Menu
▾
▴
psidev-pi-dev
|
From: <cod...@go...> - 2008-11-05 17:21:10
|
Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #13 by a.bertsch0815: Here (attached) is a list of CV terms which are not mapped to the schema at the moment (along with their parents). Just write where to put specific CV terms (subtrees of the ontology) per Mail, and I'll fix the mapping file. Attachments: unused_cv_terms.txt 8.9 KB -- 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...> - 2008-11-05 17:54:41
|
Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #14 by philip.j.r.jones: (Regarding comment 12 above). I have checked with Richard whether OLS uses an OBO file of NEWT / NCBI taxonomy for loading. Unfortunately this is not the case, so will need to look elsewhere for a solution. -- 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...> - 2008-11-11 12:50:39
|
Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #15 by a.bertsch0815: Unused cvParam locations (mapping cannot be defined, because we have no valid terms at the moment) /psi-pi:AnalysisXML/psi-pi:SequenceCollection/psi-pi:Peptide/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:SequenceCollection/psi-pi:Peptide/psi-pi:Modification/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:SequenceCollection/psi-pi:Peptide/psi-pi:SubstitutionModification/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:AnalysisCollection/psi-pi:SpectrumIdentification/psi-pi:_runtimeParams/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:AnalysisCollection/psi-pi:ProteinDetection/psi-pi:_analysisParams/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:AnalysisProtocolCollection/psi-pi:SpectrumIdentificationProtocol/psi-pi:ModificationParams/psi-pi:SearchModification/psi-pi:ModName /psi-pi:AnalysisXML/psi-pi:AnalysisProtocolCollection/psi-pi:SpectrumIdentificationProtocol/psi-pi:MassTable/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:AnalysisProtocolCollection/psi-pi:SpectrumIdentificationProtocol/psi-pi:MassTable/psi-pi:AmbiguousResidue/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:DataCollection/psi-pi:Inputs/psi-pi:SearchDatabase/pf:fileFormat/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:DataCollection/psi-pi:AnalysisData/psi-pi:SpectrumIdentificationList/psi-pi:SpectrumIdentificationResult/psi-pi:SpectrumIdentificationItem/psi-pi:PeptideEvidence/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:DataCollection/psi-pi:AnalysisData/psi-pi:SpectrumIdentificationList[3]/psi-pi:SpectrumIdentificationResult[4]/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:DataCollection/psi-pi:AnalysisData/psi-pi:SpectrumIdentificationList[5]/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:DataCollection/psi-pi:AnalysisData/psi-pi:ProteinDetectionList/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:DataCollection/psi-pi:AnalysisData/psi-pi:ProteinDetectionList/psi-pi:ProteinAmbiguityGroup/pf:cvParam/@accession -- 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...> - 2008-11-11 12:55:41
|
Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #16 by a.bertsch0815: http://psi-pi.googlecode.com/svn/trunk/cv/axml-mapping.html is a html-page which contains all mapping rules and the cv-terms which can be used. This may help to correct the example instance documents, validation errors of the examples will follow. -- 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...> - 2008-11-11 12:59:36
|
Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #17 by a.bertsch0815: Please find attached an output of the sematic validator for the example instance documents. Some errors might be due two missing CVTerms or missing mapping rules. Attachments: sematic_validation_output_examples.txt 22.7 KB -- 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...> - 2008-11-12 16:29:19
|
Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #18 by a.bertsch0815: update list of unused cv terms Attachments: unused_cv_terms.txt 12.2 KB -- 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...> - 2008-11-19 16:16:05
|
Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #19 by eisenachM: There is a "spectrum descriptions" branch with "spectrum quality descriptions". If it is calculated by a search engine, I would prefer to move the branch directly below "search result details" and rename it to "spectrum result information". -- 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...> - 2008-11-19 16:21:12
|
Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #20 by eisenachM: In the CV there is a "search engine specific score" branch containing e.g. "mascot:expectation value" and others. It is good to have the search engine specific scores under one parent term, but most of them should (additionally) be child terms of "peptide result information" or "protein result information". I think that would improve the validator mapping. We can give them multiple parents... -- 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...> - 2008-11-19 19:41:55
|
Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #21 by dcreasy: For the mapping file, PI:00088 needs to be allowed under: SequenceCollection/DBSequence We seem to have two sets of fragment types. For example [Term] id: PI:00220 name: frag: y ion is_a: PI:00221 ! fragmentation information [Term] id: PI:00262 name: param: y ion is_a: PI:00066 ! ions series considered in search Maybe this is OK, but maybe we can just have one lot? For the params, also need: "TODO: Need CV terms for a-NH3 and also a - NH3 if a significant and fragment includes RKNQ"; "TODO: Need CV terms for a-H20 and a - H2O if a significant and fragment includes STED"; "TODO: Need CV terms for b-NH2 and also b - NH3 if b significant and fragment includes RKNQ" "TODO: Need CV terms for b-H20 and b - H2O if b significant and fragment includes STED"; "TODO: Need CV terms for y - NH3 and also y - NH3 if y significant and fragment includes RKNQ"; "TODO: Need CV terms for y - H20 and also y - H2O if y significant and fragment includes STED"; "TODO: Need CV terms for internal yb"; "TODO: Need CV terms for z+1 series"; "TODO: Need CV terms for z+2 series"; I think that this one shouldn't require any value: id: PI:00020 name: DB filter taxonomy def: "The taxonomy filter applied (if any) to the database search." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PI:00019 ! database filtering See the relevant section of: http://code.google.com/p/psi-pi/wiki/NotesForDocumentation -- 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...> - 2008-11-20 10:01:05
|
Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #22 by andrewrobertjones: For parameters that require units, we should follow the PSI-MS structure as follows, linking explicitly to the Unit CV [Term] id: MS:1000004 name: sample mass def: "Total mass of sample used." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000548 ! sample attribute relationship: has_units UO:0000002 ! mass 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...> - 2008-11-20 10:43:10
|
Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #23 by andrewrobertjones: Some of the XSD data types look to be incorrect (e.g. see below), several instances of xsd:decimal should be xsd:float or xsd:double [Term] id: PI:00154 name: sequest:probability def: "The SEQUEST result 'Probability'." [PSI:PI] xref: value-type:xsd\:decimal "The allowed value-type for this CV term." is_a: PI:00153 ! 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...> - 2008-11-20 10:55:22
|
Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #24 by andrewrobertjones: The CV needs a version number e.g. added as "remark" at the top of the file, following the convention of PSI-MS. The spec doc (copied from mzML) states: A new psi-pi.obo should then be released by updating the file on the CVS server without changing the name of the file (this would alter the propagation of the file to the OBO website and to other ontology services that rely on file stable URI). For this reason an internal version number with two decimals (x.y.z) should be increased: • x should be increased when a first level term are renamed added deleted or rearranged in the structure. Such rearrangement is suppose to be rare and is very likely to have repercussion on the mapping. • y should be increased when any other term except the first level one is altered. • z should be increased when there is no term addition or deletion but just editing on the definitions or other minor 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: <cod...@go...> - 2008-11-20 14:55:25
|
Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #25 by dcreasy: For the mapping file: Error: CV term used in invalid element: 'UO:0000187 - percent' at element '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ParentTolerance' Error: Value of CVTerm not allowed: 'UO:0000187 - percent, value=0.1' at element '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ParentTolerance' Error: Value of CVTerm not allowed: 'UO:0000221 - dalton, value=0.5' at element '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/FragmentTolerance' -- 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...> - 2008-11-20 15:10:25
|
Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #26 by dcreasy: Please add [Term] id: PI:0??? name: text file is_a: PI:00043 ! input data type For a simple text file of m/z [intensity] values for a PMF (or single MS-MS?) search -- 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...> - 2008-11-20 16:55:18
|
Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #27 by delagoya: From phone conf 11/20: Change Quality estimate score "by eye" term to "manual validation" or something like that. Term needed for "number of matched/unmatched peaks"? -- 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...> - 2008-11-21 14:37:53
|
Comment #28 on issue 42 by eisenachM: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Edited OBO to fufill comments 20-27. TODOs: - NEWT.obo (Phil?) - comment 22 (units like in PSI-MS) - comment 25 (problem with values in validation) - comment 27 (terms for matched/unmacthed peaks: we have terms "number of peaks matched", "number of peaks submitted", "number of peaks used"; enough?) -- 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...> - 2008-11-21 14:50:18
