MetaboLights Bots

Python scripts for MetaboLights data management * This documentation is not extensive and is still in development.

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MetaboLights Study Bots

Automated tasks / routines over study data that fetches study factors, file extensions / MIME types, assay details and various other files related information like file counts etc. Also performs analysis to a certain extent (Getting better and better).

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MetStudyBot

Usage:

$ python MetStudyBot.py {studyid} # python MetStudyBot.py MTBLS35

A python script for extracting sample and assay data in the study This script accepts the following command line argument(s): - study : MetaboLights Study Identifier (String)

Output:

https://raw.githubusercontent.com/CS76/MetaboLightsBots/master/MetStudyBot/MTBLS35_sample_assay_mapping.json

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Bulk_head

Usage:

$ python bulk_head.py

A python script for mapping and counting file formats to studies

Output:

ftp://ftp.ebi.ac.uk/pub/databases/metabolights/study_file_extensions/ml_file_extension.json

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Bumble_bee

Usage:

$ python bumble_bee.py

A python script for travesing study file system and generates a folder tree.

It unzips the compressed files and includes the underlying files / folders in to the parent tree

Output:

ftp://ftp.ebi.ac.uk/pub/databases/metabolights/study_file_extensions/study_file_details/MTBLS1.json

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MetaboLights Compound Bots

MLCompoundsBot.py

Usage:

$ python MLCompoundsBot.py --compound "MTBLC115354" <working_directory> <destination_directory>

The script accepts the following command line argument(s):

-- compound : MetaboLights Compound Identifier (String) ( default: all)

-- working directory (temporary staging area for log, mappings and other files)

-- destination directory (output and spectra files are stored in this location)

• Output example:

http://wwwdev.ebi.ac.uk/metabolights/webservice/beta/compound/MTBLC15355

Utils

MetaboLightsBots/MetCompoundBot/utils.py

Helper module for the MLCompoundsBot

Functions in this module query different rest services to fetch information based on the InChiKey input ( Chemical identification data, Metabolights study mappings, Pathways data from KEGG, Wikipathways and Reactome, Reactions data from Rhea, Citations from European Pubmed Central, Spectroscopic data from MONA - mass bank/hmdb, SPLASH - spectral hash from MONA etc. )

• Generates the MetaboLights Study Compound mapping file

https://raw.githubusercontent.com/CS76/MetaboLightsBots/master/resources/mapping.json

• Generates the Reactome JSON file

https://raw.githubusercontent.com/CS76/MetaboLightsBots/master/resources/reactome.json

MetCompoundSpeciesMapper

Usage:

$ python MetCompoundSpeciesMapper.py

A python script for mapping compounds and species with species accessions

Output:

https://raw.githubusercontent.com/CS76/MetaboLightsBots/master/resources/compoundSpeciesMappingComplete.csv

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Wikipathways Bots

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MetStudyBot

Script to generate Wikipathways - MetaboLights Enrichment spread sheet

Usage:

$ python MetStudyBot.py {studyid} # python MetStudyBot.py MTBLS35

Output: https://gist.github.com/CS76/12e72c79561bd07944cab0ed3961616b

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