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About MiMI


Overview

MiMI (Michigan Molecular Interactions) is part of the NIH's National Center for Integrative Biomedical Informatics (NCIBI).

MiMI provides access to the knowledge and data merged and integrated from numerous protein interactions databases. It augments this information from many other biological sources. MiMI merges data from these sources with "deep integration" (see The MiMI Merge Process section) into its single database. A simple yet powerful user interface enables you to query the database, freeing you from the onerous task of having to know the data format or having to learn a query language. MiMI allows you to query all data, whether corroborative or contradictory, and specify which sources to utilize.

MiMI displays results of your queries in easy-to-browse interfaces and provides you with workspaces to explore and analyze the results. Among these workspaces is an interactive network of protein-protein interactions displayed in Cytoscape and accessed through MiMI via a MiMI Cytoscape plug-in.

MiMI gives you access to more information than you can get from any one protein interaction source such as:

A count of the interactions in MiMI is available at MiMI Counts.


LicensingLicensing and Terms of Use- Back to Top

MiMI is both a web service that integrates data and the application of research and open source software to the problem of supporting that web service. The data integration service is supplied under the conditions of the original data sources and the specific terms of use for MiMI. Access to this website 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 website 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.

How to Cite MiMI

Please use the following citation for this web site (the PubMed Citation):

V. Glenn Tarcea, Terry Weymouth, Alex Ade, Aaron Bookvich, Jing Gao, Vasudeva Mahavisno, Zach Wright, Adriane Chapman, Magesh Jayapandian, Arzucan Ozgur, Yuanyuan Tian, Jim Cavacoli, Barbara Mirel, Jignesh Patel, Dragomir Radev, Brian Athey, David States and H.V. Jagadish: Michigan molecular interactions r2: from interacting proteins to pathways. Nucleic Acids Research, 2008 Database issue.

The URL: link

The abstract: Molecular interaction data exists in a number of repositories, each with its own data format, molecule identifier and information coverage. Michigan molecular interactions (MiMI) assists scientists searching through this profusion of molecular interaction data. The original release of MiMI gathered data from well-known protein interaction databases, and deep merged this information while keeping track of provenance. Based on the feedback received from users, MiMI has been completely redesigned. This article describes the resulting MiMI Release 2 (MiMIr2). New functionality includes extension from proteins to genes and to pathways; identification of highlighted sentences in source publications; seamless two-way linkage with Cytoscape; query facilities based on MeSH/GO terms and other concepts; approximate graph matching to find relevant pathways; support for querying in bulk; and a user focus-group driven interface design. MiMI is part of the NIH's; National Center for Integrative Biomedical Informatics (NCIBI) and is publicly available at: http://mimi.ncibi.org.


Magesh Jayapandian, Adriane Chapman, V. Glenn Tarcea, Cong Yu, Aaron Elkiss, Angela Ianni, Bin Liu, Arnab Nandi, Carlos Santos, Philip Andrews, Brian Athey, David States, H.V. Jagadish: Michigan Molecular Interactions (MiMI): Putting the Jigsaw Puzzle Together. Nucleic Acids Research, 2007, Vol. 35, Database issue D566-D571.

The URL: http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D566

The abstract: Protein interaction data exists in a number of repositories. Each repository has its own data format, molecule identifier and supplementary information. Michigan Molecular Interactions (MiMI) assists scientists searching through this overwhelming amount of protein interaction data. MiMI gathers data from well-known protein interaction databases and deep-merges the information. Utilizing an identity function, molecules that may have different identifiers but represent the same real-world object are merged. Thus, MiMI allows the users to retrieve information from many different databases at once, highlighting complementary and contradictory information. To help scientists judge the usefulness of a piece of data, MiMI tracks the provenance of all data. Finally, a simple yet powerful user interface aids users in their queries, and frees them from the onerous task of knowing the data format or learning a query language. MiMI allows scientists to query all data, whether corroborative or contradictory, and specify which sources to utilize. MiMI is part of the National Center for Integrative Biomedical Informatics (NCIBI) and is publicly available at: http://mimi.ncibi.org/.


Data Source Terms of Use

Sources of data and their terms of use are as follows:

