From f1e8a3b4518ec4045582c1d3ce599e55b96b309c Mon Sep 17 00:00:00 2001 From: Nithu John <85367999+nithujohn@users.noreply.github.com> Date: Thu, 31 Oct 2024 10:21:22 +0000 Subject: [PATCH 01/12] Update psi-ms.obo New terms added for software --- psi-ms.obo | 64 +++++++++++++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 61 insertions(+), 3 deletions(-) diff --git a/psi-ms.obo b/psi-ms.obo index 2cb0613..382de3a 100644 --- a/psi-ms.obo +++ b/psi-ms.obo @@ -1,7 +1,7 @@ format-version: 1.2 -data-version: 4.1.181 -date: 11:10:2024 07:15 -saved-by: Joshua Klein +data-version: 4.1.182 +date: 31:10:2024 10:20 +saved-by: Nithu Sara John auto-generated-by: OBO-Edit 2.3.1 default-namespace: MS namespace-id-rule: * MS:$sequence(7,0,9999999)$ @@ -24,6 +24,7 @@ remark: creator: Wout Bittremieux uantwerpen.be> remark: creator: Nils Hoffmann < nils.hoffmann <-at-> cebitec.uni-bielefeld.de> remark: creator: Julian Uszkoreit ruhr-uni-bochum.de> remark: creator: Mathias Walzer ebi.ac.uk> +remark: creator: Nithu Sara John ebi.ac.uk> remark: publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics Working Group remark: When appropriate the definition and synonyms of a term are reported exactly as in the chapter 12 of IUPAC orange book. See http://www.iupac.org/projects/2003/2003-056-2-500.html and http://mass-spec.lsu.edu/msterms/index.php/Main_Page remark: For any queries contact psidev-ms-vocab@lists.sourceforge.net @@ -22655,6 +22656,63 @@ name: selected fragment theoretical m/z observed intensity spectrum def: "Spectrum for which the peaks are limited to a subset of known product ions that are important for subsequent identification, whose m/z values are corrected to theoretical values, and intensity values are experimentally derived." [PSI:PI] is_a: MS:1003072 ! spectrum origin type +[Term] +id: MS:1003426 +name: xQuest/xProphet +def: "A software to identify cross-linked peptides from LC-MS/MS spectra." [PSI:MS] +is_a: MS:1001139 ! quantitation software name +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003427 +name: PeakView +def: "A software for spectral analysis and data interrogation in qualitative review of LC-MS and MS/MS data." [PSI:MS] +is_a: MS:1001139 ! quantitation software name +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003428 +name: perseus +def: "A software for interpreting protein quantification, interaction and post-translational modification data." [PSI:MS] +is_a: MS:1001139 ! quantitation software name +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003429 +name: FragPipe +def: "A computational platform for analyzing mass spectrometry-based proteomics data." [PSI:MS] +is_a: MS:1001139 ! quantitation software name +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003430 +name: OpenMS +def: "A software for LC-MS data management and analysis." [PSI:MS] +is_a: MS:1001139 ! quantitation software name +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003431 +name: OpenMS +def: "A software for LC-MS data management and analysis." [PSI:MS] +is_a: MS:1001139 ! quantitation software name +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003432 +name: pLink +def: "A tool for the analysis of chemically cross-linked proteins using mass spectrometry." [PSI:MS] +is_a: MS:1001139 ! quantitation software name +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003433 +name: pLink2 +def: "Upgraded version of pLink tool, provides a graphical user interface and faster with newly designed index