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From: Eric D. <eri...@is...> - 2023-04-05 16:26:22
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Hi Bill, yes, these definitions are excellent, thank you. The pull request is still undergoing a few final refinements and approvals, but I think we’re nearly there. I think it is 99% safe to use the identifiers as listed in the PR: https://github.com/HUPO-PSI/psi-ms-CV/pull/189/files It should be fully merged by the end of the week. Thanks, Eric *From:* William Stafford Noble <wn...@uw...> *Sent:* Wednesday, April 5, 2023 4:24 AM *To:* Eric Deutsch <eri...@is...> *Cc:* psi...@li...; Attila Kertesz-Farkas < att...@gm...>; Eric Deutsch <ede...@sy...> *Subject:* Re: [Psidev-ms-vocab] Request for psi-ms-cv ID terms Hi Eric, Can you please let me know if the definitions we sent are sufficient, and if so, when we might expect to hear back about the new ID terms? Thanks! Bill On Wed, Mar 22, 2023 at 4:24 PM William Stafford Noble <wn...@uw...> wrote: Thanks, Eric. Here are the definitions we came up with. Please let me know if these are sufficient. Bill 1. Xcorr rank: The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the XCorr score. 2. exact p-value: A p-value for the XCorr score, calculated using dynamic programming. (PMID: 24895379) 3. refactored xcorr: A modified version of the XCorr score that is made amenable to dynamic programming calculation of p-values by changing a max operation to a sum. (PMID: 30221945) 4. res-ev score: The residue-evidence (res-ev) score measures the quality of a match between a peptide and observed spectrum using a method similar to XCorr, but considering all pairs of observed peaks. (PMID: 30221945) 5. res-ev rank: The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the res-ev score. (PMID: 30221945) 6. res-ev p-value: The residue-evidence p-value is computed from the residue-evidence score using a dynamic programming procedure. (PMID: 30221945) 7. combined p-value: A p-value that is computed by taking the product of the exact p-value and the res-ev p-value and then adjusting for dependencies between them (PMID: 30221945) 8. combined p-value rank: The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the combined p-value. (PMID: 30221945) 9. tailor score: A calibrated version of the XCorr score, computed by dividing the XCorr by the 99th percentile of the distribution of all scores for a particular spectrum. (PMID: 32175744) On Mon, Mar 20, 2023 at 1:34 PM Eric Deutsch <eri...@is...> wrote: Hi Bill, great, yes happy to add terms. What we need is a good definition for each. Would you provide a nice definition for each so that someone can readily understand (at a high level, just a sentence or two) what these scores convey? And also a PMID or DOI where one could learn more. Ideally posted as a single issue here: https://github.com/HUPO-PSI/psi-ms-CV/issues <https://urldefense.com/v3/__https:/github.com/HUPO-PSI/psi-ms-CV/issues__;!!K-Hz7m0Vt54!hBouDBsDVYf-Jbh2Y0H92mYfdo_CBKPYCJFh4UPbwYfOpjyeEnkfymts0z1fquZ8AHmhKgYJET0UB14aBYwFbeig$> Thanks! Eric *From:* William Stafford Noble <wn...@uw...> *Sent:* Monday, March 20, 2023 10:50 AM *To:* psi...@li... *Cc:* Attila Kertesz-Farkas <att...@gm...> *Subject:* [Psidev-ms-vocab] Request for psi-ms-cv ID terms Dear PSI-MSS working group, We are modifying our Tide search engine <https://urldefense.com/v3/__http:/crux.ms/commands/tide-search.html__;!!K-Hz7m0Vt54!hBouDBsDVYf-Jbh2Y0H92mYfdo_CBKPYCJFh4UPbwYfOpjyeEnkfymts0z1fquZ8AHmhKgYJET0UB14aBZXUbkUp$> to produce files in mzTab file format. Currently, Tide is capable of producing a variety of scores that are not standardized in the PSI-ms-CV specification. Would it be possible to create ID terms for the following scores? 1. Xcorr rank 2. exact p-value 3. refactored xcorr 4. res-ev p-value 5. res-ev score 6. combined p-value 7. res-ev rank 8. combined p-value rank 9. tailor score Please let me know if you need any additional information about these scores. Thanks. Bill Noble Department of Genome Sciences University of Washington |
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From: William S. N. <wn...@uw...> - 2023-04-05 11:25:27
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Hi Eric, Can you please let me know if the definitions we sent are sufficient, and if so, when we might expect to hear back about the new ID terms? Thanks! Bill On Wed, Mar 22, 2023 at 4:24 PM William Stafford Noble <wn...@uw...> wrote: > Thanks, Eric. Here are the definitions we came up with. Please let me > know if these are sufficient. > > Bill > > > > > > > 1. > > Xcorr rank: The rank of this PSM relative to all other PSMs involving > this spectrum, when sorting by the XCorr score. > 2. > > exact p-value: A p-value for the XCorr score, calculated using dynamic > programming. (PMID: 24895379) > 3. > > refactored xcorr: A modified version of the XCorr score that is made > amenable to dynamic programming calculation of p-values by changing a max > operation to a sum. (PMID: 30221945) > 4. > > res-ev score: The residue-evidence (res-ev) score measures the quality > of a match between a peptide and observed spectrum using a method similar > to XCorr, but considering all pairs of observed peaks. (PMID: 30221945) > 5. > > res-ev rank: The rank of this PSM relative to all other PSMs involving > this spectrum, when sorting by the res-ev score. (PMID: 30221945) > 6. > > res-ev p-value: The residue-evidence p-value is computed from the > residue-evidence score using a dynamic programming procedure. (PMID: > 30221945) > 7. > > combined p-value: A p-value that is computed by taking the product of > the exact p-value and the res-ev p-value and then adjusting for > dependencies between them (PMID: 30221945) > 8. > > combined p-value rank: The rank of this PSM relative to all other PSMs > involving this spectrum, when sorting by the combined p-value. (PMID: > 30221945) > 9. > > tailor score: A calibrated version of the XCorr score, computed by > dividing the XCorr by the 99th percentile of the distribution of all scores > for a particular spectrum. (PMID: 32175744) > > > On Mon, Mar 20, 2023 at 1:34 PM Eric Deutsch <eri...@is...> > wrote: > >> Hi Bill, great, yes happy to add terms. What we need is a good definition >> for each. Would you provide a nice definition for each so that someone can >> readily understand (at a high level, just a sentence or two) what these >> scores convey? >> >> >> >> And also a PMID or DOI where one could learn more. >> >> >> >> Ideally posted as a single issue here: >> https://github.com/HUPO-PSI/psi-ms-CV/issues >> <https://urldefense.com/v3/__https://github.com/HUPO-PSI/psi-ms-CV/issues__;!!K-Hz7m0Vt54!hBouDBsDVYf-Jbh2Y0H92mYfdo_CBKPYCJFh4UPbwYfOpjyeEnkfymts0z1fquZ8AHmhKgYJET0UB14aBYwFbeig$> >> >> >> >> Thanks! >> >> Eric >> >> >> >> >> >> >> >> *From:* William Stafford Noble <wn...@uw...> >> *Sent:* Monday, March 20, 2023 10:50 AM >> *To:* psi...@li... >> *Cc:* Attila Kertesz-Farkas <att...@gm...> >> *Subject:* [Psidev-ms-vocab] Request for psi-ms-cv ID terms >> >> >> >> Dear PSI-MSS working group, >> >> >> >> We are modifying our Tide search engine >> <https://urldefense.com/v3/__http://crux.ms/commands/tide-search.html__;!!K-Hz7m0Vt54!hBouDBsDVYf-Jbh2Y0H92mYfdo_CBKPYCJFh4UPbwYfOpjyeEnkfymts0z1fquZ8AHmhKgYJET0UB14aBZXUbkUp$> >> to produce files in mzTab file format. Currently, Tide is capable of >> producing a variety of scores that are not standardized in the PSI-ms-CV >> specification. >> >> >> >> Would it be possible to create ID terms for the following scores? >> >> 1. Xcorr rank >> 2. exact p-value >> 3. refactored xcorr >> 4. res-ev p-value >> 5. res-ev score >> 6. combined p-value >> 7. res-ev rank >> 8. combined p-value rank >> 9. tailor score >> >> Please let me know if you need any additional information about these >> scores. >> >> >> >> Thanks. >> >> Bill Noble >> >> Department of Genome Sciences >> >> University of Washington >> >> >> >> >> >> >> > |
