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From: Wout B. <wo...@uw...> - 2018-08-16 18:21:05
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Dear colleagues, You can find the minutes from today's teleconference here: https://github.com/HUPO-PSI/qcML-development/blob/master/meeting_notes/20180816_telco.md Enjoy the last weeks of summer and make sure to check out Julian's work on the new CV in pull request 44! Best, Wout > On 15 Aug 2018, at 08:14, Wout Bittremieux <wo...@uw...> wrote: > > Dear colleagues, > > This is a reminder that our next teleconference is scheduled for Thursday, August 16th, at 14h00 GMT (15h00 London, 16h00 Western Europe & Cape Town, 7h00 Seattle, 22h00 Beijing). > > You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 > > Apologies for the late notification, I'm trying to finish a dozen different things before I take some time off at the end of the week. > > Based on our action items from last month I propose the following agenda items: > > - Evaluate a QC metric spanning multiple files. > - Overview of the use of QC in metabolomics. > - Any other item that needs to be discussed... > > Thanks, > Wout > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Wout B. <wo...@UW...> - 2018-08-15 15:16:20
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Dear colleagues, This is a reminder that our next teleconference is scheduled for Thursday, August 16th, at 14h00 GMT (15h00 London, 16h00 Western Europe & Cape Town, 7h00 Seattle, 22h00 Beijing). You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 Apologies for the late notification, I'm trying to finish a dozen different things before I take some time off at the end of the week. Based on our action items from last month I propose the following agenda items: - Evaluate a QC metric spanning multiple files. - Overview of the use of QC in metabolomics. - Any other item that needs to be discussed... Thanks, Wout |
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From: Wout B. <wo...@uw...> - 2018-07-25 23:40:55
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Dear colleagues, Thank you all for attending our teleconference last week. You can now find the updated meeting notes on our Github repository: https://github.com/HUPO-PSI/qcML-development/blob/master/meeting_notes/20180718_telco.md Best, Wout > On 16 Jul 2018, at 16:56, Wout Bittremieux <wo...@uw...> wrote: > > Dear colleagues, > > This is a reminder that our next teleconference is scheduled for Thursday, July 19th, at 14h00 GMT (15h00 London, 16h00 Western Europe & Cape Town, 7h00 Seattle, 22h00 Beijing). > > You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 > > In between all sunshine, vacation, wedding preparations, etc, I hope you will still be able to make some time for our teleconference. I propose the following agenda items: > > - More JSON. Please have a look at Dave's recent draft mzQC JSON file. I will still try to provide an initial version of a JSON schema file for validation purposes, but I have a pretty busy week ahead of me so I'm not making any promises. > > - MIAPE-QC: Depending on the people that manage to attend the call it would be relevant to address the MIAPE-QC recommendations to construct a paragraph based on Dave's written feedback. > > Thanks, > Wout > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Julian U. <jul...@ru...> - 2018-07-19 14:05:45
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Hi all, I am still in a discussion... might be a bit late. But also have some questions and comments regarding the CV side. See you, Julian On 19.07.2018 06:59, David Tabb wrote: > Thank you for keeping us on schedule, Wout! I look forward to > speaking with you all this afternoon / morning / evening! > > Dave > > On 7/17/2018 1:56 AM, Wout Bittremieux wrote: >> Dear colleagues, >> >> This is a reminder that our next teleconference is scheduled >> for *Thursday, July 19th, at 14h00 GMT* (15h00 London, 16h00 Western >> Europe & Cape Town, 7h00 Seattle, 22h00 Beijing). >> >> You can connect to our teleconference on Google Hangouts through the >> following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 >> >> In between all sunshine, vacation, wedding preparations, etc, I hope >> you will still be able to make some time for our teleconference. I >> propose the following agenda items: >> >> - More JSON. Please have a look at Dave's recent draft mzQC JSON >> file. I will still try to provide an initial version of a JSON schema >> file for validation purposes, but I have a pretty busy week ahead of >> me so I'm not making any promises. >> >> - MIAPE-QC: Depending on the people that manage to attend the call it >> would be relevant to address the MIAPE-QC recommendations to >> construct a paragraph based on Dave's written feedback. >> >> Thanks, >> Wout >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> >> >> _______________________________________________ >> Psidev-qc-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > > > <http://www.sun.ac.za/english/Pages/Water-crisis.aspx> > > The integrity and confidentiality of this email is governed by these > terms. Disclaimer <http://www.sun.ac.za/emaildisclaimer%20> > Die integriteit en vertroulikheid van hierdie e-pos word deur die > volgende bepalings gereël. Vrywaringsklousule > <http://www.sun.ac.za/emaildisclaimer%20> > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: David T. <dt...@su...> - 2018-07-19 06:35:17
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Thank you for keeping us on schedule, Wout! I look forward to speaking with you all this afternoon / morning / evening! Dave On 7/17/2018 1:56 AM, Wout Bittremieux wrote: Dear colleagues, This is a reminder that our next teleconference is scheduled for Thursday, July 19th, at 14h00 GMT (15h00 London, 16h00 Western Europe & Cape Town, 7h00 Seattle, 22h00 Beijing). You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 In between all sunshine, vacation, wedding preparations, etc, I hope you will still be able to make some time for our teleconference. I propose the following agenda items: - More JSON. Please have a look at Dave's recent draft mzQC JSON file. I will still try to provide an initial version of a JSON schema file for validation purposes, but I have a pretty busy week ahead of me so I'm not making any promises. - MIAPE-QC: Depending on the people that manage to attend the call it would be relevant to address the MIAPE-QC recommendations to construct a paragraph based on Dave's written feedback. Thanks, Wout ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Psidev-qc-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx> The integrity and confidentiality of this email is governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> |
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From: Wout B. <wo...@uw...> - 2018-07-16 23:56:46
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Dear colleagues, This is a reminder that our next teleconference is scheduled for Thursday, July 19th, at 14h00 GMT (15h00 London, 16h00 Western Europe & Cape Town, 7h00 Seattle, 22h00 Beijing). You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 In between all sunshine, vacation, wedding preparations, etc, I hope you will still be able to make some time for our teleconference. I propose the following agenda items: - More JSON. Please have a look at Dave's recent draft mzQC JSON file. I will still try to provide an initial version of a JSON schema file for validation purposes, but I have a pretty busy week ahead of me so I'm not making any promises. - MIAPE-QC: Depending on the people that manage to attend the call it would be relevant to address the MIAPE-QC recommendations to construct a paragraph based on Dave's written feedback. Thanks, Wout |
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From: David T. <dt...@su...> - 2018-06-26 10:59:45
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Hi, all. I have given an hour to the problem of creating a draft mzQC JSON file. You can find the product here: https://github.com/HUPO-PSI/qcML-development/blob/master/schema/v0_0_10/examples/20180626-1091_Pool_start_v0.1.qc.json As I mentioned in my notes, I used CV 0.0.11 (though this example falls in the 0.0.10 folder). I am missing these CV terms: * QuaMeter IDFree (software term) * MS1-Count * MS2-Count * MS2-PrecZ-Known * MS2-PrecZ-Unknown Thanks for explaining your template in the last call, Wout! Dave [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx> The integrity and confidentiality of this email is governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> |
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From: Tenzer, S. <te...@un...> - 2018-06-21 07:59:31
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Hi everyone, unfortunately, I have to excuse myself for today, too - we are having an instrument demo today (was planned to be 1 day only, but we need the additional day to discuss data) Sorry for short notice, Stefan Am 21.06.2018 um 07:11 schrieb Jinmeng Jia <jia...@16...<mailto:jia...@16...>>: Hi everyone, I am outside on a meeting these days that I am unable to join tonight's teleconferece. I have updated the MIAPE-QC paragraph based on David's written feedback. Hope we can discuss it next time. My appology. Best, Jinmeng At 2018-06-19 23:37:59, "Wout Bittremieux" <wo...@uw...<mailto:wo...@uw...>> wrote: Dear colleagues, This is a reminder that our next teleconference is scheduled for Thursday, June 21st, at 14h00 GMT (15h00 London, 16h00 Western Europe & Cape Town, 7h00 Seattle, 22h00 Beijing). You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 I propose the following agenda items for the teleconference: 1) Evaluation of JSON examples (Mathias's example<https://github.com/HUPO-PSI/qcML-development/blob/master/schema/v0_0_10/examples/handcrafted_json.qcML>, Dave's example<https://github.com/HUPO-PSI/qcML-development/blob/master/schema/v0_0_10/examples/20180403-1091_Pool_start_v0.1.qc.json>, Wout's example<https://gist.github.com/bittremieux/52d215895d3bdf4e8ca3483c107491a6>). The structure of the files can be used to start the discussion, I've added some comments to my example as well. 2) CV: follow-up on the recent request for new entries<https://github.com/HUPO-PSI/qcML-development/issues/42>. 3) MIAPE-QC: continue discussion from last month with updated MIAPE-QC paragraph and Dave's written feedback. 4) ASMS: overview of QC stuff Dave & Wout saw at ASMS. Thanks, Wout -- Jinmeng, Jia Ph.D. candidate,Tieliu Shi's Lab Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biology Institute of Biomedical Sciences and School of Life Sciences East China Normal University Minhang Campus: 500 Dongchuan RD., Shanghai 200241 ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org<http://Slashdot.org>! http://sdm.link/slashdot_______________________________________________ Psidev-qc-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Jinmeng J. <jia...@16...> - 2018-06-21 05:11:42
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Hi everyone, I am outside on a meeting these days that I am unable to join tonight's teleconferece. I have updated the MIAPE-QC paragraph based on David's written feedback. Hope we can discuss it next time. My appology. Best, Jinmeng At 2018-06-19 23:37:59, "Wout Bittremieux" <wo...@uw...> wrote: Dear colleagues, This is a reminder that our next teleconference is scheduled for Thursday, June 21st, at 14h00 GMT (15h00 London, 16h00 Western Europe & Cape Town, 7h00 Seattle, 22h00 Beijing). You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 I propose the following agenda items for the teleconference: 1) Evaluation of JSON examples (Mathias's example, Dave's example, Wout's example). The structure of the files can be used to start the discussion, I've added some comments to my example as well. 2) CV: follow-up on the recent request for new entries. 3) MIAPE-QC: continue discussion from last month with updated MIAPE-QC paragraph and Dave's written feedback. 4) ASMS: overview of QC stuff Dave & Wout saw at ASMS. Thanks, Wout -- Jinmeng, Jia Ph.D. candidate,Tieliu Shi's Lab Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biology Institute of Biomedical Sciences and School of Life Sciences East China Normal University Minhang Campus: 500 Dongchuan RD., Shanghai 200241 |