|
Comment #29 on issue 42 by eisenachM: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 more TODOs: - add 2nd parent for Sequest scores (Martin) - add 2nd parent for Paragon scores -- 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...> - 2008-11-21 15:55:27
|
Comment #30 on issue 42 by eisenachM: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 There was an action defined in TeleCon November 12th to look in the schema, where to place search statistics. This is solved because already in the mapping file: terms below search statistics can be CVParams of SpectrumIdentificationList and ProteinDetectionList. -- 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...> - 2008-11-21 17:09:58
|
Comment #31 on issue 42 by eisenachM: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 more TODOs: - add 2nd parent for Paragon scores -- 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...> - 2008-11-23 19:58:35
|
Comment #32 on issue 42 by dcreasy: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 [Term] id: PI:00056 name: modification specificity rule def: "The specificity rules for the modifications applied by the search engine (fixed, variable)." [PSI:PI] is_a: PI:00055 ! modification parameters Remove ("fixed, variable)" from the def line Also, remove PI:00187 and PI:00188 as agreed at telecon on 2008-11-20 -- 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...> - 2008-11-23 20:02:36
|
Comment #33 on issue 42 by dcreasy: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 [Term] id: PI:00146 name: param: a ion-NH3 def: "Ion a - NH3 if a significant and fragment includes RKNQ." [PSI:PI] is_a: PI:00066 ! ions series considered in search Some search engines will only consider a-NH3 ions if the fragment includes RKN or Q residues. Other search engines don't require the RKQN residues. Hence in http://code.google.com/p/psi-pi/issues/detail?id=42#c21 I requested: "TODO: Need CV terms for a-NH3 and also a - NH3 if a significant and fragment includes RKNQ"; Either make an additional term for each of these, or remove the " if a significant and fragment includes RKNQ." etc. from the defline. -- 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...> - 2008-11-23 20:06:36
|
Comment #34 on issue 42 by dcreasy: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 [Term] id: PI:00365 name: frag: internal yb ion is_a: PI:00066 ! ions series considered in search is_a: PI:00221 ! fragmentation information At the telecon on 2008-11-20, we agreed to keep ions series found and ions series considered in search separate. The four new ones have been added as single term, but should be separated? -- 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...> - 2008-11-26 12:03:26
|
Comment #35 on issue 42 by jensiepen: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Terms need adding for X!Tandem and OMSSA: scoring xtandem: expect xtandem: hyperscore omssa: e_value omssa: p_value source file format omssa csv file xtandem xml file -- 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...> - 2008-11-26 13:51:37
|
Comment #36 on issue 42 by a.bertsch0815: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Units in terms: We agreed to use the following a structure for units in the CV (stolen from mzML): [Term] id: MS:1000004 name: sample mass def: "Total mass of sample used." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000548 ! sample attribute relationship: has_units UO:0000002 ! mass unit An example in mzML would look like this. <cvParam cvRef="MS" accession="MS:1000016" name="scan time" value="5.8905" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/> Which would be straightforward for semantic validation. Any term which has a "has_units" relationship, must have a unit. However, at the moment, cvParam cannot have an unitAccession or unitName or unitCvRef attribute (PropertyValue not included in cvParamType) in the schema. Do I miss something or do we need a schema change if we want to do it similar to mzML, which would be my favorite. -- 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...> - 2008-11-27 13:59:09
|
Comment #37 on issue 42 by dcreasy: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Under <SpectrumIdentificationResult> I would like additional CV to help determine which spectrum in an MGF file the <SpectrumIdentificationResult> came from. As discussed previously, the SpectrumID parameter is sufficient for mzML, but there are several possible indexes for an MGF file (depending on how the file was created). I suggest the following 4 cv terms: mgf title mgf scans mgf rtinseconds mgf rawscans -- 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 |
×
Want the latest updates on software, tech news, and AI?
Get latest updates about software, tech news, and AI from SourceForge directly in your inbox once a month.
Thanks for helping keep SourceForge clean.
X