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From: William S. N. <wn...@uw...> - 2023-03-22 15:25:22
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Thanks, Eric. Here are the definitions we came up with. Please let me know if these are sufficient. Bill 1. Xcorr rank: The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the XCorr score. 2. exact p-value: A p-value for the XCorr score, calculated using dynamic programming. (PMID: 24895379) 3. refactored xcorr: A modified version of the XCorr score that is made amenable to dynamic programming calculation of p-values by changing a max operation to a sum. (PMID: 30221945) 4. res-ev score: The residue-evidence (res-ev) score measures the quality of a match between a peptide and observed spectrum using a method similar to XCorr, but considering all pairs of observed peaks. (PMID: 30221945) 5. res-ev rank: The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the res-ev score. (PMID: 30221945) 6. res-ev p-value: The residue-evidence p-value is computed from the residue-evidence score using a dynamic programming procedure. (PMID: 30221945) 7. combined p-value: A p-value that is computed by taking the product of the exact p-value and the res-ev p-value and then adjusting for dependencies between them (PMID: 30221945) 8. combined p-value rank: The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the combined p-value. (PMID: 30221945) 9. tailor score: A calibrated version of the XCorr score, computed by dividing the XCorr by the 99th percentile of the distribution of all scores for a particular spectrum. (PMID: 32175744) On Mon, Mar 20, 2023 at 1:34 PM Eric Deutsch <eri...@is...> wrote: > Hi Bill, great, yes happy to add terms. What we need is a good definition > for each. Would you provide a nice definition for each so that someone can > readily understand (at a high level, just a sentence or two) what these > scores convey? > > > > And also a PMID or DOI where one could learn more. > > > > Ideally posted as a single issue here: > https://github.com/HUPO-PSI/psi-ms-CV/issues > <https://urldefense.com/v3/__https://github.com/HUPO-PSI/psi-ms-CV/issues__;!!K-Hz7m0Vt54!hBouDBsDVYf-Jbh2Y0H92mYfdo_CBKPYCJFh4UPbwYfOpjyeEnkfymts0z1fquZ8AHmhKgYJET0UB14aBYwFbeig$> > > > > Thanks! > > Eric > > > > > > > > *From:* William Stafford Noble <wn...@uw...> > *Sent:* Monday, March 20, 2023 10:50 AM > *To:* psi...@li... > *Cc:* Attila Kertesz-Farkas <att...@gm...> > *Subject:* [Psidev-ms-vocab] Request for psi-ms-cv ID terms > > > > Dear PSI-MSS working group, > > > > We are modifying our Tide search engine > <https://urldefense.com/v3/__http://crux.ms/commands/tide-search.html__;!!K-Hz7m0Vt54!hBouDBsDVYf-Jbh2Y0H92mYfdo_CBKPYCJFh4UPbwYfOpjyeEnkfymts0z1fquZ8AHmhKgYJET0UB14aBZXUbkUp$> > to produce files in mzTab file format. Currently, Tide is capable of > producing a variety of scores that are not standardized in the PSI-ms-CV > specification. > > > > Would it be possible to create ID terms for the following scores? > > 1. Xcorr rank > 2. exact p-value > 3. refactored xcorr > 4. res-ev p-value > 5. res-ev score > 6. combined p-value > 7. res-ev rank > 8. combined p-value rank > 9. tailor score > > Please let me know if you need any additional information about these > scores. > > > > Thanks. > > Bill Noble > > Department of Genome Sciences > > University of Washington > > > > > > > |
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From: Eric D. <eri...@is...> - 2023-03-20 21:02:39
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Hi Bill, great, yes happy to add terms. What we need is a good definition for each. Would you provide a nice definition for each so that someone can readily understand (at a high level, just a sentence or two) what these scores convey? And also a PMID or DOI where one could learn more. Ideally posted as a single issue here: https://github.com/HUPO-PSI/psi-ms-CV/issues Thanks! Eric *From:* William Stafford Noble <wn...@uw...> *Sent:* Monday, March 20, 2023 10:50 AM *To:* psi...@li... *Cc:* Attila Kertesz-Farkas <att...@gm...> *Subject:* [Psidev-ms-vocab] Request for psi-ms-cv ID terms Dear PSI-MSS working group, We are modifying our Tide search engine <http://crux.ms/commands/tide-search.html> to produce files in mzTab file format. Currently, Tide is capable of producing a variety of scores that are not standardized in the PSI-ms-CV specification. Would it be possible to create ID terms for the following scores? 1. Xcorr rank 2. exact p-value 3. refactored xcorr 4. res-ev p-value 5. res-ev score 6. combined p-value 7. res-ev rank 8. combined p-value rank 9. tailor score Please let me know if you need any additional information about these scores. Thanks. Bill Noble Department of Genome Sciences University of Washington |
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From: William S. N. <wn...@uw...> - 2023-03-20 17:50:50
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Dear PSI-MSS working group, We are modifying our Tide search engine <http://crux.ms/commands/tide-search.html> to produce files in mzTab file format. Currently, Tide is capable of producing a variety of scores that are not standardized in the PSI-ms-CV specification. Would it be possible to create ID terms for the following scores? 1. Xcorr rank 2. exact p-value 3. refactored xcorr 4. res-ev p-value 5. res-ev score 6. combined p-value 7. res-ev rank 8. combined p-value rank 9. tailor score Please let me know if you need any additional information about these scores. Thanks. Bill Noble Department of Genome Sciences University of Washington |
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From: Vagisha S. <vs...@uw...> - 2022-03-16 16:08:05
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Hi, A Panorama Public user requested the addition of Agilent's 6470 Triple Quadrupole LC/MS instrument to the PSI-MS CV. This is the product details page on the Agilent website: 6470B Triple quadrupole LC/MS <https://www.agilent.com/en/product/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-instruments/triple-quadrupole-lc-ms/6470b-triple-quadrupole-lc-ms>. The user acquired their data on Model# G6470A but I can't see it on the website. The current model is 6470B. Should we add two terms, similar to the 6495 series (MS:1002800, 6495A Triple Quadrupole LC/MS and MS:1002801, 6495B Triple Quadrupole LC/MS)? [Term] id: MS:100xxxx name: 6470A Triple Quadrupole LC/MS def: "The 6470A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:100xxxx name: 6470B Triple Quadrupole LC/MS def: "The 6470B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model I see another instrument in the 6495 series on the Agilent website that is not in the CV - 6495C Triple Quadrupole LC/MS <https://www.agilent.com/en/product/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-instruments/triple-quadrupole-lc-ms/6495c-triple-quadrupole-lc-ms>. Can this be added as well? [Term] id: MS:100xxxx name: 6495C Triple Quadrupole LC/MS def: "The 6495C Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model Thank you! -Vagisha |
