About and Citation

About

The Génie web server is dedicated to scientists interested to rank genes for a selected biomedical topic. Genes are ranked using a text-minig approach based on gene-related scientific abstracts. A genome wide ranking is processed in a few seconds and orthology information can be used. Please see the cited article below for details on methods.

Citation

  • Fontaine JF, Priller F, Barbosa-Silva A and Andrade-Navarro MA. Génie: literature-based gene prioritization at multi genomic scale. Nucleic Acids Research 2011 Jul;39(Web Server issue):W455-61. doi: 10.1093/nar/gkr246.

Credits

The web server is maintained by members of the Computational Biology and Data Mining group (CBDM) of Prof. Miguel Andrade-Navarro at the Johannes Gutenberg University Mainz, Mainz, Germany. Please contact Dr. Jean Fred Fontaine for questions or bug report (fontaine << at >> uni-mainz.de).

External data provider

This webserver uses data from NCBI. Please see NCBI's Disclaimer and Copyright notice.

History

  • 2015-05-07: Daily updates of PubMed are now active.
  • 2015-03-24: Migration to servers in Mainz and update of all data from NCBI. Daily updates of PubMed are still not active.
  • 2014-12-01: Minor bug fixes and update to latest NCBI information (Gene, Taxonomy and Homologene 68).
  • 2014-01-27: Implementation of a performance boost when using a MeSH term as input (Direct MeSH lookup in abstract annotations overwrites the Bayesian document classifier). Replacing Top 10 PMIDs by coloured symbols. Update of the gene data (NCBI Gene, Taxonomy and Homologene 67). Minor bug fixes (including homolog searches).
  • 2013-01-14: Bug fixes on homolog species list.
  • 2011-11-10: Update of local copies of NCBI databases (including Homologene 66, Taxonomy, and gene-abstracts links).
  • 2011-11-10: Fixing a bug hidding addtional parameters on the query page.
  • 2011-08-03: Fixing tax id links between Entrez Gene and Homologene 65.
  • 2011-08-02: Testing introduction of some biointeraction terms in abstract profiles.
  • 2011-08-01: Databases update (Homologene 65, Entrez Gene, Taxonomy).
  • 2011-04-04: Bug fixes (automatic cutoff, P-value calculation).
  • 2011-03-30: Adding MEDLINE daily updates and minor bug fixes.
  • 2011-03-18: Bug fixes (broken links to Homologene in the output table).
  • 2011-03-17: New feature (query species by scientific name).
  • 2011-03-08: Bug fixes on date annotations.
  • 2011-02-08: Bug fixes on annotation data parsing.
  • 2011-02-01: Not available for maintenance. Minor bug fixes.
  • 2011-01-27: Bug fix on querying a gene list and using ortholog species.
  • 2011-01-18: Bug fixes on MEDLINE 2011 data and UTF8 support.
  • 2011-01-10: MEDLINE 2011 DTD changes implemented. Updates reactivated.
  • 2010-12-07: Update of the Word highlighter (fixing bugs and display of available MeSH terms)
  • 2010-11-27/28: Server down for maintenance
  • 2010-11-04/05: Server down for maintenance
  • 2010-06-21: New tutorials (6 and 7)
  • 2010-06-16: Wizard implementation
  • 2010-06-15: Performance improvement of SQL queries
  • 2010-02-16/19: Off-line for maintenance
  • 2009: Start of the project

Copyright and license

Copyright Fontaine 2012

THIS SERVICE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SERVICE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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