About Gene2MeSH

What is Metab2Mesh?

Metab2MeSH is part of the NIH's National Center for Integrative Biomedical Informatics (NCIBI).

Metab2MeSH uses a statistical approach (Fisher’s Exact test) to reliably and automatically annotate compounds with the concepts defined in MeSH (Medical Subject Headings), the National Library of Medicine’s controlled vocabulary for biology and medicine. The Metab2MeSH web application searches compounds or MeSH terms and displays resulting pairs of compounds and MeSH terms that match the search term. The compound / MeSH term pairs displayed are those that are significantly associated in PubMed abstracts and are ordered highest to lowest by significance score.

How MetabMeSH is Created

The NCIBI PubMed database is downloaded from the NLM, parsed and loaded into a relational database. MeSH indexing terms are used as provided by the NLM distribution. The significance of association between compounds and MeSH terms is calculated using Fisher's exact test in the R statistics package.

Metab2MeSH is updated bi-annually.

Metab2MeSH Quick Start Guide

Using Metab2MeSH


Interpreting the Results Columns

The following columns are provided in the Metab2MeSH query results:

Compound Name
:     Preferred PubChem Compound Name (links are provided to query this compound in PubChem and to query Metab2MeSH by this compound)

Compound ID(s):      PubChem Compound ID(s)

MeSH Headings(s):   Medical Subject Heading from top level of MeSH hierarchy (http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi)

MeSH Descriptor:     Medical Subject Heading (MeSH) term (links are provided to query this MeSH term in MeSH and to query Metab2MeSH by this MeSH term)

MeSH Qualifier:        There are a small number of MeSH qualifiers, which are subheadings that can be added to MeSH terms to narrow down the topic

PubMed Articles:      Number of pubmed articles linked to both the MeSH descriptor and the compound (link to top 200 articles in PubMed)

p-value:           p-value from a two-sided Fisher’s Exact test, testing the co-occurrence frequency of the compound-MeSH term pair. Displayed results are sorted by this column.

q-value:           q-value calculated from the p-values using the Benjamini-Hochberg FDR adjustment

Fold Change: For a specific compound and MeSH descriptor:  Fold Change=  (p ⁄ c)/(d ⁄ t),
where p is the number of articles that have the compound and MeSH descriptor pair, c is the total number of articles that contain the compound, d is the total number of articles that contain the MeSH descriptor, and t is the total number of articles considered.

ChiSq:            The chi-square statistic for testing the co-occurrence frequency of the compound-MeSH term pair. This is only used for sorting results when the p-value = 0.

Metab2MeSH Web Service

NCIBI provides web service access to Metab2MeSH and other NCIBI databases outside of the regular web page interface. Programmatic access may be useful for integrating Metab2MeSH data into an analytic workflow or data pipeline, and for performing batch queries.

Click here to go to the NCIBI web services information page for Metab2MeSH.

Licensing and Terms of UseLicensing and Terms of Use

Metab2MeSH 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. 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 Metab2MeSH

Ade, AS; States, DJ; Wright, ZC; Karnovsky, A; Sartor, MA. Metab2MeSH [Internet]. Ann Arbor (MI): National Center for Integrative Biomedical Informatics. 2011 Mar. Available from http://metab2mesh.ncibi.org

Additional Help and Support

For additional Metab2MeSH support and/or any questions regarding Metab2MeSH email ncibi-list@umich.edu

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