- What is Gene2MeSH?
- Using Gene2MeSH
- Gene2MeSH Programmatic Interface
- How Gene2MeSH is Created
- Gene2MeSH Data Policy
- Citing Gene2MeSH
Overview
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
Using Gene2MeSH
- 1. Select whether you'd like to search MeSH terms, gene symbols, or both.
- 2. Enter your search term into the search field and click "Gene2MeSH Search"
- 3. Click on any MeSH term or gene symbol to search again with that specific term
- 4. Use the history tracker to go back to previous search results
Tips:
- 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 tab-delimited results" to download the results into a tab delimited text file
Gene2MeSH Programmatic Interface
NCIBI provides web service access to the Gene2MeSH database outside of the regular web page interface. Programmatic access may be useful for integrating Gene2MeSH data into an analytic workflow or data pipeline.
Base URL
http://gene2mesh.ncibi.org/fetch?
URL Parameters
geneid
Geneid is the entrez gene ID.
genesymbol
Genesymbol is the entrez gene symbol.
taxid
Taxid is the taxonomy ID from the NCBI taxonomy database.
mesh
MeSH is a Medical Subject Headings (MeSH) descriptor.
limit
Optional. Limit sets the maximum number of returned results; it defaults to 1000 if not set.
tool
Optional. Tool is a string with no internal spaces that identifies the resource using the service. Inclusion of this parameter allows us to track usage of the service.
email
Optional. Email associates an email address with the request. Inclusion of this parameter allows us to contact users if there are problems or if the software interface changes.
The following are valid parameter combinations:
geneid, genesymbol, genesymbol & taxid, mesh, mesh & taxid
Examples
http://gene2mesh.ncibi.org/fetch?geneid=1436
http://gene2mesh.ncibi.org/fetch?genesymbol=csf1r
http://gene2mesh.ncibi.org/fetch?genesymbol=csf1r&taxid=9606
http://gene2mesh.ncibi.org/fetch?mesh=diabetes
http://gene2mesh.ncibi.org/fetch?mesh=diabetes&taxid=9606
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. The result set returned is ordered by the p-value of the Fisher’s Exact Test.
NOTICE: We've recently changed the XML schema for the Gene2MeSH programmatic interface. Please update your scripts accordingly.
Licensing and Terms of Use
Gene2MeSH is both a website that integrates data and the application of research and open source software to the problem of supporting that website. The data integration service is supplied under the conditions of the original data sources and the specific terms of use for Gene2MeSh. 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 Gene2MeSH
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 gene2mesh-help@umich.edu
