examples? -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-17 19:23:22
|
Comment #79 on issue 42 by pierrealainbinz: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 A string would be minimally ok, but I would suggest a kind of binary value: true /false or accepted/rejected -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-17 16:36:13
|
Comment #78 on issue 42 by andrewrobertjones: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 In response to comment 77, I think you should use: id: MS:1001125 name: manual validation I'm not sure about user comments. Currently, values are not allowed for this CV term but we could allow a string value to be populated with comments. Any opinions? -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-17 16:21:45
|
Comment #77 on issue 42 by patri...@matrixscience.com: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 We need to be able to record that users have manually accepted or rejected proteins and peptides. Could I use the CVParam 'Quality estimation by manual estimation' to do this (at both the protein and peptide level)? Is there a CVTerm to record user comments about why a protein or peptide was accepted or rejected? -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2009-06-17 13:19:00
|
Comment #76 on issue 42 by eisenachM: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 The MPC example does not validate, because it uses "prot:FDR threshold", but "prot:global FDR" is allowed in the mapping file. I remember, that "prot:global FDR" was created as a result (being a child of "spectrum identification result details") and "prot:FDR threshold" as search input, because it is used as input in the Threshold element (being part of "Protocol"). Same for "pep:FDR threshold" and "pep:global FDR". -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
42 messages has been excluded from this view by a project administrator.
