WormBase: network access to the genome and biology of Caenorhabditis elegans

By Lincoln D. Stein, P. Sternberg, Richard Durbin, Jean Thierry-Mieg, J. Spieth. Nucleic Acids Res., 2001

362 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/171bf081f4012fa659f93c53e837d7d9132a8424

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Citations in the corpus

Annotation of the Drosophila melanogaster euchromatic genome: a systematic review (2002, background): “WormBase [39,40] currently reports 392 pseudogenes in C.”
Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes (2013, methodology): “Phenotype and disease data from SGD [ 77 ] , MGI [ 78 ] , Wormbase [ 79 ] , Flybase [ 80 ] , GSEA [ 20 ] , Zfin [ 81 ] were incorporated into our functional networks by summing the co - occurrences of gene pairs in all phenotypes / diseases and normalizing by the size of the phenotype / disease .”
The Pathway Tools software (2002, methodology): “The Pathway/Genome Navigator provides query, visualization , and analysis services for PGDBs, both as a local application and as a Web server.”
The Distributed Annotation System (2001, methodology): “The first reference DAS server was written for Worm-Base [ 11 ] and piggybacks on the WormBase software architecture: an Apache/mod_perl web server communicating with an ACeDB database via the AcePerl database access library.”
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics (2003, methodology): “Some of the genes taken from WS77 have alternative splices, so the 20,621 C. elegans genes have 21,578 different splice variants.”
WormBase: a multi-species resource for nematode biology and genomics (2004, background): “elegans and related nematodes into a webaccessible, highly curated resource (3,4).”
The Sequence Ontology: a tool for the unification of genome annotations (2005, background): “Other centers such as The Institute for Genomic Research (TIGR) [2] and the Joint Genome Institute (JGI) [3] also maintain and distribute annotations, as do many model organism databases such as FlyBase [4], WormBase [5], The Arabidopsis Information Resource (TAIR) [6] and the Saccharomyces Genome D”
The human genome browser at UCSC. (2002, methodology): “The WormBase project (Stein et al. 2001) is actively adapting parts of ACEDB for use in their web-based display.”
Textpresso: An Ontology-Based Information Retrieval and Extraction System for Biological Literature (2004, methodology): “We also wanted to support a new database curation effort involving manual literature curation (Stein et al. 2001).”
GOToolBox: functional analysis of gene datasets based on Gene Ontology (2004, background): “The hierarchical organization of the gene ontology is particularly well adapted to computational processing and is used for the functional annotations of gene products of several model organisms such as budding yeast [2], Drosophila [3], mouse [4], nematode [5] and Arabidopsis [6].”