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From: Angel P. <an...@ma...> - 2006-08-29 17:27:11
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It was pointed out today that not everyone may know the location of the Document Store and what parts pertain to the PSI-PI working group. Here is that information: PSI Document Store http://psidev.sourceforge.net/docstore/ There is a link on top for anonymous read access to all the documents. If you want/need to update one of the contained documents and are not sure if you have an account, please contact myself or Randy Julian <rkj...@in...> for account information The PSI-PI working group documents are under the "PSI_PI" folder. The contents (so far) are listed below, folders have asterisks. *PSI_PI PSI-PI Charter.doc == PSI-PI working group charter document * analysisXML - documents associated with analysisXML efforts analysisXML draft schema == analysisXML.zip AnalysisXML use cases == analysis_xml_use_cases.doc PSI-PI UML model == PSI-PI.zip Requirements for AnalysisXML == analysis_xml_use_cases.doc search_engine_outputs.xls == search_engine_outputs.xls *Meeting Minutes = contains working group meeting minutes -- Angel Pizarro Director, Bioinformatics Facility Institute for Translational Medicine and Therapeutics University of Pennsylvania 806 BRB II/III 421 Curie Blvd. Philadelphia, PA 19104-6160 P: 215-573-3736 F: 215-573-9004 E: an...@ma... |
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From: Angel P. <an...@ma...> - 2006-08-29 13:40:15
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Hello folks, I have posted the minutes for our last meeting in the docstore. -angel -- Angel Pizarro Director, Bioinformatics Facility Institute for Translational Medicine and Therapeutics University of Pennsylvania 806 BRB II/III 421 Curie Blvd. Philadelphia, PA 19104-6160 P: 215-573-3736 F: 215-573-9004 E: an...@ma... |
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From: Angel P. <an...@ma...> - 2006-08-29 13:02:15
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Hello folks, Sorry for the late notice, but we are scheduled for a conference call today. Should be a short one: UML AnalysisXML model - anybody try out the zip file I sent with MagicDraw 11.5 Community edition? PSI Fall '06 mtg in Washington: Deliverables and proposed agenda. Teleconference details: For today's PSI-MS teleconference: http://www.timeanddate.com/worldclock/fixedtime.html?year=2006&month=8&day=29&hour=15&min=0&sec=0 (16:00 British Summer Time) Please dial the most convenient number to access the teleconference: UK: +44 870 240 7821 or +44 207 819 3600 US: West coast: +1 4089616553 East coast: +1 7183541169 Switzerland: +41 1800 9449 (If you require access from any other location, please email:pj...@eb...). The passcode to access the conversation is: 8885686# I will start the teleconference at 5 minutes before the hour. Cheers! -- Angel Pizarro Director, Bioinformatics Facility Institute for Translational Medicine and Therapeutics University of Pennsylvania 806 BRB II/III 421 Curie Blvd. Philadelphia, PA 19104-6160 P: 215-573-3736 F: 215-573-9004 E: an...@ma... |
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From: Angel P. <an...@ma...> - 2006-08-22 14:00:39
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Hi Folks, last message of the morning. I posted the UML Model for AnalysisXML along with the needed FuGE and AndroMDA profiles here at the docstore: http://psidev.sourceforge.net/docstore/download.php?sess=895d52db6336d6208d6bbb954ea6f520&parent=19&expand=1&order=name&binary=1&id=101 You should be able to just open the file in MagicDraw 11.5, but please tell me if this is not the case. I made the model this morning, since (a) The first model was just a demonstration of UML syntax and not rigerous; (b) I had to convert to UML2 profiles for MD11.5; (c) I lost the original model file ;) So the model is nowhere near complete and a lot of the associations need to be named/discussed/approved etc., but this should not be a one-man effort and should be a worthwhile session in Washington DC BTW, the metro in DC is very good so if you can't find a hotel near the venue, look for hotels near subway stations or in the burbs near a metro station. -angel -- Angel Pizarro Director, Bioinformatics Facility Institute for Translational Medicine and Therapeutics University of Pennsylvania 806 BRB II/III 421 Curie Blvd. Philadelphia, PA 19104-6160 P: 215-573-3736 F: 215-573-9004 E: an...@ma... |
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From: Angel P. <an...@ma...> - 2006-07-31 19:50:39
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Folks, We have a conference call scheduled tomorrow. Sorry for the late notice, but been a little busy. Agenda: AnalysisUML Model --------------------- Last conference call, I had created a straw man UML model directly from the XML now (in)famous XML schema that myself, Randy Julian, Sean Seymour, David Shteynberg, and a few others (sorry I forget who all was there) for analysisXML. We used the ISB's pepXML and protXML as a starting point. There were a few questions regarding the model over the email list (archives found here: http://sourceforge.net/mailarchive/forum.php?thread_id=22147996&forum_id=48874 ) We will be going over these comments. Requirements spreadsheet for search engines ------------------------------------------------------------------------ David Creasy had started collating a list of search engine requirments. Status and overview of the spreadsheet, available here: http://psidev.sourceforge.net/docstore/view.php?