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From: Wout B. <wo...@uw...> - 2018-06-19 15:40:15
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Dear colleagues, This is a reminder that our next teleconference is scheduled for Thursday, June 21st, at 14h00 GMT (15h00 London, 16h00 Western Europe & Cape Town, 7h00 Seattle, 22h00 Beijing). You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 I propose the following agenda items for the teleconference: 1) Evaluation of JSON examples (Mathias's example <https://github.com/HUPO-PSI/qcML-development/blob/master/schema/v0_0_10/examples/handcrafted_json.qcML>, Dave's example <https://github.com/HUPO-PSI/qcML-development/blob/master/schema/v0_0_10/examples/20180403-1091_Pool_start_v0.1.qc.json>, Wout's example <https://gist.github.com/bittremieux/52d215895d3bdf4e8ca3483c107491a6>). The structure of the files can be used to start the discussion, I've added some comments to my example as well. 2) CV: follow-up on the recent request for new entries <https://github.com/HUPO-PSI/qcML-development/issues/42>. 3) MIAPE-QC: continue discussion from last month with updated MIAPE-QC paragraph and Dave's written feedback. 4) ASMS: overview of QC stuff Dave & Wout saw at ASMS. Thanks, Wout |
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From: Bittremieux W. <wou...@ua...> - 2018-05-30 23:18:07
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Dear colleagues, I have now made a handcrafted JSON file as well, which you can find here: https://gist.github.com/bittremieux/52d215895d3bdf4e8ca3483c107491a6 I tried to give a few examples and tried to remove some (unnecessary?) extra levels of encapsulation that were caused by a direct translation from XML to JSON. See the comments throughout the file for some of my reasoning. Some things are represented differently in my file versus Dave's file or Mathias's file. This is logical as we'll need to settle on a uniform way of representing our data in JSON, but I feel that by cutting back on the verbosity this example is already more readable than our previous XML files. Instead of a direct translation of the previous XML schema I deviated a bit in some places to take advantage of the additional flexibility JSON gives us. @Dave: Your JSON file seems reasonably ok compared to Mathias's example. I have done a few things differently which I think could be advantageous, but we'll have to discuss that. One major thing that will change is how multiple values are encoded. You added those as a string value after the "__text" key, but that obviously doesn't take advantage of the fact that we have a full JSON object and don't need to encoded our JSON values as a string anymore. Instead this should become a native JSON object. The current string encoding in yours and Mathias's file comes from a naive conversion of the previous XML schema. However, if we have a native JSON format we can directly encode values in JSON. Best, Wout > On 22 May 2018, at 00:34, David Tabb <dt...@su...> wrote: > > Hi, folks. > > I've made a first effort at JSON output for QuaMeter IDFree. You can > find it here: > https://github.com/HUPO-PSI/qcML-development/blob/master/schema/v0_0_10/examples/20180403-1091_Pool_start_v0.1.qc.json. > > Unlike my prior attempt at a qcML output, this example spans only two > metrics. I feel considerably less sure of myself in how these should be > formatted, but at least it seems to be legit JSON, courtesy of the > validator at jsonlint.com. > > Your feedback and guidance on what goes where would be welcome! > > Thanks, > Dave > [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx> > > The integrity and confidentiality of this email is governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> > Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: David T. <dt...@su...> - 2018-05-22 07:49:27
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Hi, folks. I've made a first effort at JSON output for QuaMeter IDFree. You can find it here: https://github.com/HUPO-PSI/qcML-development/blob/master/schema/v0_0_10/examples/20180403-1091_Pool_start_v0.1.qc.json. Unlike my prior attempt at a qcML output, this example spans only two metrics. I feel considerably less sure of myself in how these should be formatted, but at least it seems to be legit JSON, courtesy of the validator at jsonlint.com. Your feedback and guidance on what goes where would be welcome! Thanks, Dave [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx> The integrity and confidentiality of this email is governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> |
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From: Tabb, D. P. [<dt...@su...> - 2018-05-21 06:45:39
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Hi, all. Henning and Pierre-Alain suggested that our QC Working Group discussion at Heidelberg on the way forward for MIAPE-QC was ambiguous and not particularly supportive of the work that Jinmeng Jia has carried out on this project. We felt it might be better if I wrote out our appraisal and plan for the minimum information effort. I'm attaching a two-pager I've assembled over the last couple of weeks. I hope that it better conveys what we hope for this part of the quality project! Thanks, Dave [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx> The integrity and confidentiality of this email is governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> |
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From: Wout B. <wo...@uw...> - 2018-05-17 21:12:10
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Dear colleagues, Please find the meeting notes of today's teleconference here: https://github.com/HUPO-PSI/qcML-development/blob/master/meeting_notes/20180517_telco.md Be sure to check out the meeting notes for a summary on our important discussion about whether to stick to the hybrid XML-JSON format or switch to a native JSON format. Best, Wout > On 14 May 2018, at 20:13, Wout Bittremieux <wo...@uw...> wrote: > > Dear colleagues, > > This is a reminder that our next teleconference is scheduled for Thursday, May 17th, at 14h00 GMT (15h00 London, 16h00 Western Europe & Cape Town, 7h00 Seattle, 22h00 Beijing). We're back to daylight savings time in most places, so please verify that you've got the right time in your calendar. > > You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 > > I hope that everyone has been able to recover a bit from our productive meeting in Heidelberg. To keep the flow going I want to propose the following two agenda items: > > 1) Follow-up on the MIAPE discussion from Heidelberg. > > 2) Discussion about full JSON vs. XML–JSON hybrid. > This has been mentioned briefly a few times and we skirted around it during the meeting in Heidelberg last month, but we haven't had a real discussion about it. A native JSON format would have several advantages (more flexibility, easy APIs, more straightforward validation), but it would be an important departure from our work so far and historic PSI standards so we should carefully discuss this. > Mathias made a JSON example file last month during the meeting. This forms a good starting point for the discussion, so I invite everyone to check it out prior to the teleconference: https://github.com/HUPO-PSI/qcML-development/blob/master/schema/v0_0_10/examples/handcrafted_json.qcML > > Thanks, > Wout > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Wout B. <wo...@uw...> - 2018-05-15 03:16:12
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Dear colleagues, This is a reminder that our next teleconference is scheduled for Thursday, May 17th, at 14h00 GMT (15h00 London, 16h00 Western Europe & Cape Town, 7h00 Seattle, 22h00 Beijing). We're back to daylight savings time in most places, so please verify that you've got the right time in your calendar. You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 I hope that everyone has been able to recover a bit from our productive meeting in Heidelberg. To keep the flow going I want to propose the following two agenda items: 1) Follow-up on the MIAPE discussion from Heidelberg. 2) Discussion about full JSON vs. XML–JSON hybrid. This has been mentioned briefly a few times and we skirted around it during the meeting in Heidelberg last month, but we haven't had a real discussion about it. A native JSON format would have several advantages (more flexibility, easy APIs, more straightforward validation), but it would be an important departure from our work so far and historic PSI standards so we should carefully discuss this. Mathias made a JSON example file last month during the meeting. This forms a good starting point for the discussion, so I invite everyone to check it out prior to the teleconference: https://github.com/HUPO-PSI/qcML-development/blob/master/schema/v0_0_10/examples/handcrafted_json.qcML Thanks, Wout |
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From: David T. <dt...@su...> - 2018-04-20 12:48:06
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Hi, all.
I am attaching the slides (see "wrapup") to describe our highly
productive meeting at EMBL! Thank you all for contributing so much
effort to our success! I am also attaching the slides ("Update") to
show what we planned.
Thanks,
Dave
[http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx>
The integrity and confidentiality of this email is governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer>
Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer>
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From: Hugo L. F. <hlf...@uv...> - 2018-04-17 08:34:14
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Hi David, please, find attached the draft qcML document that our Mass-Up could create from the quality control analysis. We created it using data from a real QC analysis on the "Cancer dataset" available at the Mass-Up downloads page (https://www.sing-group.org/mass-up/downloads/datasets/Cancer-Dataset.zip). As in the example you sent me, we also put a few comments about some things that were unclear. Regarding the QC metrics, there are two types: replicates (or spectra) and samples. The first 5 QC metrics in the document are related to replicates so in this case they have 60 values (12 samples x 5 replicates each). The remaining 11 QC metrics are related to samples: the first 8 samples QC metrics have 12 values, one for each sample; and the remaining 3 samples QC metrics have, at the same time, different sets of 12 values. Each set corresponds to a POP (Percentage of Presence) value. For instance, the "matching-pop" metric have five sets of 12 values for POP values of 0.2, 0.4, 0.6, 0.8 and 1.0. Regarding the sets of values in replicates metrics: they are provided in the same order as replicates are presented in the metadata section. The same applies for samples metrics: they are provided in the same order as samples are presented in the metadata section because replicates with the same "sampleId" appear consecutively. To avoid possible misunderstandings, we discussed an alternative option for indicating samples order: adding a "userParam" with the ordered "sampleId"s. I hope this draft is useful for your meeting. Please, let me know if you need anything else. Best regards, Hugo. El 11/04/18 a las 10:52, David Tabb escribió: > I really appreciate it, sir! > > Our meeting will take place from April 18-20th. If we can discuss it > during the 19th, that would be ideal! > > I have included your image in the update I will be providing at the > start of the meeting (see attached). > > Merci, > Dave > > On 4/11/2018 11:40 AM, Hugo López Fernández wrote: >> Hi David, >> >> sure, I would be pleased to provide such draft. Please, let me know >> the deadline for sending you the document. I will have a meeting >> tomorrow or the day after tomorrow with my Mass-Up collaborators to >> address this. >> >> Regards, >> >> Hugo. >> >> El 11/04/18 a