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Thesaurus-Based Feedback to Support Mixed Search and Browsing Environments [chapter]

Edgar Meij, Maarten de Rijke
2007 Lecture Notes in Computer Science  
from a controlled vocabulary (as typically used in digital library settings).  ...  We present an account of per-topic results, which helps understand for what type of queries our feedback mechanism is particularly helpful.  ...  Using part-of-speech patterns to reduce query ambiguity. In SIGIR '02, pages 307-314, 2002.  ... 
doi:10.1007/978-3-540-74851-9_21 fatcat:5m2gsanyizezvavyhes5nwbnd4

Application of computers in biochemical education – the african challenge

N Tonukari
2009 African Journal of Biomedical Research  
Digital libraries are offering a wealth of information to a large community of users and will become an increasingly valuable part of the Internet as they are developed in a coherent and imaginative way  ...  By accessing online resources, faculty can also bring more of the dynamic nature of genomics and bioinformatics to students (Afr. J. Biomed. Res. 9  ...  Many consider the World Wide Web to be "the" digital library. Digital libraries should have a coherent, organizing principle, sorting materials by topic or by type of material, for instance.  ... 
doi:10.4314/ajbr.v9i1.48767 fatcat:t6wtj3liwbf7lp3tonpufot54e

Towards a combined model for search and navigation of annotated documents

Edgar Meij
2008 Proceedings of the 31st annual international ACM SIGIR conference on Research and development in information retrieval - SIGIR '08  
Such annotations-or concepts-have typically been used for query expansion, to suggest alternative or related query formulations, and to facilitate browsing of the document collection.  ...  In the context of a digital library setting, I have shown that integrating conceptual knowledge in this way can be beneficial both to retrieval performance as well as to facilitate navigation [1].  ...  Such annotations-or concepts-have typically been used for query expansion, to suggest alternative or related query formulations, and to facilitate browsing of the document collection.  ... 
doi:10.1145/1390334.1390573 dblp:conf/sigir/Meij08 fatcat:dp7i5m7m65dyzouwh74hijr2ky

Report on the TREC 2009 Experiments: Chemical IR Track

Julien Gobeill, Douglas Teodoro, Emilie Pasche, Patrick Ruch
2009 Text Retrieval Conference  
Query expansion, driven my chemical named entity recognition resulted in some modest improvement (+2 to 3%). Filtering based on IPC codes did not result in any significant improvement.  ...  Regarding this objective, for the Prior Art subtask, our runs performed significantly better that runs submitted by other participating teams.  ...  IPC codes are keywords assigned to patents, as for instance Medical Subject headings or CAS Registry Number are assigned to Literature articles in the MEDLINE digital library; see TREC Genomics track reports  ... 
dblp:conf/trec/GobeillTPR09 fatcat:oknwq3gob5hllgjtsqhy5zjtce

Evolution of Genome Size and Complexity in Pinus

Alison M. Morse, Daniel G. Peterson, M. Nurul Islam-Faridi, Katherine E. Smith, Zenaida Magbanua, Saul A. Garcia, Thomas L. Kubisiak, Henry V. Amerson, John E. Carlson, C. Dana Nelson, John M. Davis, Mark A. Batzer
2009 PLoS ONE  
Genome evolution in the gymnosperm lineage of seed plants has given rise to many of the most complex and largest plant genomes, however the elements involved are poorly understood.  ...  Acknowledgments We thank Emmarita Golden and Philippe Chouvarine for technical support and Christopher Dervinis for helpful discussions.  ...  We thank Ron Sederoff, Brad Barbazuk Steve Strauss and Connie Mulligan for helpful comments on previous drafts. Author Contributions  ... 
doi:10.1371/journal.pone.0004332 pmid:19194510 pmcid:PMC2633040 fatcat:doocsyia7fbkbgmzq5il4opmba

Genome stability is in the eye of the beholder: recent retrotransposon activity varies significantly across avian diversity [article]

