release 4.9.7

sirius-ms · Oct 25, 2021 · d5bc51e · d5bc51e
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diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
 [![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-blueviolet.svg)](https://www.gnu.org/licenses/agpl-3.0)
-[![Generic badge](https://img.shields.io/badge/Version-4.9.6-informational.svg)](https://shields.io/)
+[![Generic badge](https://img.shields.io/badge/Version-4.9.7-informational.svg)](https://shields.io/)
 [![Build and Pubish](https://github.com/boecker-lab/sirius/actions/workflows/distribute.yaml/badge.svg?branch=release-4-pre)](https://github.com/boecker-lab/sirius/actions/workflows/distribute.yaml)
 
 *<span style="color: #808080;">Our methods are offered to the scientific community as freely available resources. (Re-)distribution of the
@@ -25,17 +25,17 @@ graphical user interface and the command line version of SIRIUS seamlessly integ
 
 <!--begin download-->
 
-### SIRIUS+CSI:FingerID GUI and CLI - Version 4.9.6 (2021-10-19)
+### SIRIUS+CSI:FingerID GUI and CLI - Version 4.9.7 (2021-10-25)
 ##### These versions include the Java Runtime Environment, so there is no need to install Java separately! Just download, install/unpack and execute.
-- for Windows (64bit): [msi](https://github.com/boecker-lab/sirius/releases/download/v4.9.6/sirius-4.9.6-win64.msi) / [zip](https://github.com/boecker-lab/sirius/releases/download/v4.9.6/sirius-4.9.6-win64.zip)
-- for Linux (64bit): [zip](https://github.com/boecker-lab/sirius/releases/download/v4.9.6/sirius-4.9.6-linux64.zip)
-- for Mac (64bit): [pkg](https://github.com/boecker-lab/sirius/releases/download/v4.9.6/sirius-4.9.6-osx64.pkg) / [zip](https://github.com/boecker-lab/sirius/releases/download/v4.9.6/sirius-4.9.6-osx64.zip)
+- for Windows (64bit): [msi](https://github.com/boecker-lab/sirius/releases/download/v4.9.7/sirius-4.9.7-win64.msi) / [zip](https://github.com/boecker-lab/sirius/releases/download/v4.9.7/sirius-4.9.7-win64.zip)
+- for Linux (64bit): [zip](https://github.com/boecker-lab/sirius/releases/download/v4.9.7/sirius-4.9.7-linux64.zip)
+- for Mac (64bit): [pkg](https://github.com/boecker-lab/sirius/releases/download/v4.9.7/sirius-4.9.7-osx64.pkg) / [zip](https://github.com/boecker-lab/sirius/releases/download/v4.9.7/sirius-4.9.7-osx64.zip)
 
-### SIRIUS+CSI:FingerID Command-Line Interface only - Version 4.9.6 (2021-10-19)
+### SIRIUS+CSI:FingerID Command-Line Interface only - Version 4.9.7 (2021-10-25)
 ##### These versions include the Java Runtime Environment, so there is no need to install Java separately! Just download, install/unpack and execute.
-- for Windows (64bit): [msi](https://github.com/boecker-lab/sirius/releases/download/v4.9.6/sirius-4.9.6-win64-headless.msi) / [zip](https://github.com/boecker-lab/sirius/releases/download/v4.9.6/sirius-4.9.6-win64-headless.zip)
-- for Linux (64bit): [zip](https://github.com/boecker-lab/sirius/releases/download/v4.9.6/sirius-4.9.6-linux64-headless.zip)
-- for Mac (64bit): [pkg](https://github.com/boecker-lab/sirius/releases/download/v4.9.6/sirius-4.9.6-osx64-headless.pkg) / [zip](https://github.com/boecker-lab/sirius/releases/download/v4.9.6/sirius-4.9.6-osx64-headless.zip)
+- for Windows (64bit): [msi](https://github.com/boecker-lab/sirius/releases/download/v4.9.7/sirius-4.9.7-win64-headless.msi) / [zip](https://github.com/boecker-lab/sirius/releases/download/v4.9.7/sirius-4.9.7-win64-headless.zip)
+- for Linux (64bit): [zip](https://github.com/boecker-lab/sirius/releases/download/v4.9.7/sirius-4.9.7-linux64-headless.zip)
+- for Mac (64bit): [pkg](https://github.com/boecker-lab/sirius/releases/download/v4.9.7/sirius-4.9.7-osx64-headless.pkg) / [zip](https://github.com/boecker-lab/sirius/releases/download/v4.9.7/sirius-4.9.7-osx64-headless.zip)
 
 
 <!--end download-->
@@ -97,8 +97,8 @@ Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Alexander A. Aksenov, Alexey V.
 
