The collection and merging of interaction and metabolomic data is an activity of the NIH's National Center for Integrative Biomedical Informatics (NCIBI).
MiMI/Metabolomics Quick Start Guide
NCIBI has provided web service access to the MiMI and Metabolomics databases. These databases are large, merged collections of interaction, gene and metabolomics (pathways, compounds, reactions and enzymes) data. The data includes pubmed entries, interactions, provenance, and other information. Programmatic access may be useful for integrating interactions and metabolomic data into an analytic workflow or data pipeline.
Search term to perform a general MiMI free-text search.
Geneid is the Entrez GeneId for a gene.
Cid is the KEGG compound ID
Rid is the KEGG reaction ID.
Type is the type of data to return. Currently supported types are "reactions", "interactions", and "compounds." If not specified then the default is "interactions".
The types return the following information:
interactions - A list interactions (and associated data) for the given geneid.
reactions - A list of reactions (and associated data) that the given geneid participates in as an enzyme
compounds - A list of compounds (and associated data) with which a given geneid is associated.
nlp - A list of literature derived interactions (and relevant sentence) discovered using Natural Language Processing.
The following are valid parameter combinations:
geneid & type
The XML returned is divided into two sections. The Request section echos the input parameters and the values of unset parameters. The Response section holds the data from the query.
Sample Code For Retrieving and Parsing NCIBI Mimi/Metabolomics Data
The following three examples show how to interact with the NCIBI MiMI web service by querying for interactions and reactions. Samples 1 and 2 query the NCIBI-MiMI-WS. Sample 3 shows a combined query to the NCIBI-MiMI-WS and eUtils. The examples are shown in Java and Perl. Sample 4 shows a query combining NCBI's Eutils and three of NCIBI's web services: NLP, Gene2MeSH, and MiMI.
Sample 4 - Perl
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Additional Help and Support
For additional MiMI web services support and/or any questions regarding the MiMI web services E-mail: firstname.lastname@example.org