&action=xls_show&id=84 email thread discussing the spreadsheet available here: http://sourceforge.net/mailarchive/forum.php?thread_id=22351418&forum_id=48874 Other agenda items as needed --------------------------------------------------- Phil Jones will not be present to set up the conference call, but his colleague Lennart Martins has kindly agreed to step in and set up the conference call logistics. Please contact him for teleconf details, but they should be the same as last time. len...@eb... Cheers! -- C Angel Pizarro Director, Bioinformatics Facility Institute for Translational Medicine and Therapeutics University of Pennsylvania 806 BRB II/III 421 Curie Blvd. Philadelphia, PA 19104-6160 P: 215-573-3736 F: 215-573-9004 E: an...@ma... |
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From: David C. <dc...@ma...> - 2006-07-11 17:58:44
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Hi, Philip Jones wrote: > Hi, > > Based upon the draft analysisXML UML model that Angel circulated a month > or so ago, here are a few requirements that may need to be addressed. > > It is very likely that many of these requirements are already addressed > in the draft model or by the FuGE model that it extends, especially > taking into account that the majority of the classes in the diagram do > not have fields included, but hopefully this list may provoke some > discussion... > > The current draft UML model can be retrieved from: > > http://psidev.sourceforge.net/proteomics-informatics/documents/analysisUML.ppt > > Information that may need to be captured: > > 1. Polypeptide (mostly obvious stuff, probably just fields that are > present but have not been included in the Powerpoint diagram): > * Sequence (esp. for peptides) [0..1] I don't think we should have this proteins - would be huge when you are searching the human genome... For a denovo search this may be an ambiguous sequence - e.g. ACQ[I|L]K We need to define a syntax for that I guess. > * database name / version [0..1] - /Appears to be addressed by > SequenceDatabase class, The current model suggests that all > proteins identified in one XML need to be identified from > the same database - presumably this is a safe assumption?/ I think that we have to allow multiple databases. See the whole "database searched" section in the spreadsheet. > * accession / accession version [0..1], mandatory for proteins? Yes, I think so. It would be hard to justify making it optional? > * database cross references [0..*] 0 is certainly possible for a denovo search. > * Start and end coordinates of peptides in relation to any > proteins that they identify [0..1] or [0..*] ?? Guess it depends on the structure of the XML... > * Upstream / Downstream flanking regions for peptides Remember that this won't be available for denovo sequencing. Not all the search engines have this (see the spreadsheet) > > Will polypeptide be sub-classed to allow (for example) > accession to be enforced for protein identifications? > > It's also worth reading Brian Searle's comments on the comments tab in the spreadsheet: "... Is it possible to add in the specifications a recommendation for reporting at least one peptide score for every spectrum?..." > 2. Presumably the 'SearchProtocol' class will handle details of: > > * search engine identity > * search engine version > * search input parameters / settings (Is this CV parameterised > stuff with CVs from individual search engine vendors?) We've agreed to use CVs as little as possible. The spreadsheet will help us get the largest possible number of parameters defined in the schema. > > 3. Protein modifications - CustomModification class: > > * Are the monoisotopicMass & averageMass values expected or > observed? Does analysisXML need to store both? Are expected > values [1..*]? The UML doesn't look nearly complete to me - I'm certainly not very clear what it is supposed to be... > > 4. Protein modifications - Modification class > > * 'position' field declared as mandatory, however the position > of the PTM is often unknown. Ability to handle 'fuzzy' or > approximate location? (Does this last requirement even exist?) Yes, it mustn't be mandatory - for PMF searches you certainly don't know the location. I guess approximate location may be useful. Any search engines support it? > > 5. SearchHypothesis / Search result: > > * As mentioned at the last PSI-PI teleconference, just to flag > up the need for a clear plan of how to (for example) connect > to a gel spot recorded in GelML format etc. > > Best regards, > > Phil. > -- David Creasy Matrix Science 8 Wyndham Place London W1H 1PP Tel +44 (0)20 7723 2142 Fax +44 (0)20 7725 9360 dc...@ma... http://www.matrixscience.com |
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From: David C. <dc...@ma...> - 2006-07-11 17:57:34
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Hi, I've updated the search_engine_outputs.xls spreadsheet with feedback from a number of different vendors (thanks very much to all of you). It's available at: http://psidev.sourceforge.net/docstore/view.php?&action=xls_show&id=84 It's now getting to the stage where it's nearly useful enough to decide what needs to be analysisXML. The 'rule' that we decided on at the last teleconference is: If an item has a Y in 2 or more columns, should be a node in analysisXML. (e.g. - Database taxonomy filter should be a node) Are there still 'big' things missing from the spreadsheet? Looks as though we will need to add quite a bit more detail as we go along. Pierre-Alan - could I ask you to fill in the MIAPE column when you have time. Thanks, David -- David Creasy Matrix Science 8 Wyndham Place London W1H 1PP Tel +44 (0)20 7723 2142 Fax +44 (0)20 7725 9360 dc...@ma... http://www.matrixscience.com |
