Projects‎ > ‎


BIOSMILE web search (BWS), a web-based NCBI-PubMed search application, which can analyze articles for selected biomedical verbs and give users relational information, such as subject, object, location, manner, time, etc. After receiving keyword query input, BWS retrieves matching PubMed abstracts and lists them along with snippets by order of relevancy to protein–protein interaction. Users can then select articles for further analysis, and BWS will find and mark up biomedical relations in the text. The analysis results can be viewed in the abstract text or in table form.

  • Update 2011/05/25: After recovering from hardware failures, we've republished BWS, which is now available at a new URL ( Please update your bookmarks.
    • The gene normalization component (for human genes only) is updated to the one developed in our paper:
      Lai P-T, et al.: Using Contextual Information to Clarify Gene Normalization Ambiguity. IEEE IRI 2009.


  • Dai H-J, Huang C-H, Lin RTK, Tsai RT-H, Hsu W-L: BIOSMILE web search: a web application for annotating biomedical entities and relations. Nucl Acids Res 2008, 36(Web Server issue):W390-W398.
  • Lai P-T, Bow Y-Y, Huang C-H, Dai H-J, Tsai RT-H, Hsu W-L: Using Contextual Information to Clarify Gene Normalization Ambiguity. In: The IEEE International Conference on Information Reuse and Integration (IEEE IRI 2009). Las Vegas, USA; 2009: 1-5.
  • Chou P-H, Dai H-J, Huang C-H, Tsai RT-H, Hsu W-L: A Web Application for Biomedical Entities and Relations Annotation Using the Unstructured Information Management Architecture. In: International Computer Symposium (ICS). Taipei, Taiwan; 2008.
  • Tsai RT-H, Chou W-C, Su Y-S, Lin Y-C, Sung C-L, Dai H-J, Yeh IT, Ku W, Sung T-Y, Hsu W-L: BIOSMILE: A semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features. BMC Bioinformatics 2007, 8:325.
BWS comment

Error Codes

  • 1: GENIATagger.GenerateAnnotationInfos: The length of the tokenized result is inconsistent with the original string.
  • 2: FileNotFoundException: Some files are missing on the server.


  1. Adobe Felx Builder:
  2. Handling and Throwing Exceptions in XML Web Services: