- What is Gene2MeSH?
- Using Gene2MeSH
- Gene2MeSH Programmatic Interface
- How Gene2MeSH is Created
- Gene2MeSH Data Policy
- Citing Gene2MeSH
Gene2Mesh is part of the NIH's National Center for Integrative Biomedical Informatics (NCIBI).
Gene2MeSH uses a statistical approach to reliably and automatically annotate genes with the concepts defined in MeSH, the National Library of Medicine’s controlled vocabulary for biology and medicine. The Gene2MeSH web application searches gene symbols or MeSH terms and displays resulting pairs of genes and MeSH terms that match the search term. The gene / MeSH term pairs displayed are those that are significantly associated in PubMed abstracts and are ordered highest to lowest by significance score.
How Gene2MeSH 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 genes and MeSH terms are calculated by using Fisher’s Exact test. Gene2MeSH is updated monthly.
Gene2MeSH Quick Start Guide
- 1. Select organism if you wish to filter your results by organism type
- 3. Start entering your search term into the search box and available genes or MeSH descriptors will be displayed
- 4. Click on the gene or MeSH descriptor you would like to search on
- 5. Click "Gene2MeSH Search"
- 6. Use the history tracker to go back to previous search results
- If you don't wish to use a suggested term, simply enter your search term into the search box and (if necessary) click outside the search box. Gene2MeSH will search both gene symbols AND MeSH descriptors in this case.
- Click the book icon to lookup the MeSH term or gene symbol in NCBI
- Click the to lookup the gene's interactions in MiMI
- Click the link to PubMed articles to see the list of articles that created the gene / MeSH term association
- Select a species to limit results to a specific taxonomy.
- Check "substances only" to restrict results to MeSH terms related to biological substances.
- Check "show all columns" to see additional information about the gene / MeSH term pair
- Click "download" to download the results into a tab delimited text file
NCIBI provides web service access to Gene2MeSH and other NCIBI databases outside of the regular web page interface. Programmatic access may be useful for integrating Gene2MeSH data into an analytic workflow or data pipeline.
Click here to go to the NCIBI web services information page for Gene2MeSH.
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.
Ade, AS; Wright, ZC; States, DJ; Gene2MeSH [Internet]. Ann Arbor (MI): National Center for Integrative Biomedical Informatics. 2007 Mar. Available from http://gene2mesh.ncibi.org
Additional Help and Support
For additional Gene2MeSH support and/or any questions regarding Gene2MeSH email firstname.lastname@example.org