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From: Philip J. <pj...@eb...> - 2006-07-11 10:12:10
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Hi, Based upon the draft analysisXML UML model that Angel circulated a month or so ago, here are a few requirements that may need to be addressed. It is very likely that many of these requirements are already addressed in the draft model or by the FuGE model that it extends, especially taking into account that the majority of the classes in the diagram do not have fields included, but hopefully this list may provoke some discussion... The current draft UML model can be retrieved from: http://psidev.sourceforge.net/proteomics-informatics/documents/analysisUML.ppt Information that may need to be captured: 1. Polypeptide (mostly obvious stuff, probably just fields that are present but have not been included in the Powerpoint diagram): * Sequence (esp. for peptides) [0..1] * database name / version [0..1] - /Appears to be addressed by SequenceDatabase class, The current model suggests that all proteins identified in one XML need to be identified from the same database - presumably this is a safe assumption?/ * accession / accession version [0..1], mandatory for proteins? * database cross references [0..*] * Start and end coordinates of peptides in relation to any proteins that they identify [0..1] or [0..*] ?? * Upstream / Downstream flanking regions for peptides Will polypeptide be sub-classed to allow (for example) accession to be enforced for protein identifications? 2. Presumably the 'SearchProtocol' class will handle details of: * search engine identity * search engine version * search input parameters / settings (Is this CV parameterised stuff with CVs from individual search engine vendors?) 3. Protein modifications - CustomModification class: * Are the monoisotopicMass & averageMass values expected or observed? Does analysisXML need to store both? Are expected values [1..*]? 4. Protein modifications - Modification class * 'position' field declared as mandatory, however the position of the PTM is often unknown. Ability to handle 'fuzzy' or approximate location? (Does this last requirement even exist?) 5. SearchHypothesis / Search result: * As mentioned at the last PSI-PI teleconference, just to flag up the need for a clear plan of how to (for example) connect to a gel spot recorded in GelML format etc. Best regards, Phil. -- _______________________________________ Phil Jones Software Engineer BioSapiens / PRIDE Project Team Sequence Database Group EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel +44 (0)1223 492 610 (Direct Line) mailto:pj...@eb... |
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From: David C. <dc...@ma...> - 2006-07-10 15:52:37
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Hi, Unfortunately, there won't be a conference call tomorrow (11th July). We need to make a little more progress before we can present some different options to make effective use of the time in a conference call. Meanwhile, any further feedback for the use cases would be great. The use cases will directly affect what's in the standard. Thanks, David David Creasy wrote: > Hi, > The psi proteomics informatics working group had its first > teleconference on 6th June. Meeting minutes are available from the home > page kindly set up by Phil Jones: > > http://psidev.sourceforge.net/proteomics-informatics/home.html > > The next teleconference will be on 11 July - again details will be on > the home page nearer the time and the agenda will be posted to this list. > > I've updated the use cases: > http://psidev.sourceforge.net/docstore/download.php?&id=83 > with feedback from the San Francisco meeting and the last > teleconference, but we would really appreciate other uses cases and > feedback on this before the next teleconference. Please email to the > list, or to me if you'd rather. > > Thanks, > > David > -- David Creasy Matrix Science 8 Wyndham Place London W1H 1PP Tel +44 (0)20 7723 2142 Fax +44 (0)20 7725 9360 dc...@ma... http://www.matrixscience.com |
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From: David C. <dc...@ma...> - 2006-06-26 10:10:47
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Hi, The psi proteomics informatics working group had its first teleconference on 6th June. Meeting minutes are available from the home page kindly set up by Phil Jones: http://psidev.sourceforge.net/proteomics-informatics/home.html The next teleconference will be on 11 July - again details will be on the home page nearer the time and the agenda will be posted to this list. I've updated the use cases: http://psidev.sourceforge.net/docstore/download.php?&id=83 with feedback from the San Francisco meeting and the last teleconference, but we would really appreciate other uses cases and feedback on this before the next teleconference. Please email to the list, or to me if you'd rather. Thanks, David -- David Creasy Matrix Science 8 Wyndham Place London W1H 1PP Tel +44 (0)20 7723 2142 Fax +44 (0)20 7725 9360 dc...@ma... http://www.matrixscience.com |
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