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From: Eric D. <ede...@sy...> - 2021-11-16 16:57:44
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Hi Franck, you may propose a term either to this list or as a GitHub issue (GitHub would be preferred). https://github.com/HUPO-PSI/psi-ms-CV/issues Please include the official name of the concept(s) as well as a nice definition. You can model it after an existing term such as: [Term] id: MS:1000922 name: Skyline def: "Software used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the MacCoss lab at the University of Washington." [ https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default ] is_a: MS:1000871 ! SRM software is_a: MS:1001139 ! quantitation software name Please include either a URL or a PubMed ID of a publication for the tool. Thanks, Eric *From:* Franck Giacomoni <fra...@in...> *Sent:* Tuesday, November 16, 2021 1:36 AM *To:* psi...@li... *Subject:* [Psidev-ms-vocab] New software tool in HUPO Mass spectrometry ontology Dear PSI-MS working group, I lead a project related to the building of a database supporting MS and NMR data (The PeakForest project). This database architecture should be published around the beginning of 2022 and will be in open access. We added export functionalities and mzML format should be supported in our next new version. To make our project compliant with your ontology specification (e.g. *custom unreleased software tool*: *Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added. [database_cross_reference: PSI:MS*]), we will be really happy to know how to propose our software as new term. Best regards Franck [image: signature_862404077] *Franck GIACOMONI* fra...@in... *Biological computing & Metabolomics* *INRAE - UMR 1019 Human Nutrition Unit – Metabolism Exploration Platform MetaboHUB – Clermont* *[image: signature_661770698]* Tel. : +33 (0)4 73 62 47 72 Fax : +33 (0)4 73 62 46 88 Centre de recherche de Clermont-Ferrand / Theix F-63122 Saint Genès Champanelle. France INRAE PFEM portal <https://www6.clermont.inrae.fr/plateforme_exploration_metabolisme> MetaboHUB consortium website <http://www.metabohub.fr/metabohub.html> MetaboHUB Open Metabolic e-resources (OMeR) <https://informatique-mia.inra.fr/omer/> Workflow4Metabolomics.org portal <http://workflow4metabolomics.org/> PhytoHub Database website <http://phytohub.eu/> |
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From: Franck G. <fra...@in...> - 2021-11-16 09:51:45
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Dear PSI-MS working group, I lead a project related to the building of a database supporting MS and NMR data (The PeakForest project). This database architecture should be published around the beginning of 2022 and will be in open access. We added export functionalities and mzML format should be supported in our next new version. To make our project compliant with your ontology specification (e.g. custom unreleased software tool: Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added. [database_cross_reference: PSI:MS]), we will be really happy to know how to propose our software as new term. Best regards Franck [signature_862404077] Franck GIACOMONI fra...@in...<mailto:fra...@in...> Biological computing & Metabolomics INRAE - UMR 1019 Human Nutrition Unit – Metabolism Exploration Platform MetaboHUB – Clermont [signature_661770698] Tel. : +33 (0)4 73 62 47 72 Fax : +33 (0)4 73 62 46 88 Centre de recherche de Clermont-Ferrand / Theix F-63122 Saint Genès Champanelle. France INRAE PFEM portal<https://www6.clermont.inrae.fr/plateforme_exploration_metabolisme> MetaboHUB consortium website<http://www.metabohub.fr/metabohub.html> MetaboHUB Open Metabolic e-resources (OMeR)<https://informatique-mia.inra.fr/omer/> Workflow4Metabolomics.org portal<http://workflow4metabolomics.org/> PhytoHub Database website<http://phytohub.eu/> |
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From: Eric D. <ede...@sy...> - 2021-09-17 05:01:20
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Hi everyone, I sent out the Zoom link to a private list of recipients so as not to post the Zoom link here on these lists. If you did not get a Zoom link from me and want to attend, please email me and I'll send you the Zoom link. Thanks, Eric -----Original Message----- From: walzer <wa...@eb...> Sent: Thursday, September 16, 2021 3:39 AM To: psi...@li...; psi...@li... Subject: Re: [Psidev-ms-vocab] QC-CV -> MS-CV Hello Everyone, thanks for the swift completion of the doodle, this Friday seems like the most viable option. On that date, there will be another call for some of you, that has graciously been postponed for half an hour, to make some time for us. So we're going to make it short and snappy, slotting 30min. on Sep 17,Fri, 8 am PST/ 11am EDT / 4pm BST / 5pm CEST to discuss the QC-CV and how to merge with MS-CV. Zoom/google link will follow shortly. later, mths On 2021-09-13 12:55, walzer wrote: > Hello Everyone, > > I just started a doodle to find a date (and a channel on HUPO-PSI > slack for the topic, but since not everyone is there, I'll also post > here). > B'cs of timezone spread Wout suggested we'd start with the USI > timeslot Fridays 8 am PST/ 11am EDT / 4pm BST / 5pm CEST > https://doodle.com/poll/c76bbv6in2h8ywv3 (admin link in slack if you > think we need to add new dates/times) > > best, > mths > > On 2021-08-17 17:49, Mathias Walzer wrote: >> Dear PSI-MS CV community, >> >> I am writing on behalf of the PSI-QC working group, as we want to get >> our QC-CV 'into the fold'. Before that however, we thought it'd be >> best to start a conversation on how. >> We have been developing a separate CV initially to have some freedoms >> on what/how things work out best for the mzQC format, which relies >> heavily on CV control. >> Our CV holds the metric definitions, relations and few additional >> 'organisational' terms, so far <300 entries, for which we chose the >> QC >> >> prefix (naturally). We ditched the `xref: value-type` declarations in >> favour of defining term values with full CV terms and relations, >> which >> >> works nicely with the format. >> The mzQC format is, unlike most PSI formats, JSON based. One of the >> goals in the design was to bring the format closer to the last miles >> of analysis >> (R/pandas/web) but also as something that works between any steps of >> a MS based study workflow (lightweight with high automation >> potential). If you want to know more, check out our specification >> document draft (https://hupo-psi.github.io/mzQC/). For mzQC, we have >> to cover a vast range of QC/MS related topics in the CV. For that, >> we've devised a set of templates and rules for adding new >> term/metrics via GitHub issues. To keep better track of the entries, >> Nils created a GitHub workflow for obo-to-markup conversion to >> enhance browsability. QC-CV is not standalone, we base as much as >> possible on existing definitions, so we >> >> imported few other CVs: UO, OBI, STATO (,NCIT) and PSI-MS of course. >> So, overall I think QC-CV would fit in nicely, either as big PR or >> piece-wise. As for the merge, maybe we can follow the same playbook >> as the PEFF integration did? >> What do you think? >> >> TL;DR: mzQC wants to merge their CV into PSI-MS. But before opening a >> gargantuan PR, we should talk. >> >> Best, >> >> -- >> Mathias Walzer >> European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome >> Campus, Hinxton, Cambridge, UK >> Office: +44 (0)1223 494 2610 >> E-mail: wa...@eb... _______________________________________________ Psidev-ms-vocab mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab |
