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Methods and strategies for gene structure curation in WormBase

G. W. Williams, P. A. Davis, A. S. Rogers, T. Bieri, P. Ozersky, J. Spieth
2011 Database: The Journal of Biological Databases and Curation  
We also describe the current strategy for gene structure curation, and introduce the WormBase 'curation tool', which integrates different data sources in order to identify new and correct gene structures  ...  in curating this genome's sequence and gene structures.  ...  Strategies At WormBase, several strategies for manual curation of the gene structures have been used before the current 'curation tool' was developed.  ... 
doi:10.1093/database/baq039 pmid:21543339 pmcid:PMC3092607 fatcat:nptcyaxhirhwpatcl6aylqeb5u

WormBase: a comprehensive resource for nematode research

Todd W. Harris, Igor Antoshechkin, Tamberlyn Bieri, Darin Blasiar, Juancarlos Chan, Wen J. Chen, Norie De La Cruz, Paul Davis, Margaret Duesbury, Ruihua Fang, Jolene Fernandes, Michael Han (+20 others)
2009 Nucleic Acids Research  
We continue to refine our curation strategy for greater efficiency, breadth and depth of coverage.  ...  In addition, we employ Textpresso for fact extraction, notably for curation of Gene Ontology (GO) cellular component terms (13) .  ... 
doi:10.1093/nar/gkp952 pmid:19910365 pmcid:PMC2808986 fatcat:msx6exctxvfvnaurwn2fr4fd7a

WormBase 2012: more genomes, more data, new website

K. Yook, T. W. Harris, T. Bieri, A. Cabunoc, J. Chan, W. J. Chen, P. Davis, N. de la Cruz, A. Duong, R. Fang, U. Ganesan, C. Grove (+27 others)
2011 Nucleic Acids Research  
To enhance the rate of curation, we have automated the identification of key data in the scientific literature and use similar methodology for data extraction.  ...  Finally, we have introduced a dramatic overhaul of the WormBase website for public beta testing.  ...  Gene model curation WormBase continues to maintain a manual gene curation program whereby gene structures are corrected in line with all currently available data for a given locus.  ... 
doi:10.1093/nar/gkr954 pmid:22067452 pmcid:PMC3245152 fatcat:4jkq3undtzc6lporuvo3nteium

Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR

K. Van Auken, P. Fey, T. Z. Berardini, R. Dodson, L. Cooper, D. Li, J. Chan, Y. Li, S. Basu, H.-M. Muller, R. Chisholm, E. Huala (+1 others)
2012 Database: The Journal of Biological Databases and Curation  
Wimpfheimer for assistance with the figures. The members of the WormBase Consortium are M. Berriman and R. Durbin  ...  Acknowledgements We would like to thank the BioCreative Workshop 2012 Steering Committee for the opportunity to participate in the workshop and, in particular, C.  ...  A table describing the different data types curated at WormBase and the various methods used for their curation is available at http://wiki.wormbase.org/index.php/ WormBase_Literature_Curation_Workflow  ... 
doi:10.1093/database/bas040 pmid:23160413 pmcid:PMC3500519 fatcat:xm263mzjpferrgyn4augokxkgm

Automatic categorization of diverse experimental information in the bioscience literature

Ruihua Fang, Gary Schindelman, Kimberly Auken, Jolene Fernandes, Wen Chen, Xiaodong Wang, Paul Davis, Mary Tuli, Steven J Marygold, Gillian Millburn, Beverley Matthews, Haiyan Zhang (+3 others)
2012 BMC Bioinformatics  
, gene expression, gene product interaction, overexpression phenotype, gene interaction, and gene structure correction.  ...  It has been in use in production for automatic categorization of 10 different experimental datatypes in the biocuration process at WormBase for the past two years and it is in the process of being adopted  ...  We thank the past and present members of WormBase and FlyBase for curating the papers used in this study.  ... 
doi:10.1186/1471-2105-13-16 pmid:22280404 pmcid:PMC3305665 fatcat:pgt5hyh44rdzhlfxdn2tc5hvfa

Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community

Gary Schindelman, Jolene S Fernandes, Carol A Bastiani, Karen Yook, Paul W Sternberg
2011 BMC Bioinformatics  
This standardized phenotype ontology will therefore allow for more complex data queries and enhance bioinformatic analyses.  ...  Results: We describe a hierarchically structured, controlled vocabulary of terms that can be used to standardize phenotype descriptions in C. elegans, namely the Worm Phenotype Ontology (WPO).  ...  suggestions; Norie de la Cruz for his work on the phenotype ontology search tool and fellow curators at WormBase for their valuable input.  ... 
doi:10.1186/1471-2105-12-32 pmid:21261995 pmcid:PMC3039574 fatcat:j7nmqr5wirfxpnxd65zx3lfmay

Single cell tools for WormBase [article]

Eduardo da Veiga Beltrame, Valerio Arnaboldi, Paul W Sternberg
2021 bioRxiv   pre-print
We present two web apps for interactively performing common tasks with single cell RNA sequencing data: scdefg for interactive differential expression and wormcells-viz for visualization of gene expression  ...  They can also be readily deployed for use with any other datasets using the source code available at https://github.com/WormBase/scdefg/ and at https://github.com/WormBase/wormcells-viz.  ...  Acknowledgements The authors would like to thank Paulo Nuin for reviewing the code, Tom Morrell for assistance with CaltechData, and Valentine Svensson for suggestions on the manuscript.  ... 
doi:10.1101/2021.07.04.451030 fatcat:6rp44yz3s5cwhos47kgh4vbjce

A Comparative Chemogenomics Strategy to Predict Potential Drug Targets in the Metazoan Pathogen, Schistosoma mansoni

Conor R. Caffrey, Andreas Rohwer, Frank Oellien, Richard J. Marhöfer, Simon Braschi, Guilherme Oliveira, James H. McKerrow, Paul M. Selzer, Jennifer Keiser
2009 PLoS ONE  
Using the genome comparison software Genlight, two separate in silico workflows were implemented to derive a set of parasite proteins for which gene disruption of the orthologs in both the model organisms  ...  Subsequent in depth manual curation of the combined workflow output revealed 57 candidate proteins.  ...  Further curation included removal of sequences (i) not confirmed as orthologs by reciprocal blastp searches with both Wormbase and Flybase, (ii) for which targeted gene disruption of the appropriate ortholog  ... 
doi:10.1371/journal.pone.0004413 pmid:19198654 pmcid:PMC2635471 fatcat:7zulu6372rdf3c267jlyqe4cnq

Genomix: a method for combining gene-finders' predictions, which uses evolutionary conservation of sequence and intron–exon structure

Avril Coghlan, Richard Durbin
2007 Computer applications in the biosciences : CABIOS  
Results: We present a method for combining gene-finders called Genomix.  ...  Genomix selects the predicted exons that are best conserved within and/or between species in terms of sequence and intron-exon structure, and combines them into a gene structure.  ...  JIGSAW, Venky Iyer for Drosophila gene sets, and Des Higgins (University College Dublin) for hosting A.C. in his group during part of this work.  ... 
doi:10.1093/bioinformatics/btm133 pmid:17483502 pmcid:PMC2880447 fatcat:onzrc76r25e2no5i5mcmigwrdy

Textpresso: An Ontology-Based Information Retrieval and Extraction System for Biological Literature

Hans-Michael Müller, Eimear E Kenny, Paul W Sternberg, Michael Ashburner
2004 PLoS Biology  
identify sentences; in searches for two uniquely named genes and an interaction term, the ontology confers a 3-fold increase of search efficiency.  ...  Textpresso is a useful curation tool, as well as search engine for researchers, and can readily be extended to other organism-specific corpora of text.  ...  HMM was a participant in the Initiative in Computational Molecular Biology, which was funded by the Burroughs Wellcome Fund Interfaces program, and was a Howard Hughes Medical Institute Associate, with  ... 
doi:10.1371/journal.pbio.0020309 pmid:15383839 pmcid:PMC517822 fatcat:dcxfopl5ibf4pbbpmvafoj35ri

