DESIGN OF A STANDOFF OBJECT-ORIENTED MARKUP LANGUAGE (SOOML) FOR ANNOTATING BIOMEDICAL LITERATURE

Jing Ding, Daniel Berleant

2005

Abstract

With the rapid growth of electronically available scientific literature, text mining is attracting increasing attention. While numerous algorithms, tools, and systems have been developed for extracting information from text, little effort has been focused on how to mark up the information. We present the design of a standoff, object-oriented markup language (called SOOML), which is simple, expressive, flexible, and extensible, satisfying the demanding needs of biomedical text mining.

References

  1. Bird, S. and Liberman, M. (1999) A Formal Framework for Linguistic Annotation. Technical Report MS-CIS99-01, Department of Computer and Information Science, University of Pennsylvania.
  2. Doedens, C.-J. (1994) in Text Databases. One Database Model and Several Retrieval Languages. Amsterdam and Atlanta, GA.
  3. Hucka, M., et al. (2003) The Systems Biology Markup Language (SBML): A Medium for Representation and Exchange of Biochemical Network Models. Bioinformatics 19: 524-531.
  4. Kim, J.D., Ohta, T., Tateisi, Y., and Tsujii, J. (2003) GENIA Corpus - A Semantically Annotated Corpus for Bio-textmining. Bioinformatics 19: i180-i182.
Download


Paper Citation


in Harvard Style

Ding J. and Berleant D. (2005). DESIGN OF A STANDOFF OBJECT-ORIENTED MARKUP LANGUAGE (SOOML) FOR ANNOTATING BIOMEDICAL LITERATURE . In Proceedings of the Seventh International Conference on Enterprise Information Systems - Volume 3: ICEIS, ISBN 972-8865-19-8, pages 382-385. DOI: 10.5220/0002509603820385


in Bibtex Style

@conference{iceis05,
author={Jing Ding and Daniel Berleant},
title={DESIGN OF A STANDOFF OBJECT-ORIENTED MARKUP LANGUAGE (SOOML) FOR ANNOTATING BIOMEDICAL LITERATURE},
booktitle={Proceedings of the Seventh International Conference on Enterprise Information Systems - Volume 3: ICEIS,},
year={2005},
pages={382-385},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002509603820385},
isbn={972-8865-19-8},
}


in EndNote Style

TY - CONF
JO - Proceedings of the Seventh International Conference on Enterprise Information Systems - Volume 3: ICEIS,
TI - DESIGN OF A STANDOFF OBJECT-ORIENTED MARKUP LANGUAGE (SOOML) FOR ANNOTATING BIOMEDICAL LITERATURE
SN - 972-8865-19-8
AU - Ding J.
AU - Berleant D.
PY - 2005
SP - 382
EP - 385
DO - 10.5220/0002509603820385