title: Filling the gaps between tools and users: a tool comparator, using protein-protein interaction as an example.
abstract: Recently, several text mining programs have reached a near-practical level of performance. Some systems are already being used by biologists and database curators. However, it has also been recognized that current Natural Language Processing (NLP) and Text Mining (TM) technology is not easy to deploy, since research groups tend to develop systems that cater specifically to their own requirements. One of the major reasons for the difficulty of deployment of NLP/TM technology is that re-usability and interoperability of software tools are typically not considered during development. While some effort has been invested in making interoperable NLP/TM toolkits, the developers of end-to-end systems still often struggle to reuse NLP/TM tools, and often opt to develop similar programs from scratch instead. This is particularly the case in BioNLP, since the requirements of biologists are so diverse that NLP tools have to be adapted and re-organized in a much more extensive manner than was originally expected. Although generic frameworks like UIMA (Unstructured Information Management Architecture) provide promising ways to solve this problem, the solution that they provide is only partial. In order for truly interoperable toolkits to become a reality, we also need sharable type systems and a developer-friendly environment for software integration that includes functionality for systematic comparisons of available tools, a simple I/O interface, and visualization tools. In this paper, we describe such an environment that was developed based on UIMA, and we show its feasibility through our experience in developing a protein-protein interaction (PPI) extraction system.
authors.affiliation: Department of Computer Science, University of Tokyo Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Tokyo.
authors.forename: Yoshinobu
authors.initials: Y
authors.lastname: Kano
authors.forename: Ngan
authors.initials: N
authors.lastname: Nguyen
authors.forename: Rune
authors.initials: R
authors.lastname: Saetre
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Yoshida
authors.forename: Yusuke
authors.initials: Y
authors.lastname: Miyao
authors.forename: Yoshimasa
authors.initials: Y
authors.lastname: Tsuruoka
authors.forename: Yuichiro
authors.initials: Y
authors.lastname: Matsubayashi
authors.forename: Sophia
authors.initials: S
authors.lastname: Ananiadou
authors.forename: Jun'ichi
authors.initials: J
authors.lastname: Tsujii
mesh_terms: D019295:Computational Biology; D016247:Information Storage and Retrieval; D009323:Natural Language Processing; D025941:Protein Interaction Mapping / Q000706:statistics & numerical data*