las 09:41, David Tabb escribió: >>> Hi, Hugo. >>> >>> Would you be willing to assemble a draft qcML document that might be >>> created by your Mass-Up software? We will be looking at such examples >>> at our annual HUPO-PSI meeting in a week. I am providing a pointer >>> to a >>> draft qcML example of the quality metrics that are produced within the >>> QuaMeter "IDFree" mode. >>> https://github.com/HUPO-PSI/qcML-development/blob/master/20180403-1091_Pool_start_v0.8.qc.xml >>> >>> >>> >>> Thanks, >>> Dave >>> >>> On 1/20/2017 1:31 PM, Hugo López Fernández wrote: >>>> Hello David, >>>> >>>> I am Hugo, we met last week in Semmering. I hope this email finds you >>>> well and that you had a good trip to back home. >>>> >>>> As we talked in the EuBIC, I am writing you to let you know more about >>>> the quality control analysis that we have included in Mass-Up >>>> (http://sing-group.org/mass-up/). This quality control is intended to >>>> work with peak lists. We would like to incorporate quality control for >>>> raw data, specially to detect batch effects as I also commented you. >>>> >>>> Basically, the quality control (which is explained with most details >>>> in the paper http://doi.org/10.1186/s12859-015-0752-4) can be done at >>>> two levels: at the replicates leve and at the samples level, which >>>> includes additional information from the intra-sample m/z matching >>>> process and consensus spectrum creation (this is because our >>>> collaborators usually want to reduce replicates spectra to a unique >>>> sample "consensus" spectrum). You can find attached the quality >>>> control image included in the paper. >>>> >>>> At the replicates level, the user can check basic information about >>>> each individual spectrum (i.e. peak count, m/z range, intensity >>>> ranges, etc.) and compare all spectra in the dataset. At the samples >>>> level, the user can check the performance of the intra-sample peak >>>> matching process, by comparing the percentages of presence (POP) >>>> counts (i.e.: the counts of peaks that are present in, for example, >>>> 60%, 80% or 100% of replicates) and the POPs of each sample. >>>> >>>> In spite of being a very simple quality control it allowed us to >>>> detect some problems with datasets and we encourage our collaborators >>>> to have a quick look at this quality control metrics before any other >>>> analysis. Unfortunately they usually don't but we must encourage good >>>> practices, which is the reason why I am developing this other software >>>> (http://www.sing-group.org/s2p/), also presented in other poster at >>>> the EuBIC. Basically it is a software to manage, process and integrate >>>> different data sources (Mascot identifications, MALDI plates, 2D-gel >>>> spots). >>>> >>>> I will be happy to answer any question you may have or to receive any >>>> feedback from you. Looking forward to see you again, in other >>>> conference or wherever. >>>> >>>> Best regards, >>>> >>>> Hugo. >>>> >>> >>> [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx> >>> >>> >>> >>> The integrity and confidentiality of this email is governed by these >>> terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> >>> Die integriteit en vertroulikheid van hierdie e-pos word deur die >>> volgende bepalings gereël. >>> Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> >>> >> > > [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx> > > > The integrity and confidentiality of this email is governed by these > terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> > Die integriteit en vertroulikheid van hierdie e-pos word deur die > volgende bepalings gereël. > Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> -- --------------------------------------------------------------------------- Hugo López-Fernández, PhD Email: hlf...@uv... Web: http://www.sing-group.org/~hlfernandez/ --------------------------------------------------------------------------- SING Research Group http://www.sing-group.org ESEI: Escuela Superior de Ingeniería Informática "Politécnico" Building, Room 306 "As Lagoas" Campus 32004 - Ourense - Spain --------------------------------------------------------------------------- CINBIO: Centro de Investigaciones Biomédicas http://cinbio.es/en/si4-next-generation-computer-systems-group/ --------------------------------------------------------------------------- IISGS: Instituto de Investigación Sanitaria Galicia Sur http://www.iisgaliciasur.es/sistemas-informaticos-de-nueva-generacion-sing/ --------------------------------------------------------------------------- The information in this e-mail and in any attachments is confidential and intended exclusively for the named addressee(s). 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From: Tabb, D. P. [<dt...@su...> - 2018-04-14 11:30:32
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Hi, all. I am attaching slides for the first two talks at Heidelberg. The first talk encompasses slides 1-4, explaining how our effort has changed over the last year. The second talk spans slides 5-8, laying out the agenda for the qcML team during this meeting. I hope you find that this captures the spirit of what we've set out to accomplish. I am very grateful to work with all of you! Thanks, Dave [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx> The integrity and confidentiality of this email is governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> |
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From: Tabb, D. P. [<dt...@su...> - 2018-04-14 10:22:22
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Hi, all! Wout, thank you for your reply on the shortcomings of my "v0.8" qcML file to represent IDPicker IDFree. I have now produced a v0.9 revision that incorporates QuaMeter IDFree accessions from the 0.0.10 CV (I'm not sure why I couldn't find those before). Two metrics were missing from the CV (MS count and MS/MS count!), and I decided on a different reporting strategy for known and unknown precursor charge states than the CV had anticipated. I have employed unitAccession tags to provide units for single-value metrics. You can find the new demonstrator file here: https://github.com/HUPO-PSI/qcML-development/blob/master/20180403-1091_Pool_start_v0.9.qc.xml Thanks! Dave ________________________________ From: David Tabb <dt...@su...> Sent: Thursday, April 12, 2018 7:03:37 AM To: psi...@li... Subject: Re: [Psidev-qc-dev] Doing my homework for qcML Well done, Wout! I like that you were able to show instrument readings this way; I remember your working on capturing these readings in the iMonDB database, so it makes sense that we'd want to represent them in qcML. As we move to the outlier.qcml, I see that you're using RawFile to point to a source qcML document (I had earlier used RawFile to point to an mzML rather than a RAW). We may want to work out just what RawFile is supposed to represent or create other terms to represent later products in the pipeline. As Wout notes, though, the RawFile section allows us to specify the file type. The "Meta-analysis settings" set thresholds for variability; as I understand it, though, these thresholds would be applied on individual metrics rather than a dimensionality-reduced set (e.g. via PCA). When we dip down to the comment below below the metaDataParameters section, though, it appears that Wout is giving weights to show how to combine scores, perhaps in a linear combination of metrics to optimize the amount of variability explained? A PCA would really only be feasible for a defined set of metrics from a bunch of input files. This same transform, however, might then be applied to new qcML files that were not part of the set used to conduct PCA. The transform itself does not tell us that a qcML is an outlier or not. Instead, it accepts the quality metrics as an input and outputs the coordinates of this qcML in the transformed space; we can then compute distances in PC space between pairs of qcML files, and an abnormally large distance in PC space implies an outlier. Wout, thank you for trying the multi-file analysis for us! Yes, I think this highlights some areas where we have been vague to date. Merci, Dave On 4/11/2018 10:48 PM, Bittremieux Wout wrote: Dear colleagues, I have also prepared two handcrafted example files: - one from the iMonDB containing instrument parameters as opposed to ID-free/ID-based spectral metrics - one from a meta-analysis to detect low-quality experiments The files include some annotations about things to discuss. As you can see especially for the meta-analysis I'm currently not sure how to correctly store this information in a qcML file. Best, Wout > On 10 Apr 2018, at 10:15, Bittremieux Wout <wou...@ua...><mailto:wou...@ua...> wrote: > > Hi Dave, > > Sorry for the delayed answer to your questions. As far as I'm aware (please someone correct me if I'm wrong): > > - OBO and OWL are two alternative file formats to specify controlled vocabularies and ontologies. We use the OBO format for our CV. This is indeed a simpler format than OWL and can be viewed relatively easily in a simple text editor. Alternatively, Martin has previously recommended OBO-Edit to visualize the relationships between the various terms. > > - In our previous discussions we have indeed said that in principle every tool gets its own range of CV accessions. This would enable a new tool to easily start producing compliant qcML files without having to check dependencies on other tools. It might make sense to reuse some trivial definitions though for metrics that don't involve any computations, such the number of MS/MS scans. On the other hand, how will downstream tools handle conflicting metrics coming from different tools? Although in that case maybe the tool authors should be the main persons responsible to worry about this rather than us. > In any case, it would be useful to explicitly document how tools can get CV accessions. > > - To report the unit for a single QC metric you can use the unitAccession/unitName/unitCvRef attributes for any XML element that is derived from the CVParamType, which qualityParameter elements are. The CVParamType is specified in our XML schema. > > - This XML schema can also be used for simple syntactic validation and some semantic validation. Because we have a mix between XML and JSON unfortunately some external semantic validation will have to be explicitly coded as well though. > Any decent XML editor should have built-in functionality to validate XML files against a schema, and otherwise there are various command-line tools and linters you can use to do that as well. However, the previously linked v0.0.10 XML schema on GitHub does not seem to be fully up to date anymore at the moment, and I think the most recent XML schema is available in Mathias' ongoing pull request. > > - As to metrics numbering I don't think we have a process for that yet. I guess now it's just first-come-first-served. > > Best, > Wout > >> On 09 Apr 2018, at 23:56, David Tabb <dt...@su...><mailto:dt...@su...> wrote: >> >> Hi, all. >> >> I have not yet received an answer to the three questions below. I have, >> however, uploaded it to qcdev, where you can find it at this URL: >> https://github.com/HUPO-PSI/qcML-development/blob/master/20180403-1091_Pool_start_v0.8.qc.xml. >> >> Merci! >> Dave >> >> On 4/5/2018 11:29 AM, David Tabb wrote: >>> Hi, all. >>> >>> At long last, I have completed my "homework" for Heidelberg! I have >>> created a draft XML to represent the qcML output for computing QuaMeter >>> IDFree metrics for a single input mzML file (see text inline below). I >>> would greatly appreciate answers to the following questions to complete >>> this project: >>> >>> 1) If I am reporting only a single value for a metric (such as >>> "XIC-WideFrac"), how do I report the unit for the metric? >>> >>> 2) Do we have an easy way to validate a draft file like this, at least >>> to determine that I have matching end tags for each one I open? I've >>> been using Emacs, which tries to help, but a dedicated XML editor might >>> be preferable. >>> >>> 3) Who officially designates what each metric will be numbered in the CV? >>> >>> Thanks, >>> Dave >>> -------------------------------------------------------- >>> <?xml version="1.0" encoding="UTF-8"?