From 0f2305d60d43569e5cccd6f2dd6c42a95e10b4f0 Mon Sep 17 00:00:00 2001
From: Heinrich Lukas Weil <hl.weil@t-online.de>
Date: Tue, 6 Feb 2024 11:10:52 +0100
Subject: [PATCH] update process parameters in annotation of
TurbiIDSampleArc.cwl
---
workflows/EvalTurboID/TurboIDSampleArc.cwl | 71 +++++++++++++---------
1 file changed, 43 insertions(+), 28 deletions(-)
diff --git a/workflows/EvalTurboID/TurboIDSampleArc.cwl b/workflows/EvalTurboID/TurboIDSampleArc.cwl
index f1cc957..6c03d20 100644
--- a/workflows/EvalTurboID/TurboIDSampleArc.cwl
+++ b/workflows/EvalTurboID/TurboIDSampleArc.cwl
@@ -36,20 +36,11 @@ outputs:
glob: $(runtime.outdir)/$(inputs.runID)
-arc:has measurement type:
- - class: arc:measurement type
- arc:term accession: "http://purl.obolibrary.org/obo/OMIT_0023015"
- arc:term source REF: "OMIT"
- arc:annotation value: "Proteomics"
-
-
arc:has technology type:
- class: arc:technology type
- arc:term accession: "http://purl.obolibrary.org/obo/OMIT_0013943"
- arc:term source REF: "OMIT"
- arc:annotation value: "Mass Spectrometry"
+ arc:annotation value: "Docker Container"
-arc:technology platform: SCIEX
+arc:technology platform: ".NET"
arc:performer:
- class: arc:Person
@@ -64,7 +55,7 @@ arc:performer:
arc:has process sequence:
- class: arc:process sequence
- arc:name: "MassSpectrometry"
+ arc:name: "TurboID"
arc:has input:
- class: arc:sample
arc:name: "PR135_01"
@@ -81,29 +72,53 @@ arc:has process sequence:
- class: arc:protocol parameter
arc:has parameter name:
- class: arc:parameter name
- arc:term accession: "http://purl.obolibrary.org/obo/PATO_0000146"
- arc:term source REF: "PATO"
- arc:annotation value: "temperature"
- arc:has unit:
- - class: arc:unit
- arc:term accession: "http://purl.obolibrary.org/obo/UO_0000027"
- arc:term source REF: "UO"
- arc:annotation value: "degree Celsius"
- arc:value: 35
+ arc:term accession: "http://edamontology.org/operation_0004"
+ arc:term source REF: "EMBRACE"
+ arc:annotation value: "Operation"
+ arc:value:
+ - class: arc:ontology annotation
+ arc:term accession: "http://edamontology.org/operation_0362"
+ arc:term source REF: "EMBRACE"
+ arc:annotation value: "Genome annotation"
- class: arc:process parameter value
arc:has parameter:
- class: arc:protocol parameter
arc:has parameter name:
- class: arc:parameter name
- arc:term accession: "http://purl.obolibrary.org/obo/OBI_0000615"
- arc:term source REF: "OBI"
- arc:annotation value: "protein expression profiling assay"
+ arc:term accession: "http://edamontology.org/operation_0004"
+ arc:term source REF: "EMBRACE"
+ arc:annotation value: "Operation"
arc:value:
- class: arc:ontology annotation
- arc:term accession: "http://purl.obolibrary.org/obo/BAO_0010027"
- arc:term source REF: "BAO"
- arc:annotation value: "shotgun MS protein profiling assay"
-
+ arc:term accession: "http://edamontology.org/operation_3435"
+ arc:term source REF: "EMBRACE"
+ arc:annotation value: "Standardisation and normalisation"
+ - class: arc:process parameter value
+ arc:has parameter:
+ - class: arc:protocol parameter
+ arc:has parameter name:
+ - class: arc:parameter name
+ arc:term accession: "http://edamontology.org/operation_0004"
+ arc:term source REF: "EMBRACE"
+ arc:annotation value: "Operation"
+ arc:value:
+ - class: arc:ontology annotation
+ arc:term accession: "http://edamontology.org/operation_3557"
+ arc:term source REF: "EMBRACE"
+ arc:annotation value: "Imputation"
+ - class: arc:process parameter value
+ arc:has parameter:
+ - class: arc:protocol parameter
+ arc:has parameter name:
+ - class: arc:parameter name
+ arc:term accession: "http://purl.obolibrary.org/obo/OBCS_0000001"
+ arc:term source REF: "OBCS"
+ arc:annotation value: "statistical data analysis"
+ arc:value:
+ - class: arc:ontology annotation
+ arc:term accession: "http://purl.obolibrary.org/obo/OBCS_0000141"
+ arc:term source REF: "OBCS"
+ arc:annotation value: "significance analysis of microarrays"
$namespaces:
arc: https://github.com/nfdi4plants/ARC_ontology
--
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