James D. Galbraith, R. Daniel Kortschak, Alexander Suh, David L. Adelson
2021 bioRxiv   pre-print
Transposable elements (TEs) are a source of genome plasticity, because their high similarity enables chromosomal rearrangements through non-allelic homologous recombination, and they have potential for  ...  , and near inactivity of TEs in the cassowary and emu for millions of years.  ...  Acknowledgments We thank Valentina Peona, Jesper Boman, Julie Blommaert and Alastair Ludington for comments on an earlier version of this manuscript.  ... 
doi:10.1101/2021.04.13.439746 fatcat:6uhaqdcizngojcr5bsf3k5aup4

Access to the Maize Genome: An Integrated Physical and Genetic Map

E. Coe
2002 Plant Physiology  
, Cereon Genomics; and Antoni Rafalski, Du-Pont, for this project.  ...  We are grateful for the advice and contributions of our External Advisory Committee, Sue Wessler, chair, University of Georgia; Vicki Chandler, University of Arizona; Joe Ecker, Salk Institute; Stan Letovsky  ...  The output of such a query is a bin location, BLAST score, and database links for more information, e.g.  ... 
doi:10.1104/pp.128.1.9 pmid:11788746 fatcat:7alxujotvje4diyfjwjt3snmjq

Access to the Maize Genome: An Integrated Physical and Genetic Map

E. Coe, K. Cone, M. McMullen, S.-S. Chen, G. Davis, J. Gardiner, E. Liscum, M. Polacco, A. Paterson, H. Sanchez-Villeda, C. Soderlund, R. Wing
2002 Plant Physiology  
, Cereon Genomics; and Antoni Rafalski, Du-Pont, for this project.  ...  We are grateful for the advice and contributions of our External Advisory Committee, Sue Wessler, chair, University of Georgia; Vicki Chandler, University of Arizona; Joe Ecker, Salk Institute; Stan Letovsky  ...  The output of such a query is a bin location, BLAST score, and database links for more information, e.g.  ... 
doi:10.1104/pp.010953 fatcat:gsefamlv5fanzjndxq63cu3rxa

Essie: A Concept-based Search Engine for Structured Biomedical Text

N. C. Ide, R. F. Loane, D. Demner-Fushman
2007 JAMIA Journal of the American Medical Informatics Association  
Essie shows that a judicious combination of exploiting document structure, phrase searching, and concept based query expansion is a useful approach for information retrieval in the biomedical domain.  ...  of Medicine, incorporates a number of strategies aimed at alleviating the need for sophisticated user queries.  ...  The NLM Gateway 33 searches simultaneously in multiple library resources, and uses Essie directly for certain data sets as well as indirectly in some of the systems it queries.  ... 
doi:10.1197/jamia.m2233 pmid:17329729 pmcid:PMC2244877 fatcat:l3dg4ofxtnakbdhijktzci4p5i

Segmental and Tandem Duplications Driving the Recent NBS-LRR Gene Expansion in the Asparagus Genome

Jose Die, Patricia Castro, Teresa Millán, Juan Gil
2018 Genes  
Recent duplications are likely to have dominated the NBS expansion with both tandem genes and duplication events across multiple chromosomes.  ...  Our study provides a strong groundwork for the isolation of candidate R-genes in garden asparagus.  ...  Digital analyses play an increasingly important role for providing gene expression information and facilitating future genomic functional studies of plant growth and development.  ... 
doi:10.3390/genes9120568 fatcat:7k3leu6myfci3o5nr2omijinbm