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From: walzer <wa...@eb...> - 2021-09-16 10:39:08
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Hello Everyone, thanks for the swift completion of the doodle, this Friday seems like the most viable option. On that date, there will be another call for some of you, that has graciously been postponed for half an hour, to make some time for us. So we're going to make it short and snappy, slotting 30min. on Sep 17,Fri, 8 am PST/ 11am EDT / 4pm BST / 5pm CEST to discuss the QC-CV and how to merge with MS-CV. Zoom/google link will follow shortly. later, mths On 2021-09-13 12:55, walzer wrote: > Hello Everyone, > > I just started a doodle to find a date (and a channel on HUPO-PSI > slack for the topic, but since not everyone is there, I'll also post > here). > B'cs of timezone spread Wout suggested we'd start with the USI > timeslot Fridays 8 am PST/ 11am EDT / 4pm BST / 5pm CEST > https://doodle.com/poll/c76bbv6in2h8ywv3 (admin link in slack if you > think we need to add new dates/times) > > best, > mths > > On 2021-08-17 17:49, Mathias Walzer wrote: >> Dear PSI-MS CV community, >> >> I am writing on behalf of the PSI-QC working group, as we want to get >> our >> QC-CV 'into the fold'. Before that however, we thought it'd be best to >> start a >> conversation on how. >> We have been developing a separate CV initially to have some freedoms >> on >> what/how things work out best for the mzQC format, which relies >> heavily on >> CV control. >> Our CV holds the metric definitions, relations and few additional >> 'organisational' terms, so far <300 entries, for which we chose the QC >> >> prefix (naturally). We ditched the `xref: value-type` declarations in >> favour of defining term values with full CV terms and relations, which >> >> works nicely with the format. >> The mzQC format is, unlike most PSI formats, JSON based. One of the >> goals >> in the design was to bring the format closer to the last miles of >> analysis >> (R/pandas/web) but also as something that works between any steps of a >> MS >> based study workflow (lightweight with high automation potential). If >> you >> want to know more, check out our specification document draft >> (https://hupo-psi.github.io/mzQC/). For mzQC, we >> have to cover a vast range of QC/MS related topics in the CV. For >> that, >> we've devised a set of templates and rules for adding new term/metrics >> via >> GitHub issues. To keep better track of the entries, Nils created a >> GitHub >> workflow for obo-to-markup conversion to enhance browsability. QC-CV >> is not >> standalone, we base as much as possible on existing definitions, so we >> >> imported few other CVs: UO, OBI, STATO (,NCIT) and PSI-MS of course. >> So, overall I think QC-CV would fit in nicely, either as big PR or >> piece-wise. As for the merge, maybe we can follow the same playbook as >> the >> PEFF integration did? >> What do you think? >> >> TL;DR: mzQC wants to merge their CV into PSI-MS. But before opening a >> gargantuan PR, we should talk. >> >> Best, >> >> -- >> Mathias Walzer >> European Bioinformatics Institute (EMBL-EBI) >> Wellcome Trust Genome Campus, Hinxton, Cambridge, UK >> Office: +44 (0)1223 494 2610 >> E-mail: wa...@eb... |
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From: walzer <wa...@eb...> - 2021-09-13 11:55:37
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Hello Everyone, I just started a doodle to find a date (and a channel on HUPO-PSI slack for the topic, but since not everyone is there, I'll also post here). B'cs of timezone spread Wout suggested we'd start with the USI timeslot Fridays 8 am PST/ 11am EDT / 4pm BST / 5pm CEST https://doodle.com/poll/c76bbv6in2h8ywv3 (admin link in slack if you think we need to add new dates/times) best, mths On 2021-08-17 17:49, Mathias Walzer wrote: > Dear PSI-MS CV community, > > I am writing on behalf of the PSI-QC working group, as we want to get > our > QC-CV 'into the fold'. Before that however, we thought it'd be best to > start a > conversation on how. > We have been developing a separate CV initially to have some freedoms > on > what/how things work out best for the mzQC format, which relies > heavily on > CV control. > Our CV holds the metric definitions, relations and few additional > 'organisational' terms, so far <300 entries, for which we chose the QC > > prefix (naturally). We ditched the `xref: value-type` declarations in > favour of defining term values with full CV terms and relations, which > > works nicely with the format. > The mzQC format is, unlike most PSI formats, JSON based. One of the > goals > in the design was to bring the format closer to the last miles of > analysis > (R/pandas/web) but also as something that works between any steps of a > MS > based study workflow (lightweight with high automation potential). If > you > want to know more, check out our specification document draft > (https://hupo-psi.github.io/mzQC/). For mzQC, we > have to cover a vast range of QC/MS related topics in the CV. For > that, > we've devised a set of templates and rules for adding new term/metrics > via > GitHub issues. To keep better track of the entries, Nils created a > GitHub > workflow for obo-to-markup conversion to enhance browsability. QC-CV > is not > standalone, we base as much as possible on existing definitions, so we > > imported few other CVs: UO, OBI, STATO (,NCIT) and PSI-MS of course. > So, overall I think QC-CV would fit in nicely, either as big PR or > piece-wise. As for the merge, maybe we can follow the same playbook as > the > PEFF integration did? > What do you think? > > TL;DR: mzQC wants to merge their CV into PSI-MS. But before opening a > gargantuan PR, we should talk. > > Best, > > -- > Mathias Walzer > European Bioinformatics Institute (EMBL-EBI) > Wellcome Trust Genome Campus, Hinxton, Cambridge, UK > Office: +44 (0)1223 494 2610 > E-mail: wa...@eb... |
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From: Eric D. <ede...@sy...> - 2021-08-20 05:22:00
