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Gene name extraction using FlyBase resources

Alex Morgan, Lynette Hirschman, Alexander Yeh, Marc Colosimo
2003 Proceedings of the ACL 2003 workshop on Natural language processing in biomedicine -  
The FlyBase database has been in existence since 1993. 3  ...  tor), a model organism for genetics research: 2 Of course most of these early references in FlyBase are not in electronic form.  ...  We used the measure of unique genes in a paper because this allowed us to take advantage of the existing FlyBase expert curated resources.  ... 
doi:10.3115/1118958.1118959 dblp:conf/bionlp/MorganHYC03 fatcat:y5br6vlv5rfdtll2byszlnipd4

Gene name identification and normalization using a model organism database

Alexander A. Morgan, Lynette Hirschman, Marc Colosimo, Alexander S. Yeh, Jeff B. Colombe
2004 Journal of Biomedical Informatics  
These experiments indicate that the lexical resources provided by FlyBase are complete enough to achieve high recall on the gene list task, and that normalization requires accurate disambiguation; different  ...  We focused on listing the normalized form of genes and gene products discussed in an article. We broke this into two steps: gene mention tagging in text, followed by normalization of gene names.  ...  We describe the resources available in FlyBase and the use of abstracts from MEDLINE.  ... 
doi:10.1016/j.jbi.2004.08.010 pmid:15542014 fatcat:f2r63l3ecfhrtjxm2eo2omfxvq

FlyBase: establishing a Gene Group resource forDrosophila melanogaster

Helen Attrill, Kathleen Falls, Joshua L. Goodman, Gillian H. Millburn, Giulia Antonazzo, Alix J. Rey, Steven J. Marygold
2015 Nucleic Acids Research  
To this end, FlyBase (, the MOD for Drosophila melanogaster, has established a 'Gene Group' resource: high-quality sets of genes derived from the published literature and organized into individual  ...  It is useful for such gene collections to be presented as discrete lists within the appropriate Model Organism Database (MOD) so that researchers can readily access these data alongside other relevant  ...  ACKNOWLEDGEMENTS We wish to thank: Elspeth Bruford, Ruth Seal, Susan Tweedie and Kris Gray at the HGNC for useful dis-  ... 
doi:10.1093/nar/gkv1046 pmid:26467478 pmcid:PMC4702782 fatcat:2ljorlbf4jgkrilfxniusk6pcy


2005 Biocomputing 2006  
This paper demonstrates how Drosophila gene name recognition and anaphoric linking of gene names and their products can be achieved using existing information in FlyBase and the Sequence Ontology.  ...  We also present guidelines for annotation of gene mentions in texts and outline how the resulting system is used to aid FlyBase curation.  ...  We would like to thank Alexander Morgan for making the annotated test data available to us and for advice on replication of the experiment reported in Morgan et al. 5 , Chihiro Yamada for his expert  ... 
doi:10.1142/9789812701626_0010 fatcat:zopw5gnzobanllledtov36usum

Rutabaga by any other name: extracting biological names

Lynette Hirschman, Alexander A. Morgan, Alexander S. Yeh
2002 Journal of Biomedical Informatics  
This article examines emerging techniques to access biological resources through extraction of entity names and relations among them.  ...  We conclude by outlining a research agenda to raise performance of named entity tagging to a level where it can be used to perform tasks of biological importance. (L.  ...  As our lexical resource, we made use of the Flybase gene name list and associated synonyms.  ... 
doi:10.1016/s1532-0464(03)00014-5 pmid:12755519 fatcat:4w2eigmhuzecvnpe76dj7uu2u4


2005 Biocomputing 2006  
The proposed methods are evaluated using 10 randomly chosen genes from FlyBase and a subset of Medline abstracts about Drosophila.  ...  We present a two-stage summarization method, which involves first retrieving relevant articles and then extracting the most informative sentences from the retrieved articles to generate a structured gene  ...  three resources: the Summary pages, the Attributed data pages, and the references of each gene in FlyBase.  ... 
doi:10.1142/9789812701626_0005 fatcat:6gb3q3nzfngopkqiycvbx6coqi

Automatically generating gene summaries from biomedical literature

Xu Ling, Jing Jiang, Xin He, Qiaozhu Mei, Chengxiang Zhai, Bruce Schatz
2006 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
The proposed methods are evaluated using 10 randomly chosen genes from FlyBase and a subset of Medline abstracts about Drosophila.  ...  We present a two-stage summarization method, which involves first retrieving relevant articles and then extracting the most informative sentences from the retrieved articles to generate a structured gene  ...  three resources: the Summary pages, the Attributed data pages, and the references of each gene in FlyBase.  ... 
pmid:17094226 fatcat:vumxiut4lrg23aowwmylihngim

AphidBase: a database for aphid genomic resources

J.-P. Gauthier, F. Legeai, A. Zasadzinski, C. Rispe, D. Tagu
2007 Bioinformatics  
Text mining of the D.melanogaster literature was performed to construct a network of co-cited gene or protein names, which should facilitate functional annotation of aphid homolog sequences.  ...  For that, the Drosophila melanogaster genome has been loaded in the database using the GMOD open source software for a comparison with the 17 069 pea aphid unique transcripts (contigs) and the 13 639 gene  ...  FlyBase, SwissProt or Entrez Gene.  ... 
doi:10.1093/bioinformatics/btl682 pmid:17237053 fatcat:ptc2bx3e6jekdltwktrrjaa7oa

