About


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


MiMI/Metabolomics Programmatic Interface:

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.

Base URL:

http://mimi.ncibi.org/MimiWeb/fetch.jsp?

URL Parameters:

search
Search term to perform a general MiMI free-text search.

geneid
Geneid is the Entrez GeneId for a gene.

cid
Cid is the KEGG compound ID

rid
Rid is the KEGG reaction ID.

type
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:

The following are valid parameter combinations:

search
geneid & type
cid
rid

Examples:

http://mimi.ncibi.org/MimiWeb/fetch.jsp?search=pwp1

http://mimi.ncibi.org/MimiWeb/fetch.jsp?geneid=1436

http://mimi.ncibi.org/MimiWeb/fetch.jsp?geneid=1436&type=interactions

http://mimi.ncibi.org/MimiWeb/fetch.jsp?geneid=1436&type=reactions

http://mimi.ncibi.org/MimiWeb/fetch.jsp?geneid=7389&type=compounds

http://mimi.ncibi.org/MimiWeb/fetch.jsp?geneid=4005&type=nlp

http://mimi.ncibi.org/MimiWeb/fetch.jsp?cid=C00061

http://mimi.ncibi.org/MimiWeb/fetch.jsp?rid=R00548

Output:

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 1 - Java, Perl

Sample 2 - Java, Perl

Sample 3 - Java, Perl

Sample 4 - Perl

Licensing and Terms of UseLicensing and Terms of Use


The NCIBI MiMI and Metabolomics databases integrate data through the application of research and open source software. The data integration service is supplied under the conditions of the original data sources and the specific terms of use for the NCIBI MiMI web service. Access to this web service is provided free of charge. Permission is granted to use this software and data internally only, so long as no fee is charged, usage of this web service is cited in any resulting publications involving results from such use, and so long as the name of the University of Michigan is not used in any advertising or publicity pertaining to such use without specific, written prior authorization. Permission to redistribute this data in any form is specifically not granted.

The Regents of the University of Michigan does not check this data for errors or omissions, and by its nature, the data included herein likely contains errors and omissions. Access and use is provided as is, without representation as to its fitness for any purpose, and without warranty of any kind, either express or implied, including without limitation the implied warranties of merchantability and fitness for a particular purpose. The Regents of the University of Michigan shall not be liable for any damages, including special, indirect, incidental, or consequential damages, with respect to any claim arising out of, or in connection with, the use of this website or data, even if it has been or is hereafter advised of the possibility of such damages.

Additional Help and Support


For additional MiMI web services support and/or any questions regarding the MiMI web services E-mail: mimi-help@umich.edu