About and citation

About

The MedlineRanker web server is dedicated to scientists interested to rank the biomedical literature according to a selected topic. The query page allows to search for any biomedical topic. The web server is fast enough to process thousands of scientific abstracts from the PubMed database in few seconds.

Citation

  • Fontaine JF, Barbosa-Silva A, Schaefer M, Huska MR, Muro EM, Andrade-Navarro MA. MedlineRanker: flexible ranking of biomedical literature. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W141-6. doi: 10.1093/nar/gkp353

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).
  • 2013-12-19: Switching to PubMed/MEDLINE 2014 data and daily updates.
  • 2013-01-08: Installation of MEDLINE 2013 and daily automatic updates. Set min word weight = 0.5.
  • 2012-03-12: Adding option to deactivate leave-one-out cross validations.
  • 2012-02-01: Adding PubMed Central search, and manual setting of the minimal word weight.
  • 2012-01-18: Minor bug fixes (scoring formula, not affecting ranking).
  • 2012-01-12: Daily updates are back after MEDLINE 2012 DTD integration.
  • 2011-08-12: Minor bug fixes (highlighting words on sentence boundaries).
  • 2011-08-02: Testing introduction of some biointeraction terms in abstract profiles.
  • 2011-07-19: New feature (download results as text files).
  • 2011-05-27: New feature (highlighting words in MeSH list).
  • 2011-05-27: Bug fixes (highlighting words similar to HTML tags).
  • 2011-04-04: Bug fixes (automatic cutoff, P-value calculation).
  • 2011-03-30: Changed default search to 2 months old abstracts.
  • 2011-03-30: Adding daily updates and minor bug fixes.
  • 2011-03-21: Bug fixes (test set selection).
  • 2011-03-12: Automatic P-value cutoff to optimize classification performance (F-value = 90%).
  • 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.
  • 2011-01-18: Bug fixes on MEDLINE 2011 data and UTF8 support.
  • 2011-01-10: MEDLINE 2011 DTD changes implemented. Updates reactivated.
  • 2010-12-27: Updates frozen to implement MEDLINE DTD changes.
  • 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
  • 2010-09-21: Reactivation of the update agent after crash
  • 2010-03-23: Bug fixing to query MeSH terms containing special characters
  • 2010-02-19: New filters for extracted words
  • 2010-02-16/19: Off-line for maintenance
  • 2010-01-19: Full UTF-8 support
  • 2010-01-18: PubMed query through NCBI web services
  • 2009-05-08: Medline Ranker article publication

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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