Now showing items 1-6 of 6

    • Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documents 

      Usié Chimenos, Anabel; Karathia, Hiren; Teixidó Torrelles, Ivan; Alves, Rui; Solsona Tehàs, Francesc (PeerJ, 2014)
      One way to initiate the reconstruction of molecular circuits is by using automated text-mining techniques. Developing more efficient methods for such reconstruction is a topic of active research, and those methods are ...
    • Biblio-MetReS: A bibliometric network reconstruction application and server 

      Usié Chimenos, Anabel; Karathia, Hiren; Teixidó Torrelles, Ivan; Valls Marsal, Joan; Faus i Torà, Xavier; Alves, Rui; Solsona Tehàs, Francesc (BioMed Central, 2011)
      Background: Reconstruction of genes and/or protein networks from automated analysis of the literature is one of the current targets of text mining in biomedical research. Some user-friendly tools already perform this ...
    • CheNER: Chemical Named Entity Recognizer 

      Usié Chimenos, Anabel; Alves, Rui; Solsona Tehàs, Francesc; Vázquez, Miguel; Valéncia, Alfonso (Oxford University Press, 2013)
      Motivation: Chemical named entity recognition is used to automatically identify mentions to chemical compounds in text, and is the basis for more elaborate information extraction. However, only a small number of ...
    • Database constraints applied to metabolic pathway reconstruction tools 

      Vilaplana Mayoral, Jordi; Solsona Tehàs, Francesc; Teixidó Torrelles, Ivan; Usié Chimenos, Anabel; Karathia, Hiren; Alves, Rui; Mateo Fornés, Jordi (Hindawi Publishing Corporation, 2014)
      Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction ...
    • Methods for and results from the study of design principles in molecular systems 

      Salvadó López, Baldiri; Karathia, Hiren; Usié Chimenos, Anabel; Vilaprinyo Terré, Ester; Omholt, Stig; Sorribas Tello, Albert; Alves, Rui (Elsevier, 2011)
      Most aspects of molecular biology can be understood in terms of biological design principles. These principles can be loosely defined as qualitative and quantitative features that emerge in evolution and recur more ...
    • The CHEMDNER corpus of chemicals and drugs and its annotation principles 

      Krallinger, Martin; Rabal, Obdulia; Leitner, Florian; Vázquez, Miguel; Salgado, David; Lu, Zhiyong; Leaman, Robert; Lu, Yanan; Ji, Donghong; Lowe, Daniel M.; Sayle, Roger A.; Batista Navarro, Riza Theresa; Rak, Rafal; Huber, Torsten; Rocktäschel, Tim; Matos, Sérgio; Campos, David; Tang, Buzhou; Xu, Hua; Munkhdalai, Tsendsuren; Ho Ryu, Keun; Ramanan, SV; Nathan, Senthil; Žitnik, Slavko; Bajec, Marko; Weber, Lutz; Irmer, Matthias; Akhondi, Saber A.; Kors, Jan A.; Xu, Shuo; An, Xin; Kumar Sikdar, Utpal; Ekbal, Asif; Yoshioka, Masaharu; Dieb, Thaer M.; Choi, Miji; Verspoor, Karin; Khabsa, Madian; Lee Giles, C.; Liu, Hongfang; Elayavilli Ravikumar, Komandur; Lamurias, Andre; Coute, Francisco M.; Dai, Hong Jie; Tzong Han Tsai, Richard; Ata, Caglar; Can, Tolga; Usié Chimenos, Anabel; Alves, Rui; Segura Bedmar, Isabel; Martínez, Paloma; Oyarzabal, Julen; Valencia, Alfonso (BioMed Central, 2015)
      The automatic extraction of chemical information from text requires the recognition of chemical entity mentions as one of its key steps. When developing supervised named entity recognition (NER) systems, the availability ...