Resource capability discovery and description management system for bioinformatics Data and service Integration - an experiment with gene regulatory networks

Emdad Ahmed
2008 2008 11th International Conference on Computer and Information Technology  
In this context we also report a Java based implementation for integrating Flybase and AlignACE site.  ...  Our prototype application is based on WebFusion and an ad hoc query language BioFlow [2], [3], [4], [5], [6] a software agent that can simulate a person interacting with web search forms and extracting  ...  In response to the quick search, a overview page shows the attribute name and values e.g sequence location, gene direction etc. We extract those from the overview page.  ... 
doi:10.1109/iccitechn.2008.4802991 fatcat:h3ycejeftfhvfflkmentn2ryzq

tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles

J. M. Cejuela, P. McQuilton, L. Ponting, S. J. Marygold, R. Stefancsik, G. H. Millburn, B. Rost
2014 Database: The Journal of Biological Databases and Curation  
As part of the BioCreative IV Interactive Annotation Task, FlyBase has used tagtog to identify and extract mentions of Drosophila melanogaster gene symbols and names in full-text biomedical articles from  ...  Toward this end, we present the 'tagtog' system, a web-based annotation framework that can be used to mark up biological entities (such as genes) and concepts (such as Gene Ontology terms) in full-text  ...  They would also like to thank all members of FlyBase for their helpful comments and suggestions on the article.  ... 
doi:10.1093/database/bau033 pmid:24715220 pmcid:PMC3978375 fatcat:ibmnb46bofeivdeqcatwpbr7ce

Generating gene summaries from biomedical literature: A study of semi-structured summarization

Xu Ling, Jing Jiang, Xin He, Qiaozhu Mei, Chengxiang Zhai, Bruce Schatz
2007 Information Processing & Management  
We address the issue of gene name variation in the first stage and propose several different methods for sentence extraction in the second stage.  ...  We evaluate the proposed methods using a test set with 20 genes.  ...  FlyBase Resources Training Sentence Extraction Training Sentences Input Gene Name Gene Synonyms Query Expansion SynSet MEDLINE abstracts Sentence Scoring and Ranking IE Module Keyword  ... 
doi:10.1016/j.ipm.2007.01.018 fatcat:kusyzyzdkzbxjjblnksgznyyou

Building a pipeline to solicit expert knowledge from the community to aid gene summary curation

2019 Database: The Journal of Biological Databases and Curation  
Based on the data within the FlyBase database, we developed a computational pipeline to identify researchers who have worked extensively on each gene.  ...  One solution is to use computational methods to generate summaries, but this often fails to capture the key functions or express them eloquently.  ...  We greatly appreciate the willingness of our expert authors to respond to our request and provide helpful gene snapshots.  ... 
doi:10.1093/database/baz152 pmid:31960022 pmcid:PMC6971343 fatcat:cci3gb6iovbkdbzinb2yr4w6pi


2005 Biocomputing 2006  
(e.g., UniProt, PDB, PIR), model organism databases (e.g., FlyBase, MGI, SGD), ontologies (the Gene Ontology, as well as the growing number of ontologies in OBO -Open Biological Ontologies), and nomenclatures  ...  This session builds on two threads of work that have been well represented at past PSB meetings, namely text mining and ontologies.  ...  These papers tackle a number of biological problems using a variety of technologies: improve on named entity results for FlyBase genes and to support an ontologybased coreference resolution strategy for  ... 
doi:10.1142/9789812701626_0001 fatcat:idrwqvbmtrgwfbhbkneijgqaui

2008 BBSRC Tools and Resources Development Fund Application - pubmed2ensembl: a resource for linking biological literature to genome sequences

Casey Bergman, Goran Nenadic
2012 Figshare  
2008 BBSRC Tools and Resources Development Fund application. Awarded.  ...  be generated using gene name recognition or text-based sequence extraction.  ...  Both PIs anticipate using pubmed2ensembl resources in future research projects, including: 1) hybrid gene name recognition systems that use both text and sequence information, 2) automated methods to extract  ... 
doi:10.6084/m9.figshare.94137.v2 fatcat:63oszpocifezhoznpqvjc4nn3i

Bioinformatics web data and service integration - An experiemnt with Gene Regulatory Networks

Emdad Ahmed
2008 2008 International Conference on Electrical and Computer Engineering  
For a given set of genes, we could find a set of sequences (800˜1500 bp) from Flybase site, then we feed those into YMF site to get a motif of 6˜8 bp.  ...  The result motifs were fed into STAMP site and by combining result from Fly curated by Bergman and by TRANSFAC, we were able to get a sample correct result for a Bicoid gene, namely bin.  ...  Flyabse site has celeta gene number, CG, flybase gene number, FBgn as well as gene name. From the table, it is noted that some of the gene don't have name gene name (NULL).  ... 
doi:10.1109/icece.2008.4769175 fatcat:6nvnrygpivbmborxafxmdk4jxu
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