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Report on the TREC 2003 Experiment: Genomic and Web Searches

Jacques Savoy, Yves Rasolofo, Laura Perret
2003 Text Retrieval Conference  
This year we took part in the genomic information retrieval and information extraction tasks, as well as the named page and topic distillation searches.  ...  In carrying out the last two tasks, we made use of link anchor information and document content in order to construct Web page representatives.  ...  Acknowledgments This research was supported by the SNSF (grant 21-66'742.01).  ... 
dblp:conf/trec/SavoyRP03 fatcat:h3dvbkadtjbv7mabvi55a22kva

Task-Specific Query Expansion (MultiText Experiments for TREC 2003)

David L. Yeung, Charles L. A. Clarke, Gordon V. Cormack, Thomas R. Lynam, Egidio L. Terra
2003 Text Retrieval Conference  
INTRODUCTION For TREC 2003 the MultiText Project focused its efforts on the Genomics and Robust tracks. We also submitted passageretrieval runs for the QA track.  ...  For our TREC 2003 experiments, we set £ # ¥¤ . Fig. 1 . 1 Fig. 1. Flow diagram for the combined system of the BTRF run. appears in the corpus.  ... 
dblp:conf/trec/YeungCCLT03 fatcat:ohqnmnkgq5gj7koyqtk5vmhjse

Experiments in Terabyte Searching, Genomic Retrieval and Novelty Detection for TREC 2004

Stephen Blott, Fabrice Camous, Paul Ferguson, Georgina Gaughan, Cathal Gurrin, Gareth J. F. Jones, Noel Murphy, Noel E. O'Connor, Alan F. Smeaton, Peter Wilkins, Oisín Boydell, Barry Smyth
2004 Text Retrieval Conference  
all of the track experiments described in this document.  ...  In TREC2004, Dublin City University took part in three tracks, Terabyte (in collaboration with University College Dublin), Genomic and Novelty.  ...  The work described in section 4 is part of project GenIRL that is funded by Enterprise Ireland under the Basic Research Grants Scheme, project number SC-2003-0047-Y.  ... 
dblp:conf/trec/BlottCFGGJMOSWBS04 fatcat:jotvkjbkc5cihjhh3d4rmzpzbq

TREC 2004 Genomics Track Experiments at IUB

Kazuhiro Seki, James C. Costello, Vasanth R. Singan, Javed Mostafa
2004 Text Retrieval Conference  
This paper describes the methods we developed for the three tasks of the TREC Genomics Track, i.e., ad hoc retrieval, triage, and annotation tasks.  ...  For the annotation task, we focused on document representation and applied a variant of the kNN classifiers.  ...  Acknowledgment This project is partially supported by the NSF grant EN-ABLE #0333623.  ... 
dblp:conf/trec/SekiCSM04 fatcat:szqsd6zwv5cdxbwgqi7l6yjhne

A2A: a platform for research in biomedical literature search

Maciej Rybinski, Sarvnaz Karimi, Vincent Nguyen, Cecile Paris
2020 BMC Bioinformatics  
Our setup is guided by the NIST setup of the relevant TREC evaluation tasks in genomics, clinical decision support, and precision medicine.  ...  Our experiments report well-known information retrieval metrics such as precision at a cutoff of ranked documents.  ...  Acknowledgements We acknowledge the contributions of our colleagues in the previous versions of the A2A system: Falk Scholer (RMIT University), Sara Falamaki (ex-CSIRO), and Brian Jin (CSIRO).  ... 
doi:10.1186/s12859-020-03894-8 pmid:33349237 fatcat:dy45nsg2mvf3nlwrxf4s5wpe3a

TREC genomics special issue overview

William Hersh, Ellen Voorhees
2008 Information retrieval (Boston)  
Acknowledgements The TREC Genomics Track was supported by NSF Grant ITR-0325160. The track also appreciated the help of Lori Buckland and others at NIST for help in its administration.  ...  We were also very grateful to the National Library of Medicine, Highwire Press, and the Mouse Genome Informatics Project for providing data for use in the track.  ...  At present, articles are searched in a Web browser one at a time because full-text searching is not available for all of the journals included in MGI. 2.  ... 
doi:10.1007/s10791-008-9076-6 fatcat:e36xnnbro5eqvkmmm7x4rxj2mu

Phrases, Boosting, and Query Expansion Using External Knowledge Resources for Genomic Information Retrieval

William R. Hersh, Ravi Teja Bhupatiraju, Susan Price
2003 Text Retrieval Conference  
OMIM would probably be most useful for a more clinically focused retrieval task than the TREC 2003 Genomics Track task.  ...  In our TREC Genomics Track work, we focused on domain-specific techniques in attempting to improve retrieval performance beyond a word searching baseline.  ... 
dblp:conf/trec/HershBP03 fatcat:vyitjqyn65bdppt6en66iwru6u

Enhancing access to the Bibliome: the TREC 2004 Genomics Track

William R Hersh, Ravi Teja Bhupatiraju, Laura Ross, Phoebe Roberts, Aaron M Cohen, Dale F Kraemer
2006 Journal of Biomedical Discovery and Collaboration  
The goal of the TREC Genomics Track is to improve information retrieval in the area of genomics by creating test collections that will allow researchers to improve and better understand failures of their  ...  The TREC Genomics Track and its test collection resources provide tools that allow improvement in information retrieval systems.  ...  The test collection described in this paper is available on the TREC Genomics Track Web site http://ir.ohsu.edu/genomics and can be downloaded after signing the Data Usage Agreement and returning it to  ... 
doi:10.1186/1747-5333-1-3 pmid:16722581 pmcid:PMC1440302 fatcat:47rfw3fwafa3nm2huaaxu57de4