> >>> <qcML xmlns="http://www.prime-xs.eu/ms/qcml" >>> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" >>> xsi:schemaLocation="http://www.prime-xs.eu/ms/qcml >>> file:/home/walzer/psi/qcML-development/schema/v0_0_10/qcML_0_0_10.xsd" >>> version="0.0.10"> >>> <runQuality ID="ID001"> >>> <metaDataParameters ID="fileprovenance001" cvRef="?" >>> accession="?" name="?" description="do we need cv for toplevel" >>> value="all cv attributes are optional anyway"> >>> <InputFiles> >>> <RawFile >>> location="C:\Research\20171124-Lizex-Chia\1091_Pool_start.mzML" >>> id="ID001" name="1091_Pool_start.mzML"> >>> <FileFormat> >>> <cvParam cvRef="PSI-MS" accession="MS:1000584" >>> name="mzML format"/> >>> </FileFormat> >>> <!-- In the following line, I computed the md5sum for the >>> peak-picked mzML, not the RAW! --> >>> <cvParam cvRef="PSI-MS" accession="MS:1000568" name="MD5" >>> value="b583f6d2a91b4749d5a75885330f6e5d" /> >>> <cvParam cvRef="PSI-MS" accession="MS:1000747" >>> name="completion time" value="2017-12-08-T15:38:57Z" /> >>> </RawFile> >>> </InputFiles> >>> </metaDataParameters> >>> <!-- Question to consider: how should I link a metric below to the >>> concept of "liquid chromatography" or "electrospray ionization?" Is >>> this appropriate--> >>> <!-- Units I employ below: --> >>> <!-- UO:0000191 "fraction" --> >>> <!-- UO:0000010 "second" --> >>> <!-- UO:0010006 "ratio" --> >>> <!-- UO:0000189 "count" --> >>> <!-- UO:0000106 "hertz" --> >>> <!-- When a line gives a single metric, where do I indicate the >>> unit type? UO:0000191 "fraction" --> >>> <qualityParameter ID="XIC-WideFrac" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Fraction of precursor ions >>> accounting for the top half of all peak width" value="0.206807"/> >>> <qualityParameter ID="XIC-FWHM" cvRef="PSI-QC-CV" accession="QC:" >>> name="QuaMeter IDFree Metric- Distribution of peak widths for the wide >>> XICs"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" >>> value="3">{'UO:0000010':[12.5377,14.2244,16.9234]}</content></qualityParameter> >>> >>> <!-- UO:0010006 is "ratio" rather than "log ratio"--> >>> <qualityParameter ID="XIC-Height" cvRef="PSI-QC-CV" accession="QC:" >>> name="QuaMeter IDFree Metric- Distribution of peak log ratio heights for >>> the wide XICs"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" >>> value="3">{'UO:0010006':[0.776393,0.93114,6.6283]}</content></qualityParameter> >>> >>> <!-- In the following, where do I indicate the unit type? >>> UO:0000010 "second" --> >>> <qualityParameter ID="RT-Duration" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Highest scan time observed >>> minus the lowest scan time observed" value="4920.17"/> >>> <qualityParameter ID="RT-TIC" cvRef="PSI-QC-CV" accession="QC:" >>> name="QuaMeter IDFree Metric- Distribution of TIC accumulation as >>> fraction of RT-Duration"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" >>> value="4">{'UO:0000191':[0.301236,0.13286,0.174576,0.391328]}</content></qualityParameter> >>> >>> <qualityParameter ID="RT-MS" cvRef="PSI-QC-CV" accession="QC:" >>> name="QuaMeter IDFree Metric- Distribution of MS1 acquisition as >>> fraction of RT-Duration"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" >>> value="4">{'UO:0000191':[0.217794,0.272976,0.275845,0.233385]}</content></qualityParameter> >>> >>> <qualityParameter ID="RT-MSMS" cvRef="PSI-QC-CV" accession="QC:" >>> name="QuaMeter IDFree Metric- Distribution of MS2 acquisition as >>> fraction of RT-Duration"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" >>> value="4">{'UO:0000191':[0.268157,0.233516,0.236373,0.261954]}</content></qualityParameter> >>> >>> <qualityParameter ID="MS1-TIC-Change" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Distribution of log ratios >>> of MS1 scan-to-scan TIC changes"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" >>> value="3">{'UO:0010006':[0.870774,0.900585,4.66521]}</content></qualityParameter> >>> >>> <qualityParameter ID="MS1-TIC" cvRef="PSI-QC-CV" accession="QC:" >>> name="QuaMeter IDFree Metric- Log ratios of MS1 scan TICs"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" >>> value="3">{'UO:0010006':[0.568866,0.815636,1.18124]}</content></qualityParameter> >>> >>> <!-- In the following, where do I indicate the unit type? >>> UO:0000189 "count" --> >>> <qualityParameter ID="MS1-Count" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Number of MS1 scans >>> acquired" value="7832"/> >>> <!-- In the following, where do I indicate the unit type? >>> UO:0000106 "hertz" --> >>> <qualityParameter ID="MS1-Freq-Max" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Maximum frequency for MS1 >>> scan acquisition" value="2.41814"/> >>> <qualityParameter ID="MS1-Density" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Distribution of peak >>> counts for MS1 scans"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" >>> value="3">{'UO:0000189:[693,1205,1424]}</content></qualityParameter> >>> <!-- In the following, where do I indicate the unit type? >>> UO:0000189 "count" --> >>> <qualityParameter ID="MS2-Count" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Number of MS2 scans >>> acquired" value="33495"/> >>> <!-- In the following, where do I indicate the unit type? >>> UO:0000106 "hertz" --> >>> <qualityParameter ID="MS2-Freq-Max" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Maximum frequency for MS2 >>> scan acquisition" value="7.33107"/> >>> <qualityParameter ID="MS2-Density" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Distribution of peak >>> counts for MS2 scans"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" >>> value="3">{'UO:0000189:[27,44,70]}</content></qualityParameter> >>> <!-- How do we specify that the values of a vector sum to 1? How >>> about this case, where two vectors together sume to 1?--> >>> <qualityParameter ID="MS2-PrecZ-Known" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Fraction of known >>> precursor charges for +1, +2, ..., n, more than n"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" >>> value="4">{'UO:0000191':[0,0.15047,0.0687565,0.00877743,0.000507538,0.000268697]}</content></qualityParameter> >>> >>> <!-- For the final metric, I used a reporting type where the number >>> of elements in vector is fixed: QC:3000007--> >>> <qualityParameter ID="MS2-PrecZ-Unknown" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Fraction of unknown >>> precursor charges for +1, more than +1"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000007" >>> value="2">{'UO:0000191':[0.54235,0.22887]}</content></qualityParameter> >>> </runQuality> >>> <cvList> >>> <cv fullName="The HUPO-PSI QC WG metrics ontology in obo >>> format" uri="http://www.github.com/HUPO-PSI/.../" ID="PSI-QC-CV"/> >>> </cvList> >>> </qcML> >>> -------------------------------------------------------- >>> >>> On 4/5/2018 9:47 AM, David Tabb wrote: >>>> Hi, all. >>>> >>>> In creating my hand-crafted example of qcML from QuaMeter IDFree, I've >>>> installed Protege, an ontology viewer. It's useful for perusing the >>>> HUPO-PSI MS ontology (http://purl.obolibrary.org/obo/ms/4.1.2/ms.owl). >>>> >>>> I'm a bit confused, though, in how to review the qcML ontology. At >>>> present, I can find an OBO to download >>>> (https://github.com/HUPO-PSI/qcML-development/raw/master/cv/v0_0_10/qc-cv.obo), >>>> >>>> >>>> but I do not see an OWL equivalent. Helpfully, I can simply review the >>>> OBO in a text editor. >>>> >>>> In particular, I am trying to determine which QC accessions each of my >>>> IDFree metrics will represent. Does each metric generator get a >>>> particular series of numbers that relate to that software's outputs? >>>> Can I reuse a metric accession from other software if my tool generates >>>> the same values (such as the number of MS/MS scans)? >>>> >>>> Jinmeng Jia, will you be able to share your paragraph that meets the >>>> draft MIAPE QC standard with Weimin Zhu for him to present at >>>> Heidelberg? I was sorry to hear you won't be able to attend yourself. >>>> >>>> Thanks, >>>> Dave >>>> >>>> [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx<http://cdn.sun.ac.za/100/ProductionFooter.jpg]%3Chttp://www.sun.ac.za/english/Pages/Water-crisis.aspx>> >>>> >>>> >>>> >>>> The integrity and confidentiality of this email is governed by these >>>> terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> >>>> Die integriteit en vertroulikheid van hierdie e-pos word deur die >>>> volgende bepalings gereël. >>>> Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> >>>> >>>> ------------------------------------------------------------------------------ >>>> >>>> >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>> _______________________________________________ >>>> Psidev-qc-dev mailing list >>>> Psi...@li...<mailto:Psi...@li...> >>>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev >>> >>> >>> [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx<http://cdn.sun.ac.za/100/ProductionFooter.jpg]%3Chttp://www.sun.ac.za/english/Pages/Water-crisis.aspx>> >>> >>> >>> The integrity and confidentiality of this email is governed by these >>> terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> >>> Die integriteit en vertroulikheid van hierdie e-pos word deur die >>> volgende bepalings gereël. >>> Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> >>> >>> ------------------------------------------------------------------------------ >>> >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> Psidev-qc-dev mailing list >>> Psi...@li...<mailto:Psi...@li...> >>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev >> >> >> [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx<http://cdn.sun.ac.za/100/ProductionFooter.jpg]%3Chttp://www.sun.ac.za/english/Pages/Water-crisis.aspx>> >> >> The integrity and confidentiality of this email is governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> >> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> Psidev-qc-dev mailing list >> Psi...@li...<mailto:Psi...@li...> >> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ > Psidev-qc-dev mailing list > Psi...@li...<mailto:Psi...@li...> > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Psidev-qc-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: David T. <dt...@su...> - 2018-04-12 05:04:04