structure." [PSI:MS] +is_a: MS:1003432 ! pLink +is_a: MS:1001139 ! quantitation software name +is_a: MS:1001456 ! analysis software + [Term] id: MS:4000000 name: PSI-MS CV Quality Control Vocabulary From 936d5052c76257c4c1fd25e2687a1f0208e5b02d Mon Sep 17 00:00:00 2001 From: Nithu John <85367999+nithujohn@users.noreply.github.com> Date: Thu, 31 Oct 2024 12:10:59 +0000 Subject: [PATCH 02/12] Update psi-ms.obo --- psi-ms.obo | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/psi-ms.obo b/psi-ms.obo index 5be4ca3..d407bea 100644 --- a/psi-ms.obo +++ b/psi-ms.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: 4.1.182 +data-version: 4.1.183 date: 31:10:2024 10:20 saved-by: Nithu Sara John date: 11:10:2024 07:15 From 6fd2f6fe2e6247c98ef5485fd8cf442748d3f5cb Mon Sep 17 00:00:00 2001 From: Nithu John <85367999+nithujohn@users.noreply.github.com> Date: Thu, 31 Oct 2024 12:21:16 +0000 Subject: [PATCH 03/12] Update psi-ms.obo --- psi-ms.obo | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/psi-ms.obo b/psi-ms.obo index d407bea..0cc2888 100644 --- a/psi-ms.obo +++ b/psi-ms.obo @@ -22705,25 +22705,19 @@ def: "A software for LC-MS data management and analysis." [PSI:MS] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software -[Term] -id: MS:1003431 -name: OpenMS -def: "A software for LC-MS data management and analysis." [PSI:MS] -is_a: MS:1001139 ! quantitation software name -is_a: MS:1001456 ! analysis software [Term] -id: MS:1003432 +id: MS:1003431 name: pLink def: "A tool for the analysis of chemically cross-linked proteins using mass spectrometry." [PSI:MS] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software [Term] -id: MS:1003433 +id: MS:1003432 name: pLink2 def: "Upgraded version of pLink tool, provides a graphical user interface and faster with newly designed index structure." [PSI:MS] -is_a: MS:1003432 ! pLink +is_a: MS:1003431 ! pLink is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software From 10bd9a66104ecc5255bcf22e7ba10091f2d70600 Mon Sep 17 00:00:00 2001 From: Nithu John <85367999+nithujohn@users.noreply.github.com> Date: Thu, 31 Oct 2024 17:55:59 +0000 Subject: [PATCH 04/12] Update psi-ms.obo --- psi-ms.obo | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/psi-ms.obo b/psi-ms.obo index 0cc2888..5de3bf0 100644 --- a/psi-ms.obo +++ b/psi-ms.obo @@ -3,7 +3,7 @@ data-version: 4.1.183 date: 31:10:2024 10:20 saved-by: Nithu Sara John date: 11:10:2024 07:15 -saved-by: Joshua Kle +saved-by: Joshua Klein auto-generated-by: OBO-Edit 2.3.1 default-namespace: MS namespace-id-rule: * MS:$sequence(7,0,9999999)$ @@ -22686,8 +22686,8 @@ is_a: MS:1001456 ! analysis software [Term] id: MS:1003428 -name: perseus -def: "A software for interpreting protein quantification, interaction and post-translational modification data." [PSI:MS] +name: Perseus +def: "A software for interpreting protein quantification, interaction and post-translational modification data." [PMID:27348712, PSI:MS] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software From c07c4d394f93a4048a6c488649b4faad05500951 Mon Sep 17 00:00:00 2001 From: Nithu John <85367999+nithujohn@users.noreply.github.com> Date: Thu, 31 Oct 2024 18:03:08 +0000 Subject: [PATCH 05/12] Update psi-ms.obo --- psi-ms.obo | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/psi-ms.obo b/psi-ms.obo index 5de3bf0..1f9ee27 100644 --- a/psi-ms.obo +++ b/psi-ms.