ASTD: The Alternative Splicing and Transcript Diversity database

Gautier Koscielny, Vincent Le Texier, Chellappa Gopalakrishnan, Vasudev Kumanduri, Jean-Jack Riethoven, Francesco Nardone, Eleanor Stanley, Christine Fallsehr, Oliver Hofmann, Meelis Kull, Eoghan Harrington, Stéphanie Boué (+17 others)
2009 Genomics  
Users can access ASTD through a variety of browsing and query tools, including expression state-based queries for the identification of tissue-specific isoforms.  ...  Alternative transcripts are derived from the mapping of transcribed sequences to the complete human, mouse and rat genomes using an extension of the computational pipeline developed for the ASD (Alternative  ...  new species; (iii) offers a powerful interface for expression pattern-based queries; (iv) is fully integrated with other genomic data and genome browsing capabilities and (v) is extensible with respect  ... 
doi:10.1016/j.ygeno.2008.11.003 pmid:19059335 fatcat:as5xp5ak7zeu7cmws5g2lhuzdm

VitisExpDB: A database resource for grape functional genomics

Harshavardhan Doddapaneni, Hong Lin, M. Andrew Walker, Jiqiang Yao, Edwin L Civerolo
2008 BMC Plant Biology  
It can be downloaded, printed and distributed freely for any purposes (see copyright notice below). Articles in BMC journals are listed in PubMed and archived at PubMed Central.  ...  We thank the author's of the PLAN server for kindly accommodating our requirement from time to time for large scale data searches.  ...  Acknowledgements We gratefully acknowledge the financial support from the California Citrus Research Board (CRB project No. 5300-05F) for a portion of this work and California Department of Food and Agriculture's  ... 
doi:10.1186/1471-2229-8-23 pmid:18307813 pmcid:PMC2359749 fatcat:nxi7ob2rorhs7h5ajpmcadkof4

Giant lungfish genome elucidates the conquest of land by vertebrates

Axel Meyer, Siegfried Schloissnig, Paolo Franchini, Kang Du, Joost Woltering, Iker Irisarri, Wai Yee Wong, Sergej Nowoshilow, Susanne Kneitz, Akane Kawaguchi, Andrej Fabrizius, Peiwen Xiong (+7 others)
2021 Nature  
The lungfish genome continues to expand (its TEs are still active) independently and by different mechanisms than enormous salamander genomes.  ...  We determined the largest chromosome-quality animal genome, the Australian lungfish, Neoceratodus forsteri.  ...  Ocampo Daza (http://www.egosumdaniel.se/) for generously sharing his vertebrate illustrations, J. Joss and P. Sordino for the gift of lungfish embryos, and L. Pennacchio for Vista enhancer images.  ... 
doi:10.1038/s41586-021-03198-8 pmid:33461212 fatcat:wqj42ctuizaplh6be4sxyav4r4

WIDIT in TREC 2004 Genomics, Hard, Robust and Web Tracks

Kiduk Yang, Ning Yu, Adam Wead, Gavin La Rowe, Yu-Hsiu Li, Christopher Friend, Yoon Lee
2004 Text Retrieval Conference  
Our main strategies for the tracks were: the use of gene name thesaurus in the Genomics track; query expansion and relevance feedback in the HARD track; query expansion with keywords from Web search in  ...  query expansion terms and best sentences from top 25 baseline results for each query.  ... 
dblp:conf/trec/YangYWRLFL04 fatcat:74oxu6cxtnaqldkfcd7lq7if4u

Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper

Wei Yin, Zong-ji Wang, Qi-ye Li, Jin-ming Lian, Yang Zhou, Bing-zheng Lu, Li-jun Jin, Peng-xin Qiu, Pei Zhang, Wen-bo Zhu, Bo Wen, Yi-jun Huang (+7 others)
2016 Nature Communications  
TEs exhibit dynamic lineagespecific expansion, and many viper TEs show brain-specific gene expression along with their nearby genes.  ...  Here, we report the high-quality genome of the five-pacer viper, Deinagkistrodon acutus, and comparative analyses with other representative snake and lizard genomes.  ...  At last, small-insert libraries of female and male individuals were used for gap closure for their respective genomes.  ... 
doi:10.1038/ncomms13107 pmid:27708285 pmcid:PMC5059746 fatcat:pqjgkfxs5zctpmouakxhbpzkie
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