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Well done, Wout! I like that you were able to show instrument readings this way; I remember your working on capturing these readings in the iMonDB database, so it makes sense that we'd want to represent them in qcML. As we move to the outlier.qcml, I see that you're using RawFile to point to a source qcML document (I had earlier used RawFile to point to an mzML rather than a RAW). We may want to work out just what RawFile is supposed to represent or create other terms to represent later products in the pipeline. As Wout notes, though, the RawFile section allows us to specify the file type. The "Meta-analysis settings" set thresholds for variability; as I understand it, though, these thresholds would be applied on individual metrics rather than a dimensionality-reduced set (e.g. via PCA). When we dip down to the comment below below the metaDataParameters section, though, it appears that Wout is giving weights to show how to combine scores, perhaps in a linear combination of metrics to optimize the amount of variability explained? A PCA would really only be feasible for a defined set of metrics from a bunch of input files. This same transform, however, might then be applied to new qcML files that were not part of the set used to conduct PCA. The transform itself does not tell us that a qcML is an outlier or not. Instead, it accepts the quality metrics as an input and outputs the coordinates of this qcML in the transformed space; we can then compute distances in PC space between pairs of qcML files, and an abnormally large distance in PC space implies an outlier. Wout, thank you for trying the multi-file analysis for us! Yes, I think this highlights some areas where we have been vague to date. Merci, Dave On 4/11/2018 10:48 PM, Bittremieux Wout wrote: > Dear colleagues, > > I have also prepared two handcrafted example files: > - one from the iMonDB containing instrument parameters as opposed to > ID-free/ID-based spectral metrics > - one from a meta-analysis to detect low-quality experiments > > The files include some annotations about things to discuss. As you can > see especially for the meta-analysis I'm currently not sure how to > correctly store this information in a qcML file. > > Best, > Wout > > > > On 10 Apr 2018, at 10:15, Bittremieux Wout > <wou...@ua...> wrote: > > > > Hi Dave, > > > > Sorry for the delayed answer to your questions. As far as I'm aware > (please someone correct me if I'm wrong): > > > > - OBO and OWL are two alternative file formats to specify controlled > vocabularies and ontologies. We use the OBO format for our CV. This is > indeed a simpler format than OWL and can be viewed relatively easily > in a simple text editor. Alternatively, Martin has previously > recommended OBO-Edit to visualize the relationships between the > various terms. > > > > - In our previous discussions we have indeed said that in principle > every tool gets its own range of CV accessions. This would enable a > new tool to easily start producing compliant qcML files without having > to check dependencies on other tools. It might make sense to reuse > some trivial definitions though for metrics that don't involve any > computations, such the number of MS/MS scans. On the other hand, how > will downstream tools handle conflicting metrics coming from different > tools? Although in that case maybe the tool authors should be the main > persons responsible to worry about this rather than us. > > In any case, it would be useful to explicitly document how tools can > get CV accessions. > > > > - To report the unit for a single QC metric you can use the > unitAccession/unitName/unitCvRef attributes for any XML element that > is derived from the CVParamType, which qualityParameter elements are. > The CVParamType is specified in our XML schema. > > > > - This XML schema can also be used for simple syntactic validation > and some semantic validation. Because we have a mix between XML and > JSON unfortunately some external semantic validation will have to be > explicitly coded as well though. > > Any decent XML editor should have built-in functionality to validate > XML files against a schema, and otherwise there are various > command-line tools and linters you can use to do that as well. > However, the previously linked v0.0.10 XML schema on GitHub does not > seem to be fully up to date anymore at the moment, and I think the > most recent XML schema is available in Mathias' ongoing pull request. > > > > - As to metrics numbering I don't think we have a process for that > yet. I guess now it's just first-come-first-served. > > > > Best, > > Wout > > > >> On 09 Apr 2018, at 23:56, David Tabb <dt...@su...> wrote: > >> > >> Hi, all. > >> > >> I have not yet received an answer to the three questions below. I > have, > >> however, uploaded it to qcdev, where you can find it at this URL: > >> > https://github.com/HUPO-PSI/qcML-development/blob/master/20180403-1091_Pool_start_v0.8.qc.xml. > >> > >> Merci! > >> Dave > >> > >> On 4/5/2018 11:29 AM, David Tabb wrote: > >>> Hi, all. > >>> > >>> At long last, I have completed my "homework" for Heidelberg! I have > >>> created a draft XML to represent the qcML output for computing > QuaMeter > >>> IDFree metrics for a single input mzML file (see text inline > below). I > >>> would greatly appreciate answers to the following questions to > complete > >>> this project: > >>> > >>> 1) If I am reporting only a single value for a metric (such as > >>> "XIC-WideFrac"), how do I report the unit for the metric? > >>> > >>> 2) Do we have an easy way to validate a draft file like this, at least > >>> to determine that I have matching end tags for each one I open? I've > >>> been using Emacs, which tries to help, but a dedicated XML editor > might > >>> be preferable. > >>> > >>> 3) Who officially designates what each metric will be numbered in > the CV? > >>> > >>> Thanks, > >>> Dave > >>> -------------------------------------------------------- > >>> <?xml version="1.0" encoding="UTF-8"?> > >>> <qcML xmlns="http://www.prime-xs.eu/ms/qcml" > >>> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" > >>> xsi:schemaLocation="http://www.prime-xs.eu/ms/qcml > >>> file:/home/walzer/psi/qcML-development/schema/v0_0_10/qcML_0_0_10.xsd" > >>> version="0.0.10"> > >>> <runQuality ID="ID001"> > >>> <metaDataParameters ID="fileprovenance001" cvRef="?" > >>> accession="?" name="?" description="do we need cv for toplevel" > >>> value="all cv attributes are optional anyway"> > >>> <InputFiles> > >>> <RawFile > >>> location="C:\Research\20171124-Lizex-Chia\1091_Pool_start.mzML" > >>> id="ID001" name="1091_Pool_start.mzML"> > >>> <FileFormat> > >>> <cvParam cvRef="PSI-MS" accession="MS:1000584" > >>> name="mzML format"/> > >>> </FileFormat> > >>> <!-- In the following line, I computed the md5sum for the > >>> peak-picked mzML, not the RAW! --> > >>> <cvParam cvRef="PSI-MS" accession="MS:1000568" name="MD5" > >>> value="b583f6d2a91b4749d5a75885330f6e5d" /> > >>> <cvParam cvRef="PSI-MS" accession="MS:1000747" > >>> name="completion time" value="2017-12-08-T15:38:57Z" /> > >>> </RawFile> > >>> </InputFiles> > >>> </metaDataParameters> > >>> <!-- Question to consider: how should I link a metric below to the > >>> concept of "liquid chromatography" or "electrospray ionization?" Is > >>> this appropriate--> > >>> <!-- Units I employ below: --> > >>> <!-- UO:0000191 "fraction" --> > >>> <!-- UO:0000010 "second" --> > >>> <!-- UO:0010006 "ratio" --> > >>> <!-- UO:0000189 "count" --> > >>> <!-- UO:0000106 "hertz" --> > >>> <!-- When a line gives a single metric, where do I indicate the > >>> unit type? UO:0000191 "fraction" --> > >>> <qualityParameter ID="XIC-WideFrac" cvRef="PSI-QC-CV" > >>> accession="QC:" name="QuaMeter IDFree Metric- Fraction of > precursor ions > >>> accounting for the top half of all peak width" value="0.206807"/> > >>> <qualityParameter ID="XIC-FWHM" cvRef="PSI-QC-CV" accession="QC:" > >>> name="QuaMeter IDFree Metric- Distribution of peak widths for the wide > >>> XICs"> > >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" > >>> > value="3">{'UO:0000010':[12.5377,14.2244,16.9234]}</content></qualityParameter> > >>> > >>> <!-- UO:0010006 is "ratio" rather than "log ratio"--> > >>> <qualityParameter ID="XIC-Height" cvRef="PSI-QC-CV" accession="QC:" > >>> name="QuaMeter IDFree Metric- Distribution of peak log ratio > heights for > >>> the wide XICs"> > >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" > >>> > value="3">{'UO:0010006':[0.776393,0.93114,6.6283]}</content></qualityParameter> > >>> > >>> <!-- In the following, where do I indicate the unit type? > >>> UO:0000010 "second" --> > >>> <qualityParameter ID="RT-Duration" cvRef="PSI-QC-CV" > >>> accession="QC:" name="QuaMeter IDFree Metric- Highest scan time > observed > >>> minus the lowest scan time observed" value="4920.17"/> > >>> <qualityParameter ID="RT-TIC" cvRef="PSI-QC-CV" accession="QC:" > >>> name="QuaMeter IDFree Metric- Distribution of TIC accumulation as > >>> fraction of RT-Duration"> > >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" > >>> > value="4">{'UO:0000191':[0.301236,0.13286,0.174576,0.391328]}</content></qualityParameter> > >>> > >>> <qualityParameter ID="RT-MS" cvRef="PSI-QC-CV" accession="QC:" > >>> name="QuaMeter IDFree Metric- Distribution of MS1 acquisition as > >>> fraction of RT-Duration"> > >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" > >>> > value="4">{'UO:0000191':[0.217794,0.272976,0.275845,0.233385]}</content></qualityParameter> > >>> > >>> <qualityParameter ID="RT-MSMS" cvRef="PSI-QC-CV" accession="QC:" > >>> name="QuaMeter IDFree Metric- Distribution of MS2 acquisition as > >>> fraction of RT-Duration"> > >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" > >>> > value="4">{'UO:0000191':[0.268157,0.233516,0.236373,0.261954]}</content></qualityParameter> > >>> > >>> <qualityParameter ID="MS1-TIC-Change" cvRef="PSI-QC-CV" > >>> accession="QC:" name="QuaMeter IDFree Metric- Distribution of log > ratios > >>> of MS1 scan-to-scan TIC changes"> > >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" > >>> > value="3">{'UO:0010006':[0.870774,0.900585,4.66521]}</content></qualityParameter> > >>> > >>> <qualityParameter ID="MS1-TIC" cvRef="PSI-QC-CV" accession="QC:" > >>> name="QuaMeter IDFree Metric- Log ratios of MS1 scan TICs"> > >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" > >>> > value="3">{'UO:0010006':[0.568866,0.815636,1.18124]}</content></qualityParameter> > >>> > >>> <!-- In the following, where do I indicate the unit type? > >>> UO:0000189 "count" --> > >>> <qualityParameter ID="MS1-Count" cvRef="PSI-QC-CV" > >>> accession="QC:" name="QuaMeter IDFree Metric- Number of MS1 scans > >>> acquired" value="7832"/> > >>> <!-- In the following, where do I indicate the unit type? > >>> UO:0000106 "hertz" --> > >>> <qualityParameter ID="MS1-Freq-Max" cvRef="PSI-QC-CV" > >>> accession="QC:" name="QuaMeter IDFree Metric- Maximum frequency > for MS1 > >>> scan acquisition" value="2.41814"/> > >>> <qualityParameter ID="MS1-Density" cvRef="PSI-QC-CV" > >>> accession="QC:" name="QuaMeter IDFree Metric- Distribution of peak > >>> counts for MS1 scans"> > >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" > >>> value="3">{'UO:0000189:[693,1205,1424]}</content></qualityParameter> > >>> <!-- In the following, where do I indicate the unit type? > >>> UO:0000189 "count" --> > >>> <qualityParameter ID="MS2-Count" cvRef="PSI-QC-CV" > >>> accession="QC:" name="QuaMeter IDFree Metric- Number of MS2 scans > >>> acquired" value="33495"/> > >>> <!-- In the following, where do I indicate the unit type? > >>> UO:0000106 "hertz" --> > >>> <qualityParameter ID="MS2-Freq-Max" cvRef="PSI-QC-CV" > >>> accession="QC:" name="QuaMeter IDFree Metric- Maximum frequency > for MS2 > >>> scan acquisition" value="7.33107"/> > >>> <qualityParameter ID="MS2-Density" cvRef="PSI-QC-CV" > >>> accession="QC:" name="QuaMeter IDFree Metric- Distribution of peak > >>> counts for MS2 scans"> > >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" > >>> value="3">{'UO:0000189:[27,44,70]}</content></qualityParameter> > >>> <!-- How do we specify that the values of a vector sum to 1? How > >>> about this case, where two vectors together sume to 1?--> > >>> <qualityParameter ID="MS2-PrecZ-Known" cvRef="PSI-QC-CV" > >>> accession="QC:" name="QuaMeter IDFree Metric- Fraction of known > >>> precursor charges for +1, +2, ..., n, more than n"> > >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" > >>> > value="4">{'UO:0000191':[0,0.15047,0.0687565,0.00877743,0.000507538,0.000268697]}</content></qualityParameter> > >>> > >>> <!