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Hi everyone, this conversation is now here: https://github.com/HUPO-PSI/psi-ms-CV/issues/80 Please participate there if you are interested in this. Thanks, Eric *From:* Mathias Walzer <wa...@eb...> *Sent:* Tuesday, August 17, 2021 9:49 AM *To:* psi...@li... *Cc:* psi...@li... *Subject:* [Psidev-ms-vocab] QC-CV -> MS-CV Dear PSI-MS CV community, I am writing on behalf of the PSI-QC working group, as we want to get our QC-CV 'into the fold'. Before that however, we thought it'd be best to start a conversation on how. We have been developing a separate CV initially to have some freedoms on what/how things work out best for the mzQC format, which relies heavily on CV control. Our CV holds the metric definitions, relations and few additional 'organisational' terms, so far <300 entries, for which we chose the QC prefix (naturally). We ditched the `xref: value-type` declarations in favour of defining term values with full CV terms and relations, which works nicely with the format. The mzQC format is, unlike most PSI formats, JSON based. One of the goals in the design was to bring the format closer to the last miles of analysis (R/pandas/web) but also as something that works between any steps of a MS based study workflow (lightweight with high automation potential). If you want to know more, check out our specification document draft ( https://hupo-psi.github.io/mzQC/). For mzQC, we have to cover a vast range of QC/MS related topics in the CV. For that, we've devised a set of templates and rules for adding new term/metrics via GitHub issues. To keep better track of the entries, Nils created a GitHub workflow for obo-to-markup conversion to enhance browsability. QC-CV is not standalone, we base as much as possible on existing definitions, so we imported few other CVs: UO, OBI, STATO (,NCIT) and PSI-MS of course. So, overall I think QC-CV would fit in nicely, either as big PR or piece-wise. As for the merge, maybe we can follow the same playbook as the PEFF integration did? What do you think? TL;DR: mzQC wants to merge their CV into PSI-MS. But before opening a gargantuan PR, we should talk. Best, -- Mathias Walzer European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge, UK Office: +44 (0)1223 494 2610 E-mail: wa...@eb... |
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From: Mathias W. <wa...@eb...> - 2021-08-17 16:49:31
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Dear PSI-MS CV community, I am writing on behalf of the PSI-QC working group, as we want to get our QC-CV 'into the fold'. Before that however, we thought it'd be best to start a conversation on how. We have been developing a separate CV initially to have some freedoms on what/how things work out best for the mzQC format, which relies heavily on CV control. Our CV holds the metric definitions, relations and few additional 'organisational' terms, so far <300 entries, for which we chose the QC prefix (naturally). We ditched the `xref: value-type` declarations in favour of defining term values with full CV terms and relations, which works nicely with the format. The mzQC format is, unlike most PSI formats, JSON based. One of the goals in the design was to bring the format closer to the last miles of analysis (R/pandas/web) but also as something that works between any steps of a MS based study workflow (lightweight with high automation potential). If you want to know more, check out our specification document draft (https://hupo-psi.github.io/mzQC/). For mzQC, we have to cover a vast range of QC/MS related topics in the CV. For that, we've devised a set of templates and rules for adding new term/metrics via GitHub issues. To keep better track of the entries, Nils created a GitHub workflow for obo-to-markup conversion to enhance browsability. QC-CV is not standalone, we base as much as possible on existing definitions, so we imported few other CVs: UO, OBI, STATO (,NCIT) and PSI-MS of course. So, overall I think QC-CV would fit in nicely, either as big PR or piece-wise. As for the merge, maybe we can follow the same playbook as the PEFF integration did? What do you think? TL;DR: mzQC wants to merge their CV into PSI-MS. But before opening a gargantuan PR, we should talk. Best, -- Mathias Walzer European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge, UK Office: +44 (0)1223 494 2610 E-mail: wa...@eb... |
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From: Juan A. V. <ju...@eb...> - 2021-04-27 13:22:54
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Hi Martin, Everything fine. Thanks a lot for this. Cheers, Juan Antionio > On 26 Apr 2021, at 15:05, Martin Eisenacher <mar...@ru...> wrote: > > Dear colleagues, > dear persons interested in the PSI developments, > > a minor update of the PSI DocProc definition has been agreed to by the > steering committee. > > It mentions "online document editing" systems for public review / removed > the mentioning of the > insecure "comment" function on psidev.info website, changes to shortened > public and > invited review phase from 60 to 45 days; changes the license model from > "Copyright" to "CC-BY-NC 4.0". > > It has to go through a 14-day public review, after which its status could be > changed to FINAL. > I attach version 1.1.2 PREFINAL_DIFF with changes marked in comparison to > 1.1.1, so please add or > comment until May 10th! > > Thank you > Martin > -- > PD DR. MARTIN EISENACHER > Department Leader > DEPARTMENT Medical Bioinformatics > Medizinisches Proteom-Center > Medical Faculty > & > Medical Proteome Analysis > Center for Proteindiagnostics (PRODI) > > Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum > Fon +49 (0)234 32-18104 | Fax +49 (0)234 32-14496 > E-mail mar...@ru... > www.medizinisches-proteom-center.de > > <20210426_PSI_Document_Process_ver_1.1.2_PREFINAL_DIFF.docx>_______________________________________________ > Psi-announce mailing list > Psi...@eb... > https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce |
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From: Eric D. <ede...@sy...> - 2021-04-26 16:05:16
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This looks good to me, thanks!
-----Original Message-----
From: Martin Eisenacher via Psidev-ms-dev
<psi...@li...>
Sent: Monday, April 26, 2021 7:06 AM
To: psi...@li...;
psi...@li...;
psi...@li...; psi...@eb...
Cc: Martin Eisenacher <mar...@ru...>
Subject: [Psidev-ms-dev] PSI DocProc minor update 1.1.2
Dear colleagues,
dear persons interested in the PSI developments,
a minor update of the PSI DocProc definition has been agreed to by the
steering committee.
It mentions "online document editing" systems for public review / removed
the mentioning of the insecure "comment" function on psidev.info website,
changes to shortened public and invited review phase from 60 to 45 days;
changes the license model from "Copyright" to "CC-BY-NC 4.0".
It has to go through a 14-day public review, after which its status could
be changed to FINAL.
I attach version 1.1.2 PREFINAL_DIFF with changes marked in comparison to
1.1.1, so please add or comment until May 10th!
Thank you
Martin
--
PD DR. MARTIN EISENACHER
Department Leader
DEPARTMENT Medical Bioinformatics
Medizinisches Proteom-Center
Medical Faculty
&
Medical Proteome Analysis
Center for Proteindiagnostics (PRODI)
Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum Fon +49
(0)234 32-18104 | Fax +49 (0)234 32-14496 E-mail mar...@ru...
www.medizinisches-proteom-center.de
|
|
From: Martin E. <mar...@ru...> - 2021-04-26 14:06:11
|
Dear colleagues,
dear persons interested in the PSI developments,
a minor update of the PSI DocProc definition has been agreed to by the
steering committee.
It mentions "online document editing" systems for public review / removed
the mentioning of the
insecure "comment" function on psidev.info website, changes to shortened
public and
invited review phase from 60 to 45 days; changes the license model from
"Copyright" to "CC-BY-NC 4.0".