The BioLink SIG Workshop at ISMB2004

Lynette Hirschman, Christian Blaschke, Alfonso Valencia
2005 Comparative and Functional Genomics  
This paper reports on work done in part at the MITRE Corporation under support from the National Science Foundation (Grant No. EIA-0326404).  ...  Acknowledgements We would like to thank the Program Committee for their careful reviewing: Luc Dehaspe, Robert Gaizauskas, William Hersh, Karin Verspoor and Alexander Yeh.  ...  Activity is organized into 'tracks' of common interest, such as questionanswering, multi-lingual IR, web searching, interactive retrieval and, as started in 2003, IR in the genomics domain.  ... 
doi:10.1002/cfg.455 pmid:18629301 pmcid:PMC2448605 fatcat:lfl62kerhbdvblziets4jxihqa

Recommended reading for IR research students

Alistair Moffat, Justin Zobel, David Hawking
2005 SIGIR Forum  
Only four venues provided more than one nominated paper: SIGIR (16), JASIST (4), IPM (3), and SIGIR Forum (2). However, TREC work featured prominently.  ...  The results are, we believe, illuminating and thoughtprovoking.  ...  We gratefully acknowledge the support of Frontiers of Science and Technology Mission and Workshop component of the Innovation Access Program. part of the Australian Government's Innovation Statement, Backing  ... 
doi:10.1145/1113343.1113344 fatcat:lx4laud5urhh7ediq3z2vi66ju

Overview of TREC 2002

Ellen M. Voorhees
2002 Text Retrieval Conference  
A known-item search is similar to an ad hoc search but the target of the search is a particular document (or a small set of documents) that the searcher knows to exist in the collection and wants to find  ...  Once again, the retrieval system's response is usually a ranked list of documents, and the system is evaluated by the rank at which the target document is retrieved.  ...  Acknowledgements Special thanks to the track coordinators who make the variety of different tasks addressed in TREC possible.  ... 
dblp:conf/trec/Voorhees02 fatcat:e4ox3d6ravhcnn72wxsoez63v4

Boosting Web Retrieval Through Query Operations [chapter]

Gilad Mishne, Maarten de Rijke
2005 Lecture Notes in Computer Science  
We explore the use of phrase and proximity terms in the context of web retrieval, which is different from traditional ad-hoc retrieval both in document structure and in query characteristics.  ...  We also analyze why phrase and proximity terms are far more effective for web retrieval than for ad-hoc retrieval.  ...  Acknowledgments The authors wish to thank Jaap Kamps for many discussions and inspiration.  ... 
doi:10.1007/978-3-540-31865-1_36 fatcat:sna7jjdfrjh6ritpvjesn3onjq

A Testbed for Indonesian Text Retrieval

Jelita Asian, Hugh E. Williams, Seyed M. M. Tahaghoghi
2004 Australasian Document Computing Symposium  
To illustrate how the test collection is used, we briefly report the effect of stemming for Indonesian text retrieval, showing -similarly to English -that it has little effect on accuracy.  ...  The TREC and TDT testbeds have provided such an environment for the evaluation of English, Mandarin, and Arabic text retrieval techniques.  ...  For example, the 2003 Web track investigates retrieval techniques for the Web, with two tasks that investigate topic and home (or named-page) finding.  ... 
dblp:conf/adcs/AsianWT04 fatcat:uggozoek2na6hpt5pgxb5x5t7i

Text similarity: an alternative way to search MEDLINE

J. Lewis, S. Ossowski, J. Hicks, M. Errami, H. R. Garner
2006 Bioinformatics  
Motivation: The most widely used literature search techniques, such as those offered by NCBI's PubMed system, require significant effort on the part of the searcher, and inexperienced searchers do not  ...  A variety of other derivative systems and visualization tools provides the user with an enhanced experience and additional capabilities.  ...  ACKNOWLEDGEMENTS The authors wish to thank Natalie Prikhodko and Alexander Pertsemlidis for the creation of the prototype eTBLAST interface.  ... 
doi:10.1093/bioinformatics/btl388 pmid:16926219 fatcat:gl6usfhjqnbw7f7jof352av65q

Robust, Web and Genomic Retrieval with Hummingbird SearchServer at TREC 2003

Stephen Tomlinson
2003 Text Retrieval Conference  
Hummingbird participated in 4 tasks of TREC 2003: the ad hoc task of the Robust Retrieval Track (find at least one relevant document in the first 10 rows from 1.9GB of news and government data), the navigational  ...  home pages of .GOV), and the primary task of the Genomics Track (find all records focusing on the named gene in 1.1GB of MEDLINE data).  ...  Web Retrieval Both tasks of the TREC 2003 Web Track used the same .GOV collection as last year. It consists of pages downloaded from the .gov domain of the World Wide Web in early 2002.  ... 
dblp:conf/trec/Tomlinson03 fatcat:4no5m5sd4jf7hfvtoudepy7eru
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