Filling the gaps between tools and users: A tool comparator, using protein-protein interaction as an example

Yoshinobu Kano, Ngan Nguyen, Rune SÆtre, Kazuhiro Yoshida, Yusuke Miyao, Yoshimasa Tsuruoka, Yuichiro Matsubayashi, Sophia Ananiadou, Junichi Tsujii

Research output: Chapter in Book/Report/Conference proceedingConference contribution

11 Citations (Scopus)


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.

Original languageEnglish
Title of host publicationPacific Symposium on Biocomputing 2008, PSB 2008
Number of pages12
Publication statusPublished - 2008
Externally publishedYes
Event13th Pacific Symposium on Biocomputing, PSB 2008 - Kohala Coast, HI, United States
Duration: 2008 Jan 42008 Jan 8

Publication series

NamePacific Symposium on Biocomputing 2008, PSB 2008


Other13th Pacific Symposium on Biocomputing, PSB 2008
Country/TerritoryUnited States
CityKohala Coast, HI

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Biomedical Engineering
  • Medicine(all)


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