It has to go through a 14-day public review, after which its status could be
changed to FINAL.
I attach version 1.1.2 PREFINAL_DIFF with changes marked in comparison to
1.1.1, so please add or
comment until May 10th!
Thank you
Martin
--
PD DR. MARTIN EISENACHER
Department Leader
DEPARTMENT Medical Bioinformatics
Medizinisches Proteom-Center
Medical Faculty
&
Medical Proteome Analysis
Center for Proteindiagnostics (PRODI)
Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum
Fon +49 (0)234 32-18104 | Fax +49 (0)234 32-14496
E-mail mar...@ru...
www.medizinisches-proteom-center.de
|
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From: Martin E. <mar...@ru...> - 2021-04-25 10:11:11
|
Dear colleagues, Please forward this request for public review into interested communities! The HUPO Proteomics Standards Initiative (PSI) develops standards for documentation and storage of Proteomics data (see http://www.psidev.info for an overview of activities). An updated specification document of PSI-MI TAB (version 2.8) has been submitted to the PSI document process. Aims of format and update: The ability to display molecular interactions in a single, unified PSI-MI XML format represented a milestone in the field of molecular interactions. A tab-delimited format, MITAB, has proven more suitable for users requiring a simple, human-readable configuration. Implementation of these standards by all leading molecular interaction databases has considerably contributed to data exchange, representation and comparison. PSI-MI TAB format and PSI-MI controlled vocabulary have been extended to include additional terms representing aspects of causal interactions for the representation and dissemination of signalling information. PSI-MITAB 2.7 has been extended by adding four more columns allowing the description of signalling data and, therefore, updated to the new PSI-MITAB 2.8 version Specification document, CV terms and use case example: attached to https://psidev.info/mi-tab-28-in-docproc The proposed document version 2.8.0 DRAFT now goes through a 30-day public comments and external review phase until May 30th, 2021. This message is to encourage you to contribute to the standards development activity by commenting on the document. We invite both positive and negative comments on the relevance, correctness, clarity and appropriateness of the specification (e.g. is it presented in accordance with the templates and clearly written, is it sufficiently detailed and comprehensively described and are the examples in agreement with the specification?). Comments can be made on the specification as a whole or on specific parts. If you do not feel experienced enough to comment on this document, but know colleagues who are, please feel free to forward this message to them. There is no requirement that people commenting should have had any prior contact with the PSI. Please send comments by e-mail directly to me until May 30th, 2021. Thank you very much in advance for your valuable help! Best regards Martin Eisenacher (PSI Editor) -- PD DR. MARTIN EISENACHER Department Leader DEPARTMENT Medical Bioinformatics Medizinisches Proteom-Center Medical Faculty & Medical Proteome Analysis Center for Proteindiagnostics (PRODI) Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum Fon +49 (0)234 32-18104 | Fax +49 (0)234 32-14496 E-mail mar...@ru... <mailto:mar...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: Eric D. <ede...@sy...> - 2021-03-12 04:33:09
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Hi Chris, yes, I want to assign someone, but I need to figure out internally who I can assign it to. Thanks, Eric *From:* Chris Mungall <cjm...@lb...> *Sent:* Wednesday, March 10, 2021 12:59 PM *To:* Eric Deutsch <ede...@sy...> *Cc:* psi...@li...; mayerg97 <ger...@ru...>; Nico Matentzoglu <nic...@gm...>; Jones, Andy < And...@li...> *Subject:* Re: [Psidev-ms-vocab] Status of sep and xlmod vocabularies On Tue, Mar 9, 2021 at 11:04 AM Eric Deutsch <ede...@sy...> wrote: Hi Chris, thanks for the note and your help. xlmod is still very relevant and (lightly) maintained. We will fix the error and want to be able to facilitate OWL translation. Thanks! I think the tracker item is the best place to follow up. Do you want to assign someone? Sep is not maintained. The information in there is pretty good and relevant, but there seems to be little to no interest in the community to use it. So in a world of limited available effort, it is deemed unmaintained. Does that translate to obsolete? As far as I’m aware, there is no other ontology that replaces it and it has some good information, but it’s unclear whether is should be discarded or not. Presumably we keep it with no maintenance until someone finds time and motivation to use it and maintain it. I have cc’ed Andy Jones who may wish to weigh in on the topic. So we have a specific category 'inactive' here. However, the sep.obo suffers the same problem, syntactically incorrect obo format. If you think you can fix this we can help you provide OWL, then we can change the status to obsolete. the advantage of the inactive status is that it clearly indicates the status but it does not hide the ontology from browsers Either way, I think it would be good to update the PSI web page to indicate the statuses of the various ontologies in language you think PSI users will understand Thanks, Eric *From:* Chris Mungall <cjm...@lb...> *Sent:* Tuesday, March 9, 2021 9:44 AM *To:* psi...@li...; mayerg97 <ger...@ru...>; Nico Matentzoglu <nic...@gm...> *Subject:* [Psidev-ms-vocab] Status of sep and xlmod vocabularies Hi all, The canonical list of Proteomics Standards vocabularies is here: https://www.psidev.info/groups/controlled-vocabularies#wgCVs Of these, 2 are unavailable in ontology browsers such as OLS: xlmod and sep. Are these vocabularies still maintained? xlmod is unavailable as there is no OWL translation, because there are syntax errors in your obo format file. This is reported here: https://github.com/HUPO-PSI/mzIdentML/issues/117 sep is unavailable as it is declared obsolete in the OBO registry, as expressed by members of this group. See: https://github.com/OBOFoundry/OBOFoundry.github.io/pull/847 If xlmod still supported? If so, we are able to help with getting a syntactically valid file. I also suggest that we synchronize the information on https://www.psidev.info with the information on OBO and ontology browsers, and that sep is marked obsolete in both places. Thanks! Chris Mungall, OBO |
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From: Eric D. <ede...@sy...> - 2021-03-12 04:32:53
