From 3b955218a75f08eb5a6c50a9dc32ceafdcbcb488 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Wed, 30 Oct 2024 10:21:52 +0000 Subject: [PATCH 1/8] quantms added --- psi-ms.obo | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/psi-ms.obo b/psi-ms.obo index 1f163b9..286c6ae 100644 --- a/psi-ms.obo +++ b/psi-ms.obo @@ -22667,6 +22667,13 @@ 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: "Is a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data" [PSI:MS] +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 9f51a628907b37d5729c3a8131e797b06791dc51 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Wed, 30 Oct 2024 10:24:03 +0000 Subject: [PATCH 2/8] version increased. --- psi-ms.obo | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/psi-ms.obo b/psi-ms.obo index 286c6ae..5952c63 100644 --- a/psi-ms.obo +++ b/psi-ms.obo @@ -1,7 +1,7 @@ format-version: 1.2 -data-version: 4.1.182 -date: 11:10:2024 07:15 -saved-by: Joshua Klein +data-version: 4.1.183 +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:$sequence(7,0,9999999)$ From 7cef8e24e25adb4be50ea518000ccd43c8c41dd2 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Wed, 30 Oct 2024 13:57:18 +0000 Subject: [PATCH 3/8] version increased. --- .github/workflows/validate-owl.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/validate-owl.yaml b/.github/workflows/validate-owl.yaml index 5961e68..62065f4 100644 --- a/.github/workflows/validate-owl.yaml +++ b/.github/workflows/validate-owl.yaml @@ -43,8 +43,8 @@ jobs: - name: Validate OWL File for OLS run: | cd ols4/dataload/rdf2json/target - wget https://raw.githubusercontent.com/ypriverol/psi-ms-CV/dev/owl-config-ols/foundry.json - wget https://raw.githubusercontent.com/ypriverol/psi-ms-CV/dev/owl-config-ols/fail_owl.json + wget https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/dev/owl-config-ols/foundry.json + wget https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/dev/owl-config-ols/fail_owl.json java -jar rdf2json-1.0-SNAPSHOT.jar --config foundry.json --output foundry_out.json if diff foundry_out.json fail_owl.json > /dev/null; then echo "The PSI-MS ontology has an error in the owl file and do not allow to import in OLS" From 5dd9834612b3f06361bf44d1fda8b76b3f8d3baf Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Wed, 30 Oct 2024 14:00:28 +0000 Subject: [PATCH 4/8] version increased. --- .github/workflows/validate-owl.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/validate-owl.yaml b/.github/workflows/validate-owl.yaml index 62065f4..bcad8f4 100644 --- a/.github/workflows/validate-owl.yaml +++ b/.github/workflows/validate-owl.yaml @@ -43,8 +43,8 @@ jobs: - name: Validate OWL File for OLS run: | cd ols4/dataload/rdf2json/target - wget https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/dev/owl-config-ols/foundry.json - wget https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/dev/owl-config-ols/fail_owl.json + wget https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/owl-config-ols/foundry.json + wget https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/owl-config-ols/fail_owl.json java -jar rdf2json-1.0-SNAPSHOT.jar --config foundry.json --output foundry_out.json if diff foundry_out.json fail_owl.json > /dev/null; then echo "The PSI-MS ontology has an error in the owl file and do not allow to import in OLS" From ddb44b2584c2708e91aaefe33a32fc750cae4b3e Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Wed, 30 Oct 2024 20:59:35 +0000 Subject: [PATCH 5/8] quantms changed --- psi-ms.obo | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/psi-ms.obo b/psi-ms.obo index 5952c63..5b5f62b 100644 --- a/psi-ms.obo +++ b/psi-ms.obo @@ -22670,7 +22670,7 @@ is_a: MS:1003072 ! spectrum origin type [Term] id: MS:1003425 name: quantms -def: "Is a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data" [PSI:MS] +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 From b10d2530893e3f0f74162ea83e85da375005e80e Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Fri, 1 Nov 2024 15:12:54 +0000 Subject: [PATCH 6/8] add reference to Scout --- psi-ms.obo | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/psi-ms.obo b/psi-ms.obo index 5b5f62b..211ecf7 100644 --- a/psi-ms.obo +++ b/psi-ms.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: 4.1.183 -date: 30:10:2024 10:15 +data-version: 4.1.184 +date: 01:11:2024 10:15 saved-by: Yasset Perez-Riverol auto-generated-by: OBO-Edit 2.3.1 default-namespace: MS @@ -22538,7 +22538,7 @@ is_a: MS:1000531 ! software [Term] id: MS:1003407 name: Scout -def: "Identifying crosslinked peptides in complex protein mixtures" [PSI:MS] +def: "Identifying crosslinked peptides in complex protein mixtures" [PMID:39482464] is_a: MS:1001456 ! analysis software [Term] From 0415d56d086185de7599014800e1aeefe3411f52 Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Sun, 10 Nov 2024 08:22:02 +0000 Subject: [PATCH 7/8] Andromeda:delta score added --- psi-ms.obo | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/psi-ms.obo b/psi-ms.obo index c8a955c..8a91f35 100644 --- a/psi-ms.obo +++ b/psi-ms.obo @@ -22724,6 +22724,14 @@ is_a: MS:1003431 ! pLink is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software +[Term] +id: MS:1003433 +name: Andromeda:delta score +def: "Score difference to the second best identified peptide with a different amino acid sequence." [PSI:PI] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1002108 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + [Term] id: MS:4000000 name: PSI-MS CV Quality Control Vocabulary From 481fb78de523b3461dd68e315f22f19d48ee22bb Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Sun, 10 Nov 2024 08:23:50 +0000 Subject: [PATCH 8/8] Andromeda:delta score added --- psi-ms.obo | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/psi-ms.obo b/psi-ms.obo index 8a91f35..c9ec1a9 100644 --- a/psi-ms.obo +++ b/psi-ms.obo @@ -1,7 +1,7 @@ format-version: 1.2 -data-version: 4.1.185 -date: 31:10:2024 10:20 -saved-by: Nithu Sara John +data-version: 4.1.186 +date: 10:11:2024 08:30 +saved-by: Yasset Perez-Riverol default-namespace: MS namespace-id-rule: * MS:$sequence(7,0,9999999)$ namespace-id-rule: * PEFF:$sequence(7,0,9999999)$