Jean F Fontaine
- CELDA -- an ontology for the comprehensive representation of cells in complex systemsStefanie Seltmann
Charite Universitatsmedizin Berlin, Berlin Brandenburg Center for Regenerative Therapies BCRT, Berlin, Germany
BMC Bioinformatics 14:228. 2013..CELDA (Cell: Expression, Localization, Development, Anatomy) is a novel ontology for the association of primary experimental data and derived knowledge to various types of cells of organisms...
- Using cited references to improve the retrieval of related biomedical documentsFrancisco M Ortuño
Computer Architecture and Computer Technology Department, University of Granada, Granada, Spain
BMC Bioinformatics 14:113. 2013..As a solution to this problem, we propose a query expansion method that extends the information related to a manuscript using its cited references...
- The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full textMartin Krallinger
Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, Madrid, Spain
BMC Bioinformatics 12:S3. 2011....
- PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queriesAdriano Barbosa-Silva
Computational Biology and Data Mining Group, Max Delbruck Center for Molecular Medicine, Robert Rössle Strasse, 10, D 13125, Berlin, Germany
BMC Bioinformatics 12:435. 2011..Current tools do not allow studying these data with a focus on concepts of relevance to a user, for example, interactions related to a disease or to a biological mechanism such as protein aggregation...
- LAITOR--Literature Assistant for Identification of Terms co-Occurrences and RelationshipsAdriano Barbosa-Silva
Max Delbruck Center for Molecular Medicine, Berlin, Germany
BMC Bioinformatics 11:70. 2010..Therefore, the study of the current literature about a selected topic deposited in public databases, facilitates the generation of novel hypotheses associating a set of bioentities to a common context...
- MedlineRanker: flexible ranking of biomedical literatureJean Fred Fontaine
Computational Biology and Data Mining Group, Max Delbruck Center for Molecular Medicine, Robert Rossle Strasse 10, D 13125, Berlin, Germany
Nucleic Acids Res 37:W141-6. 2009..We show that our tool can be highly accurate and that it is able to process millions of abstracts in a practical amount of time. MedlineRanker is free for use and is available at http://cbdm.mdc-berlin.de/tools/medlineranker...
- QiSampler: evaluation of scoring schemes for high-throughput datasets using a repetitive sampling strategy on gold standardsJean F Fontaine
Max Delbruck Center for Molecular Medicine, Robert Rossle Strasse 10, 13125 Berlin, Germany
BMC Res Notes 4:57. 2011..abstract:..
- Génie: literature-based gene prioritization at multi genomic scaleJean Fred Fontaine
Max Delbruck Center for Molecular Medicine, Robert Rossle Str 10, 13125 Berlin, Germany
Nucleic Acids Res 39:W455-61. 2011..Common run times below a minute, even when analyzing the human genome with hundreds of thousands of literature records, allows the use of Génie in routine lab work. Availability: http://cbdm.mdc-berlin.de/tools/genie/...