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Hi Nico, many thanks for the offer, we will gladly accept your help. First we need to figure out internally who can fix these errors. We will get back to you. Thanks, Eric *From:* Nico Matentzoglu <nic...@gm...> *Sent:* Wednesday, March 10, 2021 1:04 PM *To:* Chris Mungall <cjm...@lb...> *Cc:* Eric Deutsch <ede...@sy...>; psi...@li...; mayerg97 <ger...@ru...>; Jones, Andy <And...@li...> *Subject:* Re: [Psidev-ms-vocab] Status of sep and xlmod vocabularies Hey Eric, if you need any help setting up the translation, I am happy to assist! All best, Nico On Wed, 10 Mar 2021 at 20:58, Chris Mungall <cjm...@lb...> wrote: On Tue, Mar 9, 2021 at 11:04 AM Eric Deutsch <ede...@sy...> wrote: Hi Chris, thanks for the note and your help. xlmod is still very relevant and (lightly) maintained. We will fix the error and want to be able to facilitate OWL translation. Thanks! I think the tracker item is the best place to follow up. Do you want to assign someone? Sep is not maintained. The information in there is pretty good and relevant, but there seems to be little to no interest in the community to use it. So in a world of limited available effort, it is deemed unmaintained. Does that translate to obsolete? As far as I’m aware, there is no other ontology that replaces it and it has some good information, but it’s unclear whether is should be discarded or not. Presumably we keep it with no maintenance until someone finds time and motivation to use it and maintain it. I have cc’ed Andy Jones who may wish to weigh in on the topic. So we have a specific category 'inactive' here. However, the sep.obo suffers the same problem, syntactically incorrect obo format. If you think you can fix this we can help you provide OWL, then we can change the status to obsolete. the advantage of the inactive status is that it clearly indicates the status but it does not hide the ontology from browsers Either way, I think it would be good to update the PSI web page to indicate the statuses of the various ontologies in language you think PSI users will understand Thanks, Eric *From:* Chris Mungall <cjm...@lb...> *Sent:* Tuesday, March 9, 2021 9:44 AM *To:* psi...@li...; mayerg97 <ger...@ru...>; Nico Matentzoglu <nic...@gm...> *Subject:* [Psidev-ms-vocab] Status of sep and xlmod vocabularies Hi all, The canonical list of Proteomics Standards vocabularies is here: https://www.psidev.info/groups/controlled-vocabularies#wgCVs Of these, 2 are unavailable in ontology browsers such as OLS: xlmod and sep. Are these vocabularies still maintained? xlmod is unavailable as there is no OWL translation, because there are syntax errors in your obo format file. This is reported here: https://github.com/HUPO-PSI/mzIdentML/issues/117 sep is unavailable as it is declared obsolete in the OBO registry, as expressed by members of this group. See: https://github.com/OBOFoundry/OBOFoundry.github.io/pull/847 If xlmod still supported? If so, we are able to help with getting a syntactically valid file. I also suggest that we synchronize the information on https://www.psidev.info with the information on OBO and ontology browsers, and that sep is marked obsolete in both places. Thanks! Chris Mungall, OBO |
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From: Chris M. <cjm...@lb...> - 2021-03-10 21:26:16
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On Tue, Mar 9, 2021 at 11:04 AM Eric Deutsch <ede...@sy...> wrote: > Hi Chris, thanks for the note and your help. > > > > xlmod is still very relevant and (lightly) maintained. We will fix the > error and want to be able to facilitate OWL translation. > Thanks! I think the tracker item is the best place to follow up. Do you want to assign someone? > > > Sep is not maintained. The information in there is pretty good and > relevant, but there seems to be little to no interest in the community to > use it. So in a world of limited available effort, it is deemed > unmaintained. Does that translate to obsolete? As far as I’m aware, there > is no other ontology that replaces it and it has some good information, but > it’s unclear whether is should be discarded or not. Presumably we keep it > with no maintenance until someone finds time and motivation to use it and > maintain it. I have cc’ed Andy Jones who may wish to weigh in on the topic. > So we have a specific category 'inactive' here. However, the sep.obo suffers the same problem, syntactically incorrect obo format. If you think you can fix this we can help you provide OWL, then we can change the status to obsolete. the advantage of the inactive status is that it clearly indicates the status but it does not hide the ontology from browsers Either way, I think it would be good to update the PSI web page to indicate the statuses of the various ontologies in language you think PSI users will understand > > > Thanks, > > Eric > > > > > > > > > > > > *From:* Chris Mungall <cjm...@lb...> > *Sent:* Tuesday, March 9, 2021 9:44 AM > *To:* psi...@li...; mayerg97 < > ger...@ru...>; Nico Matentzoglu <nic...@gm...> > *Subject:* [Psidev-ms-vocab] Status of sep and xlmod vocabularies > > > > Hi all, > > > > The canonical list of Proteomics Standards vocabularies is here: > > > > https://www.psidev.info/groups/controlled-vocabularies#wgCVs > > > > Of these, 2 are unavailable in ontology browsers such as OLS: xlmod and > sep. Are these vocabularies still maintained? > > > > xlmod is unavailable as there is no OWL translation, because there are > syntax errors in your obo format file. This is reported here: > > > > https://github.com/HUPO-PSI/mzIdentML/issues/117 > > > > sep is unavailable as it is declared obsolete in the OBO registry, as > expressed by members of this group. See: > https://github.com/OBOFoundry/OBOFoundry.github.io/pull/847 > > > > If xlmod still supported? If so, we are able to help with getting a > syntactically valid file. > > > > I also suggest that we synchronize the information on > https://www.psidev.info with the information on OBO and ontology > browsers, and that sep is marked obsolete in both places. > > > > Thanks! > > Chris Mungall, OBO > |
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From: Nico M. <nic...@gm...> - 2021-03-10 21:03:53
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Hey Eric, if you need any help setting up the translation, I am happy to assist! All best, Nico On Wed, 10 Mar 2021 at 20:58, Chris Mungall <cjm...@lb...> wrote: > > > On Tue, Mar 9, 2021 at 11:04 AM Eric Deutsch <ede...@sy...> > wrote: > >> Hi Chris, thanks for the note and your help. >> >> >> >> xlmod is still very relevant and (lightly) maintained. We will fix the >> error and want to be able to facilitate OWL translation. >> > > Thanks! I think the tracker item is the best place to follow up. Do you > want to assign someone? > > >> >> >> Sep is not maintained. The information in there is pretty good and >> relevant, but there seems to be little to no interest in the community to >> use it. So in a world of limited available effort, it is deemed >> unmaintained. Does that translate to obsolete? As far as I’m aware, there >> is no other ontology that replaces it and it has some good information, but >> it’s unclear whether is should be discarded or not. Presumably we keep it >> with no maintenance until someone finds time and motivation to use it and >> maintain it. I have cc’ed Andy Jones who may wish to weigh in on the topic. >> > > So we have a specific category 'inactive' here. However, the sep.obo > suffers the same problem, syntactically incorrect obo format. If you think > you can fix this we can help you provide OWL, then we can change the status > to obsolete. > > the advantage of the inactive status is that it clearly indicates the > status but it does not hide the ontology from browsers > > Either way, I think it would be good to update the PSI web page to > indicate the statuses of the various ontologies in language you think PSI > users will understand > > >> >> >> Thanks, >> >> Eric >> >> >> >> >> >> >> >> >> >> >> >> *From:* Chris Mungall <cjm...@lb...> >> *Sent:* Tuesday, March 9, 2021 9:44 AM >> *To:* psi...@li...; mayerg97 < >> ger...@ru...>; Nico Matentzoglu <nic...@gm...> >> *Subject:* [Psidev-ms-vocab] Status of sep and xlmod vocabularies >> >> >> >> Hi all, >> >> >> >> The canonical list of Proteomics Standards vocabularies is here: >> >> >> >> https://www.psidev.info/groups/controlled-vocabularies#wgCVs >> >> >> >> Of these, 2 are unavailable in ontology browsers such as OLS: xlmod and >> sep. Are these vocabularies still maintained? >> >> >> >> xlmod is unavailable as there is no OWL translation, because there are >> syntax errors in your obo format file. This is reported here: >> >> >> >> https://github.com/HUPO-PSI/mzIdentML/issues/117 >> >> >> >> sep is unavailable as it is declared obsolete in the OBO registry, as >> expressed by members of this group. See: >> https://github.com/OBOFoundry/OBOFoundry.github.io/pull/847 >> >> >> >> If xlmod still supported? If so, we are able to help with getting a >> syntactically valid file. >> >> >> >> I also suggest that we synchronize the information on >> https://www.psidev.info with the information on OBO and ontology >> browsers, and that sep is marked obsolete in both places. >> >> >> >> Thanks! >> >> Chris Mungall, OBO >> > |
