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Molecular networking and chemical similarity

ConCISE

ConCISE propagates consensus chemical-class annotations by combining molecular-network relationships, library matches and in-silico class predictions.

Platform-independentUntargeted metabolomicsCommand lineDesktop graphical interfaceNotebook
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Overview

ConCISE propagates consensus chemical-class annotations by combining molecular-network relationships, library matches and in-silico class predictions. It accepts GNPS and CANOPUS-derived results through graphical, command-line or notebook workflows.

What can this tool do?

Compound-class prediction

Common uses

  • ConCISE propagates consensus chemical-class annotations by combining molecular-network relationships, library matches and in-silico class predictions.

Scientific fit

Primary function

Molecular networking and chemical similarity

Other functions

Metabolite annotation and identification

Analysis types

Untargeted metabolomics

Data compatibility

Inputs

Compound list or annotations, Statistical results

Outputs

Compound list or annotations, Human-readable report

Input formats

GNPS library/task results, CANOPUS TSV and network information

Output formats

Consensus chemical-class annotation tables

Scope and considerations

Designed for

  • ConCISE propagates consensus chemical-class annotations by combining molecular-network relationships, library matches and in-silico class predictions.

Not designed for

  • Confirmed molecular structures or class assignments independent of the quality of the underlying network and source annotations.

Important requirements

  • Compatible library-match/GNPS task information, CANOPUS summary and network-node information with consistent feature identifiers; choose ClassyFire or NPClassifier ontology inputs.

Considerations

  • README documents missing ClassyFire fields from GNPS and provides NPClassifier/manual-merge workarounds. Check ontology consistency and consensus thresholds; the macOS GUI is deprecated.

Access and documentation

Primary accessDocumentation

MIT source distribution. External datasets, dependent packages and any hosted routes retain their own terms; software operation was not tested.

License: MIT

Evidence and review

Enveda intake rechecked against official repository documentation, package/license metadata and primary publication identity on 2026-10-27. Editorial source review only; no software execution or independent benchmark. See docs/enveda-expansion-review-2026-10-27-batch3.md.

Core publications

Resource papers, direct updates and tool-specific methods. Selection policy.

  1. ConCISE: Consensus Annotation Propagation of Ion Features in Untargeted Tandem Mass Spectrometry Combining Molecular Networking and In Silico Metabolite Structure Prediction. Metabolites (2022). doi:10.3390/metabo12121275

Related tools

GNPSSimilar function · A web-based mass-spectrometry ecosystem for molecular networking, spectral-library search, repository-scale search, interactive visualization, knowledgebase curation, and public-data integration.GNPS2 Classical Molecular NetworkingSimilar function · GNPS2 workflow for organizing MS/MS spectra into molecular families using pairwise spectral similarity and spectral-library searching.GNPS2 Feature-Based Molecular Networking workflowSimilar function · Dedicated GNPS2 workflow that combines an aligned LC-MS feature table with MS/MS spectra to build quantitative molecular networks.MetGemSimilar function · Local desktop generation and exploration of MS/MS similarity networks and two-dimensional spectral projections.

Entry history

Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.

  1. 2026-10-27 · First committed entry

    Add 45 source-reviewed Enveda tool entries in third expansion batch

    View change · Entry at this revision

Full GitHub history