Source Terms of Use
BIND There are no license conditions attached to the use of BIND if you are using BIND data for internal research purposes. Unleashed Informatics Limited holds an exclusive commercial license to intellectual property including U.S. patent number 6,745,204 - "System for electronically managing, finding, and/or displaying biomolecular interactions" - also known as the BIND patent. The USPTO document can be found here. (http://patft.uspto.gov/netahtml/PTO/srchnum.htm)
For-profit organizations selling a biomolecular interaction software system or employing such a software system specification in a product for sale which falls under the claims of the above patent will require a commercial, fee-based license from Unleashed Informatics. Academic and commercial users of BOND will be unaffected by the enforcement of this patent.
BioGRID http://www.thebiogrid.org/viewdocument.php?documentid=6
CCSB at Harvard Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M.; Towards a proteome-scale map of the human protein-protein interaction network; Nature. 2005 Oct 20;437(7062):1173-8. Epub 2005 Sep 28.
PMID: 16189514
cPath http://cbio.mskcc.org/software/cpath/
DIP http://dip.doe-mbi.ucla.edu/termsofuse.html
GO http://www.geneontology.org/GO.cite.shtml
HPRD http://www.hprd.org
IntAct http://www.ebi.ac.uk/intact/site/index.jsf
InterPro http://www.ebi.ac.uk/interpro/User-FAQ-InterPro.html
IPI http://www.ebi.ac.uk/IPI/IPIhelp.html
KEGG http://www.genome.jp/kegg/kegg1.html
Max Delbreuck Center Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, Timm J, Mintzlaff S, Abraham C, Bock N, Kietzmann S, Goedde A, Toksöz E, Droege A, Krobitsch S, Korn B, Birchmeier W, Lehrach H, Wanker EE.; A human protein-protein interaction network: a resource for annotating the proteome.; Cell 2005 Sep 23;122(6):957-68.
PMID: 16169070
MiBLAST http://www.eecs.umich.edu/miblast/download.html
NCBI Gene http://www.ncbi.nlm.nih.gov/About/disclaimer.html
Organelle DB http://organelledb.lsi.umich.edu/index.php
OrthoMCL DB http://www.orthomcl.org/cgi-bin/OrthoMclWeb.cgi?rm=orthomcl#Acknowledgement
PFam http://pfam.sanger.ac.uk/help?tab=helpReferencesBlock
ProtoNet http://www.protonet.cs.huji.ac.il/prototeam.php?global=protonet|no|5|51|lifetime|1|2|2
PubMed See NCBI Gene
PubMed NLP Mining See MiMI Terms of Use
Reactome http://www.reactome.org/
MINT http://mint.bio.uniroma2.it/mint/download.do
Finley Lab http://proteome.wayne.edu/Cjejuni2.html

Downloading MiMIDownloading MiMI Data - Back to top

Downloading MiMI Data

The MiMI data is available in PSI-MITAB Format. These files represent a subset of the data available in MiMI. Only UniProt and RefSeq identifiers are included for each interactor, pathways and metabolomics data is not included, and provenance is not included for each interaction. If you need access to the full MiMI dataset please send an email to mimi-help@umich.edu.

Download MiMI


MiMI Web Service APIMiMI Web Service API - Back to top

MiMI Web Service API

The MiMI data is queryable through a web services api. To read more about this api see MiMI Web Service API.



MiMI Merge ProcessThe MiMI Merge Process - Back to Top

The MiMI Merge Process

Protein interaction data exists in a number of repositories. Each repository has its own data format, molecule identifier, and supplementary information. MiMI assists scientists searching through this overwhelming amount of protein interaction data. MiMI gathers data from well-known protein interaction databases and deep-merges the information.

Utilizing an identity function, molecules that may have different identifiers but represent the same real-world object are merged. Thus, MiMI allows the user to retrieve information from many different databases at once, highlighting complementary and contradictory information.

There are several steps needed to create the final MiMI dataset. They are:

  1. The original source datasets are obtained, and transformed into the MiMI schema, except KEGG, NCBI Gene, Uniprot, Ensembl.
  2. Molecules that can be rolled into a gene are annotated to that gene record.
  3. Using all known identifiers of a merged molecule, sources such as Organelle DB or miBLAST, are queried to annotate specific molecular fields.
  4. The resulting dataset is loaded into a relational database.

Because this is an automated process, and no curation occurs, any errors or misnomers in the original data sources will also exist in MiMI. For example, if a source indicates that the organism is unknown, MiMI will as well.

If you find that a molecule has been incorrectly merged under a gene record, please contact us immediately. Because MiMI is completely automatically generated, and there is no data curation, it is possible that we have merged molecules with gene records incorrectly. If made aware of the error, we can and will correct the situation. Please report any problems of this kind to mimi-help@umich.edu.

Rules and Assumptions

MiMI is not merged by 'experts' - everything is done automatically. When you look into genes of interest it is important to understand why your target gene contains the attributes and associated annotations; you also may want to know why conflicting data are displayed in the merged data. Some of the assumptions and rules that MiMI uses in deep merging that may be relevant to understanding and being confident in its displays include the following:

Source differences in quality

Not all sources are created equal. While each source has a particular strength, each also has its drawback. Some important things to know about the curation processes in these different databases that might affect your interpretations and confidence include:

Source content

Not only do sources have different strengths and weaknesses, they also organize content differently. For example, IntAct will associate publications with individual molecules while BIND associates publications with interactions only. MiMI remains true to individual sources and how they assign publications to molecules or interactions.

Source data not used

In general, MiMI uses all data from each source. However, there are some data from each source that are not incorporated into MiMI. For instance, sequence data is never stored within the MiMI dataset.


FundingMiMI Support and Funding - Back to Top

www.ncibi.org - For support and questions email: mimi-help@umich.edu