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Research Interests
My research is in text mining. The biomedical literature contains a deluge of information - in an attempt to keep up with the latest findings as presented in scientific publications, researchers in biomedicine almost daily search for papers related to their work, specific information within the papers and often are trying to make connections among information contained in different papers. So far I have worked on developing and evaluating text mining systems (both algorithms and user interfaces), identifying information for database annotation, as well as document clustering based on both syntactic and semantic content. All aim at making the information hunt in the literature faster and more efficient.
Currently, I am working on a Ludwig Institute of Cancer Research (LICR) project on cancer metastasis where I combine knowledge acquisition with text mining to compose a better understanding of the metastatic process in relation to the beliefs of experts.
I am also interested in knowledge representation and ontology design, the use of crowdsourcing for biomedical studies, and studying the behavior of biomedical scientists, in particular the language and media they use to communicate their ideas and findings.
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Publications
Papers:
Yao, L., Divoli, A., Mayzus, I., Evans, J.A. and Rzhetsky, A. (2011) Benchmarking Ontologies, Bigger vs Better, PLoS Computational Biology 7(1): e1001055 [PubMed]
Morgan, A.A., Lu, Z., Wang, X., Cohen, A.M., Fluck, J., Ruch, P., Divoli, A., Fundel, A., Leaman, R., Hakenberg, J., Sun, C., Liu, H., Torres, R., Krauthammer, M., Lau, W.W., Liu, H., Hsu, C-N., Schuemie, M., Cohen, K.B., Hirschman, L. (2008)
Overview of BioCreative II gene normalization, Genome Biology, 9(Suppl 2):S3
[PubMed]
Smith, L., Tanabe, L.K., Johnson nee Ando, R., Kuo, C-J., Chung, I-F., Hsu, C-N., Lin, Y-S., Klinger, R., Friedrich, C.M., Ganchev, K., Torii, M., Liu, H., Haddow, B., Struble, C.A., Povinelli, R.J., Vlachos, A., Baumgartner, W.A., Hunter, L., Carpenter, B., Tsai, R.T-H., Dai, H-J., Liu, F., Chen, Y., Sun, C., Katrenko, S., Adriaans, P., Blaschke, C., Torres, R., Neves, M., Nakov, P., Divoli, A., Mana-Lopez, M., Mata, J., Wilbur, J.W. (2008)
Overview of BioCreative II gene mention recognition,
Genome Biology, 9(Suppl 2):S2
[PubMed]
Hearst, M.A., Divoli, A., Guturu, H., Ksikes, A., Nakov, P., Wooldridge, M.A. and Ye, J. (2007)
BioText Search Engine: beyond abstract search,
Bioinformatics, 23: 2196-2197
[PubMed]
Divoli, A., Hearst, M.A., Nakov, P.I., Schwartz, A. and Ksikes, A. (2006)
BioText Team Report for the TREC 2006 Genomics Track,
The Fifteenth Text REtrieval Conference Proceedings, Gaithersburg, MD, USA
(Participation Report Paper)
Mitchell, A.L.,Divoli, A., Kim, J.-H., Hilario, M., Selimas, I. and Attwood, T.K. (2005)
METIS: Multiple Extraction Techniques for Informative Sentences,
Bioinformatics, 21: 4196-4197
[PubMed]
Short Papers, Abstracts, Posters, etc:
Mitchell, A.L., Bradley, P., Divoli, A. and Attwood, T.K. (2004)
Sequence Analysis Workshop,
MIPNETS training meeting, Liverpool, UK (Workshop Organised)
Other Selected Talks (not listed above):
Divoli, A. (2008) Usability, Interfaces and Text Mining (work with Wooldridge, M.A. and Hearst, M.A.), Dagstuhl seminar "Ontologies and text mining for Life Sciences-Current Status and Future Perspectives", Germany (Invited Session)
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Software
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BioText Search
Engine: Journal Search Engine Showing Figures and Captions
The BioText Search Engine provides biologists with new ways to access information from any Open Access article available
at PubMedCentral.
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BioIE: Extracting Informative
Sentences from the Biomedical Literature
A rule-based system for extracting informative sentences referring to
either structure, function, diseases and therapeutic compounds, localisation or familial relationships of biological entities,
particularly proteins.
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METIS:
Multiple Extraction Techniques for Informative Sentences
METIS accepts Swiss-Prot identifiers or FASTA-format
sequences, performs BLAST to find related sequences, and then retrieves textual information from Swiss-Prot as well as related
sentences from PubMed abstracts.
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BioQSpace: An interactive
visualisation tool for clustering PubMed abstracts
BioQSpace clusters abstracts based on similarity measures calculated on user-specified weighting of certain attributes and
allows for visualisation and navigation in 3D space.
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News
24 Nov 2010
Benchmarking Ontologies, Bigger vs Better
One of our group's papers was recently accepted by PLoS Computational Biology.
Lixia Yao, Anna Divoli, Ilya Mayzus, James Evans and Andrey Rzhetsky
Benchmarking Ontologies, Bigger vs Better
In this paper we introduce a family of ontology metrics and we test them on four medical ontologies and seven popular English thesauri.
9 Aug 2010
Bio-Interfaces Google Group
Together with some of the Interfaces people at EBI (if you haven't already, check out their fantastic site: http://ebiinterfaces.wordpress.com ), I have started a Google Group "Biological Interfaces".
We are hoping that this will serve as a platform for all bio-interfaces researchers around the world to discuss research matters, post CFP for pertinent meetings/conferences and advertise for related jobs. Areas covered: design, visualization, human-computer interaction, usability.
The archives of the group are public. You can read and join here:
14 Jul 2010
ISMB 2010
I just came back from ISMB which took place in Boston, MA this year. The meeting was very interesting and stimulating and I got the chance to catch up with many wonderful colleagues as well as to meet new interesting people.
There, I presented a poster entitled "Considering alternative views when modeling cancer metastasis".
14 Jul 2010
Some kind of blog...
I decided to start a "News" tab on my website. I suppose this will allow me to do something in between microblogging and proper blogging...
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Last updated: November 2010 |
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