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From: Eric D. <ede...@sy...> - 2021-03-09 19:34:39
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Hi Chris, thanks for the note and your help. xlmod is still very relevant and (lightly) maintained. We will fix the error and want to be able to facilitate OWL translation. Sep is not maintained. The information in there is pretty good and relevant, but there seems to be little to no interest in the community to use it. So in a world of limited available effort, it is deemed unmaintained. Does that translate to obsolete? As far as I’m aware, there is no other ontology that replaces it and it has some good information, but it’s unclear whether is should be discarded or not. Presumably we keep it with no maintenance until someone finds time and motivation to use it and maintain it. I have cc’ed Andy Jones who may wish to weigh in on the topic. Thanks, Eric *From:* Chris Mungall <cjm...@lb...> *Sent:* Tuesday, March 9, 2021 9:44 AM *To:* psi...@li...; mayerg97 <ger...@ru...>; Nico Matentzoglu <nic...@gm...> *Subject:* [Psidev-ms-vocab] Status of sep and xlmod vocabularies Hi all, The canonical list of Proteomics Standards vocabularies is here: https://www.psidev.info/groups/controlled-vocabularies#wgCVs Of these, 2 are unavailable in ontology browsers such as OLS: xlmod and sep. Are these vocabularies still maintained? xlmod is unavailable as there is no OWL translation, because there are syntax errors in your obo format file. This is reported here: https://github.com/HUPO-PSI/mzIdentML/issues/117 sep is unavailable as it is declared obsolete in the OBO registry, as expressed by members of this group. See: https://github.com/OBOFoundry/OBOFoundry.github.io/pull/847 If xlmod still supported? If so, we are able to help with getting a syntactically valid file. I also suggest that we synchronize the information on https://www.psidev.info with the information on OBO and ontology browsers, and that sep is marked obsolete in both places. Thanks! Chris Mungall, OBO |
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From: Chris M. <cjm...@lb...> - 2021-03-09 18:12:31
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Hi all, The canonical list of Proteomics Standards vocabularies is here: https://www.psidev.info/groups/controlled-vocabularies#wgCVs Of these, 2 are unavailable in ontology browsers such as OLS: xlmod and sep. Are these vocabularies still maintained? xlmod is unavailable as there is no OWL translation, because there are syntax errors in your obo format file. This is reported here: https://github.com/HUPO-PSI/mzIdentML/issues/117 sep is unavailable as it is declared obsolete in the OBO registry, as expressed by members of this group. See: https://github.com/OBOFoundry/OBOFoundry.github.io/pull/847 If xlmod still supported? If so, we are able to help with getting a syntactically valid file. I also suggest that we synchronize the information on https://www.psidev.info with the information on OBO and ontology browsers, and that sep is marked obsolete in both places. Thanks! Chris Mungall, OBO |
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From: Sylvie R. <syl...@un...> - 2020-12-27 22:12:16
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Dear colleagues, dear members of the Proteomics community, The HUPO Proteomics Standards Initiative (PSI) develops standards for documentation and storage of Proteomics data (see http://www.psidev.info for an overview of activities). The *specification document* *ProForma, Proteoform and Peptidoform Notation* (version 2, draft 12) has been submitted to the PSI document process. It aims to standardise the representation of proteoforms/peptidoforms supporting the main proteomics approaches, including both bottom-up (focused on peptides/peptidoforms) and top down (focused on proteins/proteoforms) approaches. *Specification document*: http://www.psidev.info/proforma-v2 *Use case examples*: https://github.com/HUPO-PSI/ProForma/) *Development background*: https://github.com/HUPO-PSI/ProForma After having passed a 30-day review of the PSI steering group with minor changes, the proposed document version 2.0.0 DRAFT now goes through *60-day public comments and external review phase until February 27th, 2021*. This message is to encourage you to contribute to the standards development activity by commenting on the document. We invite both positive and negative comments on the relevance, correctness, clarity and appropriateness of the specification (e.g. is it presented in accordance with the templates and clearly written, is it sufficiently detailed and comprehensively described and are the examples in agreement with the specification?). Comments can be made on the specification as a whole or on specific parts. If you do not feel experienced enough to comment on this document, but know colleagues who are, please feel free to forward this message to them. There is no requirement that people commenting should have had any prior contact with the PSI. *Please send comments by e-mail directly to syl...@un... *before *February 27th, 2021.* Thank you very much in advance for your valuable help. Best regards. Professor Sylvie RICARD-BLUM - *PSI Editor* Pericellular and Extracellular Supramolecular Assemblies UMR 5246 CNRS - University Lyon 1 Institute of Molecular and Supramolecular Chemistry and Biochemistry University Claude Bernard Lyon 1, 43 Boulevard du 11 novembre 1918 69622 Villeurbanne Cedex, France Phone: +33(0)4 72 44 82 32 E-mail: syl...@un... http://www.icbms.fr The French Society for Matrix Biology http://www.sfbmec.fr The International Society for Matrix Biology http://ismb.org |
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From: Eric D. <ede...@sy...> - 2020-11-17 19:11:08
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Merged. [Term] id: MS:1003144 name: Triple Quad 7500 def: "SCIEX Triple Quad 7500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model *From:* Eric Deutsch <eri...@is...> *Sent:* Tuesday, November 17, 2020 9:39 AM *To:* psi...@li... *Cc:* Eric Deutsch <ede...@sy...> *Subject:* RE: [Psidev-ms-vocab] New term needed for SCIEX Triple Quad™ 7500 Hi Vagisha, thanks for the request. Please see pull request and approve or comment: https://github.com/HUPO-PSI/psi-ms-CV/pull/49/files *From:* Vagisha Sharma <vs...@uw...> *Sent:* Monday, November 16, 2020 8:44 PM *To:* psi...@li... *Subject:* [Psidev-ms-vocab] New term needed for SCIEX Triple Quad™ 7500 Hi, We have data submitted to Panorama Public that was acquired on a SCIEX Triple Quad™ 7500 <https://sciex.com/about-us/press-releases/the-sciex-triple-quad-7500-lc-ms/ms-system-qtrap-ready-launches-at-virtual-product-experience>. There is no term for this instrument in the PSI-MS CV. Can this be added? [Term] id: MS:100xxxx name: Triple Quad 7500 def: "SCIEX Triple Quad 7500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model Thanks, Vagisha |
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