-- For the final metric, I used a reporting type where the number > >>> of elements in vector is fixed: QC:3000007--> > >>> <qualityParameter ID="MS2-PrecZ-Unknown" cvRef="PSI-QC-CV" > >>> accession="QC:" name="QuaMeter IDFree Metric- Fraction of unknown > >>> precursor charges for +1, more than +1"> > >>> <content cvRef="PSI-QC-CV" accession="QC:3000007" > >>> > value="2">{'UO:0000191':[0.54235,0.22887]}</content></qualityParameter> > >>> </runQuality> > >>> <cvList> > >>> <cv fullName="The HUPO-PSI QC WG metrics ontology in obo > >>> format" uri="http://www.github.com/HUPO-PSI/.../" ID="PSI-QC-CV"/> > >>> </cvList> > >>> </qcML> > >>> -------------------------------------------------------- > >>> > >>> On 4/5/2018 9:47 AM, David Tabb wrote: > >>>> Hi, all. > >>>> > >>>> In creating my hand-crafted example of qcML from QuaMeter IDFree, > I've > >>>> installed Protege, an ontology viewer. It's useful for perusing the > >>>> HUPO-PSI MS ontology > (http://purl.obolibrary.org/obo/ms/4.1.2/ms.owl). > >>>> > >>>> I'm a bit confused, though, in how to review the qcML ontology. At > >>>> present, I can find an OBO to download > >>>> > (https://github.com/HUPO-PSI/qcML-development/raw/master/cv/v0_0_10/qc-cv.obo), > >>>> > >>>> > >>>> but I do not see an OWL equivalent. Helpfully, I can simply > review the > >>>> OBO in a text editor. > >>>> > >>>> In particular, I am trying to determine which QC accessions each > of my > >>>> IDFree metrics will represent. Does each metric generator get a > >>>> particular series of numbers that relate to that software's outputs? > >>>> Can I reuse a metric accession from other software if my tool > generates > >>>> the same values (such as the number of MS/MS scans)? > >>>> > >>>> Jinmeng Jia, will you be able to share your paragraph that meets the > >>>> draft MIAPE QC standard with Weimin Zhu for him to present at > >>>> Heidelberg? I was sorry to hear you won't be able to attend > yourself. > >>>> > >>>> Thanks, > >>>> Dave > >>>> > >>>> > [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx > <http://cdn.sun.ac.za/100/ProductionFooter.jpg]%3Chttp://www.sun.ac.za/english/Pages/Water-crisis.aspx>> > >>>> > >>>> > >>>> > >>>> The integrity and confidentiality of this email is governed by these > >>>> terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> > >>>> Die integriteit en vertroulikheid van hierdie e-pos word deur die > >>>> volgende bepalings gereël. > >>>> Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> > >>>> > >>>> > ------------------------------------------------------------------------------ > >>>> > >>>> > >>>> Check out the vibrant tech community on one of the world's most > >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot > >>>> _______________________________________________ > >>>> Psidev-qc-dev mailing list > >>>> Psi...@li... > >>>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > >>> > >>> > >>> > [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx > <http://cdn.sun.ac.za/100/ProductionFooter.jpg]%3Chttp://www.sun.ac.za/english/Pages/Water-crisis.aspx>> > >>> > >>> > >>> The integrity and confidentiality of this email is governed by these > >>> terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> > >>> Die integriteit en vertroulikheid van hierdie e-pos word deur die > >>> volgende bepalings gereël. > >>> Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> > >>> > >>> > ------------------------------------------------------------------------------ > >>> > >>> Check out the vibrant tech community on one of the world's most > >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot > >>> _______________________________________________ > >>> Psidev-qc-dev mailing list > >>> Psi...@li... > >>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > >> > >> > >> > [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx > <http://cdn.sun.ac.za/100/ProductionFooter.jpg]%3Chttp://www.sun.ac.za/english/Pages/Water-crisis.aspx>> > >> > >> The integrity and confidentiality of this email is governed by > these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> > >> Die integriteit en vertroulikheid van hierdie e-pos word deur die > volgende bepalings gereël. > Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> > >> > >> > ------------------------------------------------------------------------------ > >> Check out the vibrant tech community on one of the world's most > >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot > >> _______________________________________________ > >> Psidev-qc-dev mailing list > >> Psi...@li... > >> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > > > > > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, Slashdot.org! > http://sdm.link/slashdot_______________________________________________ > > Psidev-qc-dev mailing list > > Psi...@li... > > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
|
From: Bittremieux W. <wou...@ua...> - 2018-04-11 20:48:21
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Dear colleagues, I have also prepared two handcrafted example files: - one from the iMonDB containing instrument parameters as opposed to ID-free/ID-based spectral metrics - one from a meta-analysis to detect low-quality experiments The files include some annotations about things to discuss. As you can see especially for the meta-analysis I'm currently not sure how to correctly store this information in a qcML file. Best, Wout > On 10 Apr 2018, at 10:15, Bittremieux Wout <wou...@ua...> wrote: > > Hi Dave, > > Sorry for the delayed answer to your questions. As far as I'm aware (please someone correct me if I'm wrong): > > - OBO and OWL are two alternative file formats to specify controlled vocabularies and ontologies. We use the OBO format for our CV. This is indeed a simpler format than OWL and can be viewed relatively easily in a simple text editor. Alternatively, Martin has previously recommended OBO-Edit to visualize the relationships between the various terms. > > - In our previous discussions we have indeed said that in principle every tool gets its own range of CV accessions. This would enable a new tool to easily start producing compliant qcML files without having to check dependencies on other tools. It might make sense to reuse some trivial definitions though for metrics that don't involve any computations, such the number of MS/MS scans. On the other hand, how will downstream tools handle conflicting metrics coming from different tools? Although in that case maybe the tool authors should be the main persons responsible to worry about this rather than us. > In any case, it would be useful to explicitly document how tools can get CV accessions. > > - To report the unit for a single QC metric you can use the unitAccession/unitName/unitCvRef attributes for any XML element that is derived from the CVParamType, which qualityParameter elements are. The CVParamType is specified in our XML schema. > > - This XML schema can also be used for simple syntactic validation and some semantic validation. Because we have a mix between XML and JSON unfortunately some external semantic validation will have to be explicitly coded as well though. > Any decent XML editor should have built-in functionality to validate XML files against a schema, and otherwise there are various command-line tools and linters you can use to do that as well. However, the previously linked v0.0.10 XML schema on GitHub does not seem to be fully up to date anymore at the moment, and I think the most recent XML schema is available in Mathias' ongoing pull request. > > - As to metrics numbering I don't think we have a process for that yet. I guess now it's just first-come-first-served. > > Best, > Wout > >> On 09 Apr 2018, at 23:56, David Tabb <dt...@su...> wrote: >> >> Hi, all. >> >> I have not yet received an answer to the three questions below. I have, >> however, uploaded it to qcdev, where you can find it at this URL: >> https://github.com/HUPO-PSI/qcML-development/blob/master/20180403-1091_Pool_start_v0.8.qc.xml. >> >> Merci! >> Dave >> >> On 4/5/2018 11:29 AM, David Tabb wrote: >>> Hi, all. >>> >>> At long last, I have completed my "homework" for Heidelberg! I have >>> created a draft XML to represent the qcML output for computing QuaMeter >>> IDFree metrics for a single input mzML file (see text inline below). I >>> would greatly appreciate answers to the following questions to complete >>> this project: >>> >>> 1) If I am reporting only a single value for a metric (such as >>> "XIC-WideFrac"), how do I report the unit for the metric? >>> >>> 2) Do we have an easy way to validate a draft file like this, at least >>> to determine that I have matching end tags for each one I open? I've >>> been using Emacs, which tries to help, but a dedicated XML editor might >>> be preferable. >>> >>> 3) Who officially designates what each metric will be numbered in the CV? >>> >>> Thanks, >>> Dave >>> -------------------------------------------------------- >>> <?xml version="1.0" encoding="UTF-8"?> >>> <qcML xmlns="http://www.prime-xs.eu/ms/qcml" >>> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" >>> xsi:schemaLocation="http://www.prime-xs.eu/ms/qcml >>> file:/home/walzer/psi/qcML-development/schema/v0_0_10/qcML_0_0_10.xsd" >>> version="0.0.10"> >>> <runQuality ID="ID001"> >>> <metaDataParameters ID="fileprovenance001" cvRef="?" >>> accession="?" name="?" description="do we need cv for toplevel" >>> value="all cv attributes are optional anyway"> >>> <InputFiles> >>> <RawFile >>> location="C:\Research\20171124-Lizex-Chia\1091_Pool_start.mzML" >>> id="ID001" name="1091_Pool_start.mzML"> >>> <FileFormat> >>> <cvParam cvRef="PSI-MS" accession="MS:1000584" >>> name="mzML format"/> >>> </FileFormat> >>> <!-- In the following line, I computed the md5sum for the >>> peak-picked mzML, not the RAW! --> >>> <cvParam cvRef="PSI-MS" accession="MS:1000568" name="MD5" >>> value="b583f6d2a91b4749d5a75885330f6e5d" /> >>> <cvParam cvRef="PSI-MS" accession="MS:1000747" >>> name="completion time" value="2017-12-08-T15:38:57Z" /> >>> </RawFile> >>> </InputFiles> >>> </metaDataParameters> >>> <!-- Question to consider: how should I link a metric below to the >>> concept of "liquid chromatography" or "electrospray ionization?" Is >>> this appropriate--> >>> <!-- Units I employ below: --> >>> <!-- UO:0000191 "fraction" --> >>> <!-- UO:0000010 "second" --> >>> <!-- UO:0010006 "ratio" --> >>> <!-- UO:0000189 "count" --> >>> <!-- UO:0000106 "hertz" --> >>> <!-- When a line gives a single metric, where do I indicate the >>> unit type? UO:0000191 "fraction" --> >>> <qualityParameter ID="XIC-WideFrac" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Fraction of precursor ions >>> accounting for the top half of all peak width" value="0.206807"/> >>> <qualityParameter ID="XIC-FWHM" cvRef="PSI-QC-CV" accession="QC:" >>> name="QuaMeter IDFree Metric- Distribution of peak widths for the wide >>> XICs"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" >>> value="3">{'UO:0000010':[12.5377,14.2244,16.9234]}</content></qualityParameter> >>> >>> <!-- UO:0010006 is "ratio" rather than "log ratio"--> >>> <qualityParameter ID="XIC-Height" cvRef="PSI-QC-CV" accession="QC:" >>> name="QuaMeter IDFree Metric- Distribution of peak log ratio heights for >>> the wide XICs"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" >>> value="3">{'UO:0010006':[0.776393,0.93114,6.6283]}</content></qualityParameter> >>> >>> <!-- In the following, where do I indicate the unit type? >>> UO:0000010 "second" --> >>> <qualityParameter ID="RT-Duration" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Highest scan time observed >>> minus the lowest scan time observed" value="4920.17"/> >>> <qualityParameter ID="RT-TIC" cvRef="PSI-QC-CV" accession="QC:" >>> name="QuaMeter IDFree Metric- Distribution of TIC accumulation as >>> fraction of RT-Duration"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" >>> value="4">{'UO:0000191':[0.301236,0.13286,0.174576,0.391328]}</content></qualityParameter> >>> >>> <qualityParameter ID="RT-MS" cvRef="PSI-QC-CV" accession="QC:" >>> name="QuaMeter IDFree Metric- Distribution of MS1 acquisition as >>> fraction of RT-Duration"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" >>> value="4">{'UO:0000191':[0.217794,0.272976,0.275845,0.233385]}</content></qualityParameter> >>> >>> <qualityParameter ID="RT-MSMS" cvRef="PSI-QC-CV" accession="QC:" >>> name="QuaMeter IDFree Metric- Distribution of MS2 acquisition as >>> fraction of RT-Duration"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" >>> value="4">{'UO:0000191':[0.268157,0.233516,0.236373,0.261954]}</content></qualityParameter> >>> >>> <qualityParameter ID="MS1-TIC-Change" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Distribution of log ratios >>> of MS1 scan-to-scan TIC changes"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" >>> value="3">{'UO:0010006':[0.870774,0.900585,4.66521]}</content></qualityParameter> >>> >>> <qualityParameter ID="MS1-TIC" cvRef="PSI-QC-CV" accession="QC:" >>> name="QuaMeter IDFree Metric- Log ratios of MS1 scan TICs"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" >>> value="3">{'UO:0010006':[0.568866,0.815636,1.18124]}</content></qualityParameter> >>> >>> <!