FlyBase: enhancing Drosophila Gene Ontology annotations

By S. Tweedie, Michael Ashburner, Kathleen Falls, P. Leyland, Peter McQuilton, Steven J. Marygold, G. Millburn, David Osumi-Sutherland, A. Schroeder, Ruth L. Seal and 1 more. Nucleic Acids Res., 2008

780 citations recorded by the source corpus.

FlyBase (http://flybase.org) is a database of Drosophila genetic and genomic information. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. This article describes recent changes to the FlyBase GO annotation strategy that are improving the quality of the GO annotation data. Many of these changes stem from our participation in the GO Reference Genome Annotation Project—a multi-database collaboration producing comprehensive GO annotation sets for 12 diverse species.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/17d61a353bb9f1b83b2f453779dbb37e2d358410

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Citations in the corpus

UniProt Knowledgebase: a hub of integrated protein data (2011, background): “Close collaborations exist with a number of species-specific resources such as the Human Gene Nomenclature Committee (HGNC) (28), the Mouse Genome Database (MGD) (29) and Flybase (30) and there is active communication between curators at UniProtKB and the various species-specific databases to ensure”
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored (2010, background): “Annotated pathway knowledge is mostly kept in a separate set of resources (22–24) and yet other interactions can be found in various organism-speciﬁc databases (25,26) or text-mining resources (27,28).”
A Protein Complex Network of Drosophila melanogaster (2011, methodology): “The raw mass spectrometry data are available in Table S1 (available online) and are accessible through FlyBase Linkouts and the DPiM website (https://interfly.med.harvard.edu/).”
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis (2009, background): “org/annotation/fungi/fgi/), 7 from Flybase (11), 7 from NCBI (12), 6 from WormBase (13), 6 from Sanger (http://www.”
RBPDB: a database of RNA-binding specificities (2010, background): “Each protein and experiment is assigned a unique internal ID number, and proteins are linked to Ensembl, FlyBase and WormBase gene annotations and RNA-bound protein structures on PDB (14–17).”
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium (2009, background): “Arabidopsis thaliana ARATH TAIR (11) Dicot plant Caenorhabditis elegans CAEEL WormBase (12) Nematode worm Danio rerio DANRE Ensembl, ZFIN (13) Zebrafish Dictyostelium discoideum DICDI DictyBase (14) Cellular slime mold Drosophila melanogaster DROME FlyBase (15) Fruit fly Escherichia coli ECOLI EcoCy”
PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals (2011, background): “Because FlyBase [19] does not accept wiggle files, PoPoolation generates a special output file that enables the polymorphism pattern to be linked with FlyBase.”
The BioGRID Interaction Database: 2011 update (2010, methodology): “BioGRID data are also available through partner model organism databases (MODs) including SGD (8), FlyBase (21), TAIR (10) and GeneDB (9), through external resources such as NCBI Entrez-Gene, DroID (22) and GermOnline (23), and through meta-databases such as STRING (24), iRefIndex (25) and Pathway C”
Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition (2011, neutral): “have been experimentally characterized [10,11,21].”
The digital revolution in phenotyping (2015, background): “Table 1: Summarizes all resources mentioned throughout the manuscript, together with their URL and reference (where applicable) Resource Link Reference Online Mendelian Inheritance in Man database http://omim.org/ [1] Mouse Genome Database http://informatics.jax.org/ [2] FlyBase http://flybase.org/ ”
Detecting differential usage of exons from RNA-seq data (2012, methodology): “We defined counting bins, as described above, based on the annotation from FlyBase 5.25 (Tweedie et al. 2009) as provided by Ensembl 62 (Flicek et al. 2011).”
Dynamic reprogramming of chromatin accessibility during Drosophila embryo development (2011, positive): “Analysis of core promoter elements The peak DNAse I cleavage density was calculated for the core promoters (-60 to +40) of each gene from the release 4.3 version of the D. melanogaster genome obtained from FlyBase [63].”