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Chemical Directionality

Chemical Directionality (ChemDir)

The Chemical Directionality (ChemDir) concept applied here is defined by relative abundance changes between two neighbouring nodes within a molecular network. By taking advantage of the feature-based molecular network workflow (FBMN), we used the raw peak area across the longitudinal (or spatial) data series as a measure of the abundance for each detected feature among events. ChemDir facilitates the prioritisation of putative transformations in tandem mass spectrometry (MS/MS) data using the Global Natural Products Social Molecular Network (GNPS) environment.

You can checkout the tool on GNPS.

FBMN Version Compatibility

We require a FBMN that is release_18 or newer. If your job is older than that, simply clone to latest to get the latest version and it should be compatible with ChemDir

Workflow Make sure you select the ChemDir workflow

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Title Name your job to be easily recognize by yourself as it will be available in your jobs tab

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Enter GNPS Network Task ID (Required) Copy and paste the FBMN task ID from your previous FBMN job

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METADATA_COLUMN Define a metadata column header based on the exact metadata table provided for the FBMN job ID you are using in this ChemDir workflow

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TIME_SERIES Provide the variables that you are interested in based on your longitudinal analysis. Example: 0,1,2,3; comma separated values, can be integers or strings; no spaces between variables. The variables provided here must match entries from the metadata column specified in METADATA_COLUMN.

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MIN_AREA_THRESHOLD Min peak area; defined during feature finding; job specific. The value used here will replace any 0 value from your dataset for ChemDir.

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METADATA_FILTER_COLUMN It is possible to filter the dataset based on the columns of interest.

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METADATA_FILTER_TERM It is possible to filter the column used from your dataset based on the specific term of interest for the analysis.

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Job status Once your job is finished, you will be able to explore the results.

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Summary table This table provides the general overview of every pair node compared via ChemDir.

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Direct Cytoscape preview This enables you to directly download and explore the data in Cytoscape.

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ChemDir dashboard This enables you to quickly explore the maximum ChemDir scores and their correspondent DeltaMZ observed from your dataset.

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Development

Source code There are two portions of the ChemDir infrastructure: ChemDir GNPS/ProteoSAFe workflow and the ChemDir Results Exploration Dashboard.

Citation

To be updated

Page Contributions

Ming Wang (10.13%), amcaraballor (87.34%), Laura-Isobel McCall (2.53%)


Last update: September 14, 2020 21:35:23