 ---
 Martin A. Hoffmann and Louis-Félix Nothias and Marcus Ludwig and Markus Fleischauer and Emily C. Gentry and Michael Witting and Pieter C. Dorrestein and Kai Dührkop and Sebastian Böcker
-[Assigning confidence to structural annotations from mass spectra with COSMIC](https://doi.org/10.1101/2021.03.18.435634)
-bioRxiv, 2021. (Cite if you are using: *CSI:FingerID*, *COSMIC*)
+[High-confidence structural annotation of metabolites absent from spectral libraries](https://doi.org/10.1038/s41587-021-01045-9)
+*Nat Biotechnology*, 2021. (Cite if you are using: *CSI:FingerID* with *COSMIC*)
 
 Kai Dührkop, Louis-Félix Nothias, Markus Fleischauer, Raphael Reher, Marcus Ludwig, Martin A. Hoffmann, Daniel Petras, William H. Gerwick, Juho Rousu, Pieter C. Dorrestein and Sebastian Böcker.
 [Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra.](https://doi.org/10.1038/s41587-020-0740-8)

diff --git a/sirius_cli/src/main/resources/cite.bibtex b/sirius_cli/src/main/resources/cite.bibtex
@@ -95,14 +95,13 @@ SIRIUS 3 can be a part of an untargeted metabolomics workflow, allowing research
   pmid      = {26392543},
 }
 
-@Article{hoffmann21assigning,
-  author    = {Martin A. Hoffmann and Louis-F\'elix Nothias and Marcus Ludwig and Markus Fleischauer and Emily C. Gentry and Michael Witting and Pieter C. Dorrestein and Kai D\"uhrkop and Sebastian B\"ocker},
-  journal   = {bioRxiv},
-  title     = {Assigning confidence to structural annotations from mass spectra with {COSMIC}},
-  year      = {2021},
-  pages     = {bioRxiv:2021.03.18.435634},
-  abstract  = {Untargeted metabolomics experiments rely on spectral libraries for structure annotation, but these libraries are vastly incomplete; in silico methods search in structure databases but cannot distinguish between correct and incorrect annotations. As biological interpretation relies on accurate structure annotations, the ability to assign confidence to such annotations is a key outstanding problem. We introduce the COSMIC workflow that combines structure database generation, in silico annotation, and a confidence score consisting of kernel density p-value estimation and a Support Vector Machine with enforced directionality of features. In evaluation, COSMIC annotates a substantial number of hits at small false discovery rates, and outperforms spectral library search for this purpose. To demonstrate that COSMIC can annotate structures never reported before, we annotated twelve novel bile acid conjugates; nine structures were confirmed by manual evaluation and two structures using synthetic standards. Second, we annotated and manually evaluated 315 molecular structures in human samples currently absent from the Human Metabolome Database. Third, we applied COSMIC to 17,400 experimental runs and annotated 1,715 structures with high confidence that were absent from spectral libraries.},
-  doi       = {10.1101/2021.03.18.435634},
-  keywords  = {CSI:FingerID; COSMIC},
-  timestamp = {2018-01-10},
+@Article{hoffmann21high-confidence,
+    author    = {Martin A. Hoffmann and Louis-F\'elix Nothias and Marcus Ludwig and Markus Fleischauer and Emily C. Gentry and Michael Witting and Pieter C. Dorrestein and Kai D\"uhrkop and Sebastian B\"ocker},
+    journal   = {Nature Biotechnology},
+    title     = {High-confidence structural annotation of metabolites absent from spectral libraries},
+    year      = {2021},
+    pages     = {1546-1696},
+    abstract  = {Untargeted metabolomics experiments rely on spectral libraries for structure annotation, but, typically, only a small fraction of spectra can be matched. Previous in silico methods search in structure databases but cannot distinguish between correct and incorrect annotations. Here we introduce the COSMIC workflow that combines in silico structure database generation and annotation with a confidence score consisting of kernel density P value estimation and a support vector machine with enforced directionality of features. On diverse datasets, COSMIC annotates a substantial number of hits at low false discovery rates and outperforms spectral library search. To demonstrate that COSMIC can annotate structures never reported before, we annotated 12 natural bile acids. The annotation of nine structures was confirmed by manual evaluation and two structures using synthetic standards. In human samples, we annotated and manually validated 315 molecular structures currently absent from the Human Metabolome Database. Application of COSMIC to data from 17,400 metabolomics experiments led to 1,715 high-confidence structural annotations that were absent from spectral libraries.},
+    doi       = {10.1038/s41587-021-01045-9},
+    keywords  = {CSI:FingerID; COSMIC},
 }
diff --git a/sirius_cli/src/main/resources/sirius_frontend.build.properties b/sirius_cli/src/main/resources/sirius_frontend.build.properties
@@ -1,5 +1,6 @@
 #here you can provide properties that may be needed during build- AND during runtime and should not be editable by the user at runtime
 de.unijena.bioinf.siriusFrontend.version=4.9.7
+
 de.unijena.bioinf.sirius.version=4.6.1
 de.unijena.bioinf.fingerid.version=1.6.0
 #