Open semantic annotation of scientific publications using DOMEO

被引：20

作者：

Paolo Ciccarese

Marco Ocana

Tim Clark

机构：

[1] Harvard Medical School and Massachusetts General Hospital, Boston, MA

[2] Balboa Systems, Newton, MA

[3] School of Computer Science, University of Manchester, Manchester

来源：

Journal of Biomedical Semantics | / 3卷 / Suppl 1期

基金：

美国国家卫生研究院;

关键词：

Citation Network; Semantic Annotation; Annotation Type; Neuroscience Information Framework; Discourse Element;

D O I：

10.1186/2041-1480-3-S1-S1

中图分类号：

学科分类号：

摘要：

Background: Our group has developed a useful shared software framework for performing, versioning, sharing and viewing Web annotations of a number of kinds, using an open representation model. Methods: The Domeo Annotation Tool was developed in tandem with this open model, the Annotation Ontology (AO). Development of both the Annotation Framework and the open model was driven by requirements of several different types of alpha users, including bench scientists and biomedical curators from university research labs, online scientific communities, publishing and pharmaceutical companies. Several use cases were incrementally implemented by the toolkit. These use cases in biomedical communications include personal note-taking, group document annotation, semantic tagging, claim-evidence-context extraction, reagent tagging, and curation of textmining results from entity extraction algorithms. Results: We report on the Domeo user interface here. Domeo has been deployed in beta release as part of the NIH Neuroscience Information Framework (NIF, http://www.neuinfo.org ) and is scheduled for production deployment in the NIF's next full release. Future papers will describe other aspects of this work in detail, including Annotation Framework Services and components for integrating with external textmining services, such as the NCBO Annotator web service, and with other textmining applications using the Apache UIMA framework. © 2012 Ciccarese et al; licensee BioMed Central Ltd.

引用

共 51 条

[1]

Jacobs I., Walsh N., Architecture of the World Wide Web, W3C Recommendation, 1, (2004)

[2]

Attwood T.K., Kell D.B., McDermott P., Marsh J., Pettifer S.R., Thorne D., Utopia documents: linking scholarly literature with research data, Bioinformatics, 26, 18, pp. i568-i574, (2010)

[3]

Singh J., Mendeley: A free research management tool for desktop and web, 1, (2010)

[4]

Altman R.B., Bergman C.M., Blake J., Blaschke C., Cohen A., Gannon F., Grivell L., Hahn U., Hersh W., Hirschman L., Et al., Text mining for biology--the way forward: opinions from leading scientists, Genome Biology, 9, (2008)

[5]

Arighi C., Lu Z., Krallinger M., Cohen K., Wilbur W., Valencia A., Hirschman L., Wu C., Overview of the BioCreative III Workshop, BMC Bioinformatics, 12, (2011)

[6]

Arighi C., Roberts P., Agarwal S., Bhattacharya S., Cesareni G., Chatr-aryamontri A., Clematide S., Gaudet P., Giglio M., Harrow I., BioCreative III Interactive Task: an Overview, BMC Bioinformatics, (2011)

[7]

Krallinger M., Vazquez M., Leitner F., Salgado D., Chatr-aryamontri A., Winter A., Perfetto L., Briganti L., Licata L., Iannuccelli M., The Protein-Protein Interaction tasks of BioCreative III: classication/ranking of articles and linking bio-ontology concepts to full text, BMC Bioinformatics, (2011)

[8]

Lu Z., Kao H., Wei C., Huang M., Liu J., Kuo C., Hsu C., Tsai R., Dai H., Okazaki N., The Gene Normalization Task in BioCreative III, BMC Bioinformatics, (2011)

[9]

Leitner F., Chatr-aryamontri A., Mardis S., Ceol A., Krallinger M., Licata L., Hirschman L., Cesareni G., Valencia A., The FEBS Letters/BioCreative II.5 experiment: making biological information accessible, Nature biotechnology, 28, pp. 897-899, (2009)

[10]

Kim J., Ohta T., Tsuruoka Y., Tateisi Y., Collier N., Introduction to the Bio-Entity Task at JNLPBA, BioCreative Challenge Evaluation Workshop, (2004)

← 1 2 3 4 5 6 →