Wormicloud: a new text summarization tool based on word clouds to explore the C. elegans literature

Valerio Arnaboldi, Jaehyoung Cho, Paul W Sternberg
2021 Database: The Journal of Biological Databases and Curation  
Wormicloud is integrated through direct links from gene interaction pages in WormBase.  ...  Biocuration and model organism databases provide a map for researchers to navigate through the complex structure of the biomedical literature by distilling knowledge into curated and standardized information  ...  Acknowledgements We thank Ranjana Kishore, Daniela Raciti and Eduardo da Veiga Beltrame for their comments and suggestions on the manuscript.  ... 
doi:10.1093/database/baab015 pmid:33787871 pmcid:PMC8011436 fatcat:rbb5hyz76bdw3p6atam5wfrv3u

The BioGRID Interaction Database: 2011 update

C. Stark, B.-J. Breitkreutz, A. Chatr-aryamontri, L. Boucher, R. Oughtred, M. S. Livstone, J. Nixon, K. Van Auken, X. Wang, X. Shi, T. Reguly, J. M. Rust (+3 others)
2010 Nucleic Acids Research  
BioGRID currently holds 347 966 interactions (170 162 genetic, 177 804 protein) curated from both high-throughput data sets and individual focused studies, as derived from over 23 000 publications in the  ...  BioGRID provides interaction data to several model organism databases, resources such as Entrez-Gene and other interaction meta-databases.  ...  Judy Blake for support and helpful discussions.  ... 
doi:10.1093/nar/gkq1116 pmid:21071413 pmcid:PMC3013707 fatcat:5e7qa7hecfbnfj7o3dvxiw4yum

GAZE: A Generic Framework for the Integration of Gene-Prediction Data by Dynamic Programming

K. L. Howe
2002 Genome Research  
We describe a method (implemented in a program, GAZE) for assembling arbitrary evidence for individual gene components (features) into predictions of complete gene structures.  ...  Our system is generic in that both the features themselves, and the model of gene structure against which potential assemblies are validated and scored, are external to the system and supplied by the user  ...  ACKNOWLEDGMENTS We thank Phil Green for allowing us to use the Genefinder tables and Kerstin Jekosch for checking the curated gene  ... 
doi:10.1101/gr.149502 pmid:12213779 pmcid:PMC186661 fatcat:wfjiyexmfzdidlaq6jxxpvgp4a

Micropublication: incentivizing community curation and placing unpublished data into the public domain

Daniela Raciti, Karen Yook, Todd W Harris, Tim Schedl, Paul W Sternberg
2018 Database: The Journal of Biological Databases and Curation  
Getting researchers to adopt a new system of data reporting and curation requires a fundamental change in behavior among all members of the research community.  ...  Large volumes of data generated by research laboratories coupled with the required effort and cost of curation present a significant barrier to inclusion of these data in authoritative community databases  ...  , Phoenix Bioinformatics), Xenbase and ZFIN for their feedback on submission forms and workflow and to the Conflict of interest.  ... 
doi:10.1093/database/bay013 pmid:29688367 pmcid:PMC5836261 fatcat:dhf2ampq4jgjzkpwnb7g63xkh4

EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression

M Inmaculada Barrasa, Philippe Vaglio, Fabien Cavasino, Laurent Jacotot, Albertha J M Walhout
2007 BMC Genomics  
We use high-throughput yeast one-hybrid assays as a gene-centered method to identify protein-DNA interactions between regulatory sequences (e.g. gene promoters) and transcription factors in the nematode  ...  Both transcription factor -and gene-centered methods can be used to systematically identify such interactions.  ...  Acknowledgements We thank the members of the Walhout laboratory and Job Dekker for discussion and critical reading of the manuscript, and NIDDK for funding (R01DK068429). We also thank D.  ... 
doi:10.1186/1471-2164-8-21 pmid:17233892 pmcid:PMC1790901 fatcat:liamp2b23vebhnlnvzgern4pp4
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