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: 4.1.183 +data-version: 4.1.184 date: 31:10:2024 10:20 saved-by: Nithu Sara John date: 11:10:2024 07:15 From 4f9f2c0489af368a560bbcb542c55660437b7d76 Mon Sep 17 00:00:00 2001 From: Nithu John <85367999+nithujohn@users.noreply.github.com> Date: Mon, 4 Nov 2024 16:15:37 +0000 Subject: [PATCH 06/12] Update psi-ms.obo --- psi-ms.obo | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/psi-ms.obo b/psi-ms.obo index 1239588..0603a2b 100644 --- a/psi-ms.obo +++ b/psi-ms.obo @@ -1,8 +1,8 @@ format-version: 1.2 -data-version: 4.1.184 +data-version: 4.1.185 date: 31:10:2024 10:20 saved-by: Nithu Sara John -date: 11:10:2024 07:15 +date: 04:11:2024 16:15 saved-by: Joshua Klein date: 30:10:2024 10:15 saved-by: Yasset Perez-Riverol From d910b56ff529aee3fbf34c7743c91a997b7a1d43 Mon Sep 17 00:00:00 2001 From: Nithu John <85367999+nithujohn@users.noreply.github.com> Date: Tue, 5 Nov 2024 13:47:31 +0000 Subject: [PATCH 07/12] Update psi-ms.obo --- psi-ms.obo | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/psi-ms.obo b/psi-ms.obo index 0603a2b..491a5a3 100644 --- a/psi-ms.obo +++ b/psi-ms.obo @@ -22674,6 +22674,13 @@ name: selected fragment theoretical m/z observed intensity spectrum def: "Spectrum for which the peaks are limited to a subset of known product ions that are important for subsequent identification, whose m/z values are corrected to theoretical values, and intensity values are experimentally derived." [PSI:PI] is_a: MS:1003072 ! spectrum origin type +[Term] +id: MS:1003425 +name: quantms +def: "Cloud-based pipeline for quantitative proteomics that enables the reanalysis of public proteomics data." [PMID:38965444] +is_a: MS:1001456 ! analysis software +is_a: MS:1001139 ! quantitation software name + [Term] id: MS:1003426 name: xQuest/xProphet @@ -22724,12 +22731,6 @@ is_a: MS:1003431 ! pLink is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software -id: MS:1003425 -name: quantms -def: "Cloud-based pipeline for quantitative proteomics that enables the reanalysis of public proteomics data." [PMID:38965444] -is_a: MS:1001456 ! analysis software -is_a: MS:1001139 ! quantitation software name - [Term] id: MS:4000000 name: PSI-MS CV Quality Control Vocabulary From 81eae126f3db93de4129a65cbb83c42f76c295a9 Mon Sep 17 00:00:00 2001 From: Nithu John <85367999+nithujohn@users.noreply.github.com> Date: Tue, 5 Nov 2024 13:50:36 +0000 Subject: [PATCH 08/12] Update psi-ms.obo --- psi-ms.obo | 4 ---- 1 file changed, 4 deletions(-) diff --git a/psi-ms.obo b/psi-ms.obo index 491a5a3..20523b2 100644 --- a/psi-ms.obo +++ b/psi-ms.obo @@ -2,12 +2,8 @@ format-version: 1.2 data-version: 4.1.185 date: 31:10:2024 10:20 saved-by: Nithu Sara John -date: 04:11:2024 16:15 -saved-by: Joshua Klein date: 30:10:2024 10:15 saved-by: Yasset Perez-Riverol -date: 01:11:2024 10:15 -saved-by: Yasset Perez-Riverol auto-generated-by: OBO-Edit 2.3.1 default-namespace: MS namespace-id-rule: * MS:$sequence(7,0,9999999)$ From a139153bf1b7c8211974d4cef576883bf0e23ad4 Mon Sep 17 00:00:00 2001 From: Nithu John <85367999+nithujohn@users.noreply.github.com> Date: Tue, 5 Nov 2024 13:52:26 +0000 Subject: [PATCH 09/12] Update psi-ms.obo --- psi-ms.obo | 2 -- 1 file changed, 2 deletions(-) diff --git a/psi-ms.obo b/psi-ms.obo index 20523b2..43dc0dd 100644 --- a/psi-ms.obo +++ b/psi-ms.obo @@ -3,8 +3,6 @@ data-version: 4.1.185 date: 31:10:2024 10:20 saved-by: Nithu Sara John date: 30:10:2024 10:15 -saved-by: Yasset Perez-Riverol -auto-generated-by: OBO-Edit 2.3.1 default-namespace: MS namespace-id-rule: * MS:$sequence(7,0,9999999)$ namespace-id-rule: * PEFF:$sequence(7,0,9999999)$ From b8f578f4401b059d69346d03f383c0317a8243e1 Mon Sep 17 00:00:00 2001 From: Nithu John <85367999+nithujohn@users.noreply.github.com> Date: Tue, 5 Nov 2024 13:54:15 +0000 Subject: [PATCH 10/12] Update psi-ms.obo --- psi-ms.obo | 1 - 1 file changed, 1 deletion(-) diff --git a/psi-ms.obo b/psi-ms.obo index 43dc0dd..aaa134a 100644 --- a/psi-ms.obo +++ b/psi-ms.obo @@ -2,7 +2,6 @@ format-version: 1.2 data-version: 4.1.185 date: 31:10:2024 10:20 saved-by: Nithu Sara John -date: 30:10:2024 10:15 default-namespace: MS namespace-id-rule: * MS:$sequence(7,0,9999999)$ namespace-id-rule: * PEFF:$sequence(7,0,9999999)$ From 2627c19c94257286cf831c773092ca9fe301b215 Mon Sep 17 00:00:00 2001 From: Nithu John <85367999+nithujohn@users.noreply.github.com> Date: Tue, 5 Nov 2024 14:20:54 +0000 Subject: [PATCH 11/12] Update psi-ms.obo --- psi-ms.obo | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/psi-ms.obo b/psi-ms.obo index aaa134a..c40cde9 100644 --- a/psi-ms.obo +++ b/psi-ms.obo @@ -22705,14 +22705,14 @@ is_a: MS:1001456 ! analysis software [Term] id: MS:1003430 name: OpenMS -def: "A software for LC-MS data management and analysis." [PSI:MS] +def: "A software for LC-MS data management and analysis." [PMID:38366242] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software [Term] id: MS:1003431 name: pLink -def: "A tool for the analysis of chemically cross-linked proteins using mass spectrometry." [PSI:MS] +def: "A tool for the analysis of chemically cross-linked proteins using mass spectrometry." [PMID:31363125] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software From 8dfa1052d6c227d7e94ee21627e8b4b4b0c847b9 Mon Sep 17 00:00:00 2001 From: Nithu John <85367999+nithujohn@users.noreply.github.com> Date: Wed, 6 Nov 2024 09:33:02 +0000 Subject: [PATCH 12/12] Update psi-ms.obo --- psi-ms.obo | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/psi-ms.obo b/psi-ms.obo index c40cde9..c8a955c 100644 --- a/psi-ms.obo +++ b/psi-ms.obo @@ -22677,7 +22677,7 @@ is_a: MS:1001139 ! quantitation software name [Term] id: MS:1003426 name: xQuest/xProphet -def: "A software to identify cross-linked peptides from LC-MS/MS spectra." [PSI:MS] +def: "A software to identify cross-linked peptides from LC-MS/MS spectra." [PMID:18327264] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software @@ -22698,7 +22698,7 @@ is_a: MS:1001456 ! analysis software [Term] id: MS:1003429 name: FragPipe -def: "A computational platform for analyzing mass spectrometry-based proteomics data." [PSI:MS] +def: "A computational platform for analyzing mass spectrometry-based proteomics data." [PMID:37878603] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software @@ -22712,14 +22712,14 @@ is_a: MS:1001456 ! analysis software [Term] id: MS:1003431 name: pLink -def: "A tool for the analysis of chemically cross-linked proteins using mass spectrometry." [PMID:31363125] +def: "A tool for the analysis of chemically cross-linked proteins using mass spectrometry." [PMID:22772728] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software [Term] id: MS:1003432 name: pLink2 -def: "Upgraded version of pLink tool, provides a graphical user interface and faster with newly designed index structure." [PSI:MS] +def: "Upgraded version of pLink tool, provides a graphical user interface and faster with newly designed index structure." [PMID:31363125] is_a: MS:1003431 ! pLink is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software