-- In the following, where do I indicate the unit type? >>> UO:0000189 "count" --> >>> <qualityParameter ID="MS1-Count" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Number of MS1 scans >>> acquired" value="7832"/> >>> <!-- In the following, where do I indicate the unit type? >>> UO:0000106 "hertz" --> >>> <qualityParameter ID="MS1-Freq-Max" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Maximum frequency for MS1 >>> scan acquisition" value="2.41814"/> >>> <qualityParameter ID="MS1-Density" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Distribution of peak >>> counts for MS1 scans"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" >>> value="3">{'UO:0000189:[693,1205,1424]}</content></qualityParameter> >>> <!-- In the following, where do I indicate the unit type? >>> UO:0000189 "count" --> >>> <qualityParameter ID="MS2-Count" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Number of MS2 scans >>> acquired" value="33495"/> >>> <!-- In the following, where do I indicate the unit type? >>> UO:0000106 "hertz" --> >>> <qualityParameter ID="MS2-Freq-Max" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Maximum frequency for MS2 >>> scan acquisition" value="7.33107"/> >>> <qualityParameter ID="MS2-Density" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Distribution of peak >>> counts for MS2 scans"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" >>> value="3">{'UO:0000189:[27,44,70]}</content></qualityParameter> >>> <!-- How do we specify that the values of a vector sum to 1? How >>> about this case, where two vectors together sume to 1?--> >>> <qualityParameter ID="MS2-PrecZ-Known" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Fraction of known >>> precursor charges for +1, +2, ..., n, more than n"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000008" >>> value="4">{'UO:0000191':[0,0.15047,0.0687565,0.00877743,0.000507538,0.000268697]}</content></qualityParameter> >>> >>> <!-- For the final metric, I used a reporting type where the number >>> of elements in vector is fixed: QC:3000007--> >>> <qualityParameter ID="MS2-PrecZ-Unknown" cvRef="PSI-QC-CV" >>> accession="QC:" name="QuaMeter IDFree Metric- Fraction of unknown >>> precursor charges for +1, more than +1"> >>> <content cvRef="PSI-QC-CV" accession="QC:3000007" >>> value="2">{'UO:0000191':[0.54235,0.22887]}</content></qualityParameter> >>> </runQuality> >>> <cvList> >>> <cv fullName="The HUPO-PSI QC WG metrics ontology in obo >>> format" uri="http://www.github.com/HUPO-PSI/.../" ID="PSI-QC-CV"/> >>> </cvList> >>> </qcML> >>> -------------------------------------------------------- >>> >>> On 4/5/2018 9:47 AM, David Tabb wrote: >>>> Hi, all. >>>> >>>> In creating my hand-crafted example of qcML from QuaMeter IDFree, I've >>>> installed Protege, an ontology viewer. It's useful for perusing the >>>> HUPO-PSI MS ontology (http://purl.obolibrary.org/obo/ms/4.1.2/ms.owl). >>>> >>>> I'm a bit confused, though, in how to review the qcML ontology. At >>>> present, I can find an OBO to download >>>> (https://github.com/HUPO-PSI/qcML-development/raw/master/cv/v0_0_10/qc-cv.obo), >>>> >>>> >>>> but I do not see an OWL equivalent. Helpfully, I can simply review the >>>> OBO in a text editor. >>>> >>>> In particular, I am trying to determine which QC accessions each of my >>>> IDFree metrics will represent. Does each metric generator get a >>>> particular series of numbers that relate to that software's outputs? >>>> Can I reuse a metric accession from other software if my tool generates >>>> the same values (such as the number of MS/MS scans)? >>>> >>>> Jinmeng Jia, will you be able to share your paragraph that meets the >>>> draft MIAPE QC standard with Weimin Zhu for him to present at >>>> Heidelberg? I was sorry to hear you won't be able to attend yourself. >>>> >>>> Thanks, >>>> Dave >>>> >>>> [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx> >>>> >>>> >>>> >>>> The integrity and confidentiality of this email is governed by these >>>> terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> >>>> Die integriteit en vertroulikheid van hierdie e-pos word deur die >>>> volgende bepalings gereël. >>>> Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> >>>> >>>> ------------------------------------------------------------------------------ >>>> >>>> >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>> _______________________________________________ >>>> Psidev-qc-dev mailing list >>>> Psi...@li... >>>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev >>> >>> >>> [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx> >>> >>> >>> The integrity and confidentiality of this email is governed by these >>> terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> >>> Die integriteit en vertroulikheid van hierdie e-pos word deur die >>> volgende bepalings gereël. >>> Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> >>> >>> ------------------------------------------------------------------------------ >>> >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> Psidev-qc-dev mailing list >>> Psi...@li... >>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev >> >> >> [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx> >> >> The integrity and confidentiality of this email is governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> >> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> Psidev-qc-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
|
From: Hugo L. F. <hlf...@uv...> - 2018-04-11 13:56:18
|
Fine, I will try to send it by April 17th. Thank you for including my
picture!
Regards,
Hugo.
El 11/04/18 a las 10:52, David Tabb escribió:
> I really appreciate it, sir!
>
> Our meeting will take place from April 18-20th. If we can discuss it
> during the 19th, that would be ideal!
>
> I have included your image in the update I will be providing at the
> start of the meeting (see attached).
>
> Merci,
> Dave
>
> On 4/11/2018 11:40 AM, Hugo López Fernández wrote:
>> Hi David,
>>
>> sure, I would be pleased to provide such draft. Please, let me know
>> the deadline for sending you the document. I will have a meeting
>> tomorrow or the day after tomorrow with my Mass-Up collaborators to
>> address this.
>>
>> Regards,
>>
>> Hugo.
>>
>> El 11/04/18 a las 09:41, David Tabb escribió:
>>> Hi, Hugo.
>>>
>>> Would you be willing to assemble a draft qcML document that might be
>>> created by your Mass-Up software? We will be looking at such examples
>>> at our annual HUPO-PSI meeting in a week. I am providing a pointer
>>> to a
>>> draft qcML example of the quality metrics that are produced within the
>>> QuaMeter "IDFree" mode.
>>> https://github.com/HUPO-PSI/qcML-development/blob/master/20180403-1091_Pool_start_v0.8.qc.xml
>>>
>>>
>>>
>>> Thanks,
>>> Dave
>>>
>>> On 1/20/2017 1:31 PM, Hugo López Fernández wrote:
>>>> Hello David,
>>>>
>>>> I am Hugo, we met last week in Semmering. I hope this email finds you
>>>> well and that you had a good trip to back home.
>>>>
>>>> As we talked in the EuBIC, I am writing you to let you know more about
>>>> the quality control analysis that we have included in Mass-Up
>>>> (http://sing-group.org/mass-up/). This quality control is intended to
>>>> work with peak lists. We would like to incorporate quality control for
>>>> raw data, specially to detect batch effects as I also commented you.
>>>>
>>>> Basically, the quality control (which is explained with most details
>>>> in the paper http://doi.org/10.1186/s12859-015-0752-4) can be done at
>>>> two levels: at the replicates leve and at the samples level, which
>>>> includes additional information from the intra-sample m/z matching
>>>> process and consensus spectrum creation (this is because our
>>>> collaborators usually want to reduce replicates spectra to a unique
>>>> sample "consensus" spectrum). You can find attached the quality
>>>> control image included in the paper.
>>>>
>>>> At the replicates level, the user can check basic information about
>>>> each individual spectrum (i.e. peak count, m/z range, intensity
>>>> ranges, etc.) and compare all spectra in the dataset. At the samples
>>>> level, the user can check the performance of the intra-sample peak
>>>> matching process, by comparing the percentages of presence (POP)
>>>> counts (i.e.: the counts of peaks that are present in, for example,
>>>> 60%, 80% or 100% of replicates) and the POPs of each sample.
>>>>
>>>> In spite of being a very simple quality control it allowed us to
>>>> detect some problems with datasets and we encourage our collaborators
>>>> to have a quick look at this quality control metrics before any other
>>>> analysis. Unfortunately they usually don't but we must encourage good
>>>> practices, which is the reason why I am developing this other software
>>>> (http://www.sing-group.org/s2p/), also presented in other poster at
>>>> the EuBIC. Basically it is a software to manage, process and integrate
>>>> different data sources (Mascot identifications, MALDI plates, 2D-gel
>>>> spots). It probably will not revolutionize bioinformatics but it is
>>>> allowing the research group to process data efficiently and in a
>>>> reproducible way, a totally different scenario than wen I came here
>>>> six months ago.
>>>>
>>>> As I mentioned previously we also would like to include quality
>>>> control metrics for MALDI-TOF raw data, with special focus in batch
>>>> effect detection (which seems to a common problem here). Regarding
>>>> batch effect, I would like to apply this statistic
>>>> (http://dx.doi.org/10.1093/bioinformatics/btt480) based on guided
>>>> principal component analysis to detect batch effects in MALDI-TOF data
>>>> (some people applied it to LC-MS metabolomic data
>>>> [http://dx.doi.org/10.1016/j.talanta.2014.07.031]). I would like to
>>>> develop this work this year if I get public MALDI-TOF datasets where
>>>> batch effect presence has been publicly reported (I found a few
>>>> reported but I could not get the data to analyze it yet).
>>>>
>>>> I will be happy to answer any question you may have or to receive any
>>>> feedback from you. Looking forward to see you again, in other
>>>> conference or wherever.
>>>>
>>>> Best regards,
>>>>
>>>> Hugo.
>>>>
>>>
>>> [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx>
>>>
>>>
>>>
>>> The integrity and confidentiality of this email is governed by these
>>> terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer>
>>> Die integriteit en vertroulikheid van hierdie e-pos word deur die
>>> volgende bepalings gereël.
>>> Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer>
>>>
>>
>
> [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx>
>
>
> The integrity and confidentiality of this email is governed by these
> terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer>
> Die integriteit en vertroulikheid van hierdie e-pos word deur die
> volgende bepalings gereël.
> Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer>
--
---------------------------------------------------------------------------
Hugo López-Fernández, PhD
Email: hlf...@uv...
Web: http://www.sing-group.org/~hlfernandez/
---------------------------------------------------------------------------
SING Research Group
http://www.sing-group.org
ESEI: Escuela Superior de Ingeniería Informática
"Politécnico" Building, Room 306
"As Lagoas" Campus
32004 - Ourense - Spain
---------------------------------------------------------------------------
CINBIO: Centro de Investigaciones Biomédicas
http://cinbio.es/en/si4-next-generation-computer-systems-group/
---------------------------------------------------------------------------
IISGS: Instituto de Investigación Sanitaria Galicia Sur
http://www.iisgaliciasur.es/sistemas-informaticos-de-nueva-generacion-sing/
---------------------------------------------------------------------------
The information in this e-mail and in any attachments is confidential and
intended exclusively for the named addressee(s). Any use of this
information not in accordance with its purpose, any dissemination or
disclosure, either whole or partial, is prohibited except if formally
approved.
|
|
From: David T. <dt...@su...> - 2018-04-11 10:08:06
|
I really appreciate it, sir! Our meeting will take place from April 18-20th. If we can discuss it during the 19th, that would be ideal! I have included your image in the update I will be providing at the start of the meeting (see attached). Merci, Dave On 4/11/2018 11:40 AM, Hugo López Fernández wrote: > Hi David, > > sure, I would be pleased to provide such draft. Please, let me know > the deadline for sending you the document. I will have a meeting > tomorrow or the day after tomorrow with my Mass-Up collaborators to > address this. > > Regards, > > Hugo. > > El 11/04/18 a las 09:41, David Tabb escribió: >> Hi, Hugo. >> >> Would you be willing to assemble a draft qcML document that might be >> created by your Mass-Up software? We will be looking at such examples >> at our annual HUPO-PSI meeting in a week. I am providing a pointer to a >> draft qcML example of the quality metrics that are produced within the >> QuaMeter "IDFree" mode. >> https://github.com/HUPO-PSI/qcML-development/blob/master/20180403-1091_Pool_start_v0.8.qc.xml >> >> >> Thanks, >> Dave >> >> On 1/20/2017 1:31 PM, Hugo López Fernández wrote: >>> Hello David, >>> >>> I am Hugo, we met last week in Semmering. I hope this email finds you >>> well and that you had a good trip to back home. >>> >>> As we talked in the EuBIC, I am writing you to let you know more about >>> the quality control analysis that we have included in Mass-Up >>> (http://sing-group.org/mass-up/). This quality control is intended to >>> work with peak lists. We would like to incorporate quality control for >>> raw data, specially to detect batch effects as I also commented you. >>> >>> Basically, the quality control (which is explained with most details >>> in the paper http://doi.org/10.1186/s12859-015-0752-4) can be done at >>> two levels: at the replicates leve and at the samples level, which >>> includes additional information from the intra-sample m/z matching >>> process and consensus spectrum creation (this is because our >>> collaborators usually want to reduce replicates spectra to a unique >>> sample "consensus" spectrum). You can find attached the quality >>> control image included in the paper. >>> >>> At the replicates level, the user can check basic information about >>> each individual spectrum (i.e. peak count, m/z range, intensity >>> ranges, etc.) and compare all spectra in the dataset. At the samples >>> level, the user can check the performance of the intra-sample peak >>> matching process, by comparing the percentages of presence (POP) >>> counts (i.e.: the counts of peaks that are present in, for example, >>> 60%, 80% or 100% of replicates) and the POPs of each sample. >>> >>> In spite of being a very simple quality control it allowed us to >>> detect some problems with datasets and we encourage our collaborators >>> to have a quick look at this quality control metrics before any other >>> analysis. Unfortunately they usually don't but we must encourage good >>> practices, which is the reason why I am developing this other software >>> (http://www.sing-group.org/s2p/), also presented in other poster at >>> the EuBIC. Basically it is a software to manage, process and integrate >>> different data sources (Mascot identifications, MALDI plates, 2D-gel >>> spots). It probably will not revolutionize bioinformatics but it is >>> allowing the research group to process data efficiently and in a >>> reproducible way, a totally different scenario than wen I came here >>> six months ago. >>> >>> As I mentioned previously we also would like to include quality >>> control metrics for MALDI-TOF raw data, with special focus in batch >>> effect detection (which seems to a common problem here). Regarding >>> batch effect, I would like to apply this statistic >>> (http://dx.doi.org/10.1093/bioinformatics/btt480) based on guided >>> principal component analysis to detect batch effects in MALDI-TOF data >>> (some people applied it to LC-MS metabolomic data >>> [http://dx.doi.org/10.1016/j.talanta.2014.07.031]). I would like to >>> develop this work this year if I get public MALDI-TOF datasets where >>> batch effect presence has been publicly reported (I found a few >>> reported but I could not get the data to analyze it yet). >>> >>> I will be happy to answer any question you may have or to receive any >>> feedback from you. Looking forward to see you again, in other >>> conference or wherever. >>> >>> Best regards, >>> >>> Hugo. >>> >> >> [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx> >> >> >> The integrity and confidentiality of this email is governed by these >> terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> >> Die integriteit en vertroulikheid van hierdie e-pos word deur die >> volgende bepalings gereël. >> Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> >> > [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx> The integrity and confidentiality of this email is governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> |
|
From: Hugo L. F. <hlf...@uv...> - 2018-04-11 09:54:13
|
Hi David,
sure, I would be pleased to provide such draft. Please, let me know the
deadline for sending you the document. I will have a meeting tomorrow or
the day after tomorrow with my Mass-Up collaborators to address this.
Regards,
Hugo.
El 11/04/18 a las 09:41, David Tabb escribió:
> Hi, Hugo.
>
> Would you be willing to assemble a draft qcML document that might be
> created by your Mass-Up software? We will be looking at such examples
> at our annual HUPO-PSI meeting in a week. I am providing a pointer to a
> draft qcML example of the quality metrics that are produced within the
> QuaMeter "IDFree" mode.
> https://github.com/HUPO-PSI/qcML-development/blob/master/20180403-1091_Pool_start_v0.8.qc.xml
>
>
> Thanks,
> Dave
>
> On 1/20/2017 1:31 PM, Hugo López Fernández wrote:
>> Hello David,
>>
>> I am Hugo, we met last week in Semmering. I hope this email finds you
>> well and that you had a good trip to back home.
>>
>> As we talked in the EuBIC, I am writing you to let you know more about
>> the quality control analysis that we have included in Mass-Up
>> (http://sing-group.org/mass-up/). This quality control is intended to
>> work with peak lists. We would like to incorporate quality control for
>> raw data, specially to detect batch effects as I also commented you.
>>
>> Basically, the quality control (which is explained with most details
>> in the paper http://doi.org/10.1186/s12859-015-0752-4) can be done at
>> two levels: at the replicates leve and at the samples level, which
>> includes additional information from the intra-sample m/z matching
>> process and consensus spectrum creation (this is because our
>> collaborators usually want to reduce replicates spectra to a unique
>> sample "consensus" spectrum). You can find attached the quality
>> control image included in the paper.
>>
>> At the replicates level, the user can check basic information about
>> each individual spectrum (i.e. peak count, m/z range, intensity
>> ranges, etc.) and compare all spectra in the dataset. At the samples
>> level, the user can check the performance of the intra-sample peak
>> matching process, by comparing the percentages of presence (POP)
>> counts (i.e.: the counts of peaks that are present in, for example,
>> 60%, 80% or 100% of replicates) and the POPs of each sample.
>>
>> In spite of being a very simple quality control it allowed us to
>> detect some problems with datasets and we encourage our collaborators
>> to have a quick look at this quality control metrics before any other
>> analysis. Unfortunately they usually don't but we must encourage good
>> practices, which is the reason why I am developing this other software
>> (http://www.sing-group.org/s2p/), also presented in other poster at
>> the EuBIC. Basically it is a software to manage, process and integrate
>> different data sources (Mascot identifications, MALDI plates, 2D-gel
>> spots). It probably will not revolutionize bioinformatics but it is
>> allowing the research group to process data efficiently and in a
>> reproducible way, a totally different scenario than wen I came here
>> six months ago.
>>
>> As I mentioned previously we also would like to include quality
>> control metrics for MALDI-TOF raw data, with special focus in batch
>> effect detection (which seems to a common problem here). Regarding
>> batch effect, I would like to apply this statistic
>> (http://dx.doi.org/10.1093/bioinformatics/btt480) based on guided
>> principal component analysis to detect batch effects in MALDI-TOF data
>> (some people applied it to LC-MS metabolomic data
>> [http://dx.doi.org/10.1016/j.talanta.2014.07.031]). I would like to
>> develop this work this year if I get public MALDI-TOF datasets where
>> batch effect presence has been publicly reported (I found a few
>> reported but I could not get the data to analyze it yet).
>>
>> I will be happy to answer any question you may have or to receive any
>> feedback from you. Looking forward to see you again, in other
>> conference or wherever.
>>
>> Best regards,
>>
>> Hugo.
>>
>
> [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx>
>
>
> The integrity and confidentiality of this email is governed by these
> terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer>
> Die integriteit en vertroulikheid van hierdie e-pos word deur die
> volgende bepalings gereël.
> Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer>
>
--
---------------------------------------------------------------------------
Hugo López-Fernández, PhD
Email: hlf...@uv...
Web: http://www.sing-group.org/~hlfernandez/
---------------------------------------------------------------------------
SING Research Group
http://www.sing-group.org
ESEI: Escuela Superior de Ingeniería Informática
"Politécnico" Building, Room 306
"As Lagoas" Campus
32004 - Ourense - Spain
---------------------------------------------------------------------------
CINBIO: Centro de Investigaciones Biomédicas
http://cinbio.es/en/si4-next-generation-computer-systems-group/
---------------------------------------------------------------------------
IISGS: Instituto de Investigación Sanitaria Galicia Sur
http://www.iisgaliciasur.es/sistemas-informaticos-de-nueva-generacion-sing/
---------------------------------------------------------------------------
The information in this e-mail and in any attachments is confidential and
intended exclusively for the named addressee(s). Any use of this
information not in accordance with its purpose, any dissemination or
disclosure, either whole or partial, is prohibited except if formally
approved.
|
|
From: David T. <dt...@su...> - 2018-04-11 08:57:00
|
Hi, Hugo. Would you be willing to assemble a draft qcML document that might be created by your Mass-Up software? We will be looking at such examples at our annual HUPO-PSI meeting in a week. I am providing a pointer to a draft qcML example of the quality metrics that are produced within the QuaMeter "IDFree" mode. https://github.com/HUPO-PSI/qcML-development/blob/master/20180403-1091_Pool_start_v0.8.qc.xml Thanks, Dave On 1/20/2017 1:31 PM, Hugo López Fernández wrote: > Hello David, > > I am Hugo, we met last week in Semmering. I hope this email finds you > well and that you had a good trip to back home. > > As we talked in the EuBIC, I am writing you to let you know more about > the quality control analysis that we have included in Mass-Up > (http://sing-group.org/mass-up/). This quality control is intended to > work with peak lists. We would like to incorporate quality control for > raw data, specially to detect batch effects as I also commented you. > > Basically, the quality control (which is explained with most details > in the paper http://doi.org/10.1186/s12859-015-0752-4) can be done at > two levels: at the replicates leve and at the samples level, which > includes additional information from the intra-sample m/z matching > process and consensus spectrum creation (this is because our > collaborators usually want to reduce replicates spectra to a unique > sample "consensus" spectrum). You can find attached the quality > control image included in the paper. > > At the replicates level, the user can check basic information about > each individual spectrum (i.e. peak count, m/z range, intensity > ranges, etc.) and compare all spectra in the dataset. At the samples > level, the user can check the performance of the intra-sample peak > matching process, by comparing the percentages of presence (POP) > counts (i.e.: the counts of peaks that are present in, for example, > 60%, 80% or 100% of replicates) and the POPs of each sample. > > In spite of being a very simple quality control it allowed us to > detect some problems with datasets and we encourage our collaborators > to have a quick look at this quality control metrics before any other > analysis. Unfortunately they usually don't but we must encourage good > practices, which is the reason why I am developing this other software > (http://www.sing-group.org/s2p/), also presented in other poster at > the EuBIC. Basically it is a software to manage, process and integrate > different data sources (Mascot identifications, MALDI plates, 2D-gel > spots). It probably will not revolutionize bioinformatics but it is > allowing the research group to process data efficiently and in a > reproducible way, a totally different scenario than wen I came here > six months ago. > > As I mentioned previously we also would like to include quality > control metrics for MALDI-TOF raw data, with special focus in batch > effect detection (which seems to a common problem here). Regarding > batch effect, I would like to apply this statistic > (http://dx.doi.org/10.1093/bioinformatics/btt480) based on guided > principal component analysis to detect batch effects in MALDI-TOF data > (some people applied it to LC-MS metabolomic data > [http://dx.doi.org/10.1016/j.talanta.2014.07.031]). I would like to > develop this work this year if I get public MALDI-TOF datasets where > batch effect presence has been publicly reported (I found a few > reported but I could not get the data to analyze it yet). > > I will be happy to answer any question you may have or to receive any > feedback from you. Looking forward to see you again, in other > conference or wherever. > > Best regards, > > Hugo. > [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/Pages/Water-crisis.aspx> The integrity and confidentiality of this email is governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings gereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> |
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