VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases

By Gloria I. Giraldo-Calderón, S. Emrich, Robert M. MacCallum, G. Maslen, E. Dialynas, P. Topalis, Nicholas Ho, S. Gesing, G. Madey, F. S. Collins and 1 more. 2014

567 citations recorded by the source corpus.

VectorBase is a National Institute of Allergy and Infectious Diseases supported Bioinformatics Resource Center (BRC) for invertebrate vectors of human pathogens. Now in its 11th year, VectorBase currently hosts the genomes of 35 organisms including a number of non-vectors for comparative analysis. Hosted data range from genome assemblies with annotated gene features, transcript and protein expression data to population genetics including variation and insecticide-resistance phenotypes. Here we describe improvements to our resource and the set of tools available for interrogating and accessing BRC data including the integration of Web Apollo to facilitate community annotation and providing Galaxy to support user-based workflows. VectorBase also actively supports our community through hands-on workshops and online tutorials. All information and data are freely available from our website at https://www.vectorbase.org/.

Subfields: Genetics, Molecular Biology

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Citations in the corpus

UniProt: the universal protein knowledgebase (2016, background): “The majority of these proteomes are based on the translation of genome sequence submissions to the International Nucleotide Sequence Database Consortium (INSDC) but also include predictions from Ensembl, RefSeq reference genomes and vector/parasitespecific databases like VectorBase (5) and WormBase ”
UniProt: a worldwide hub of protein knowledge (2018, methodology): “To ensure comprehensiveness, complementary pipelines have been developed to supplement these with genomes sequenced and / or annotated by groups such as Ensembl (3), Vectorbase (4) and WormBase ParaSite (5).”
OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs (2016, background): “Protein-coding gene translations were retrieved for vertebrates and plants from Ensembl (13), for arthropods from AgripestBase, AphidBase (14), BeetleBase (15), DiamondBackMoth-DB (16), FlyBase (17), Hymenoptera Genome Database (18), NCBI (19), SilkDB (20), VectorBase (21), wFleaBase (22), as well a”
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation (2016, background): “The flexibility of the Ensembl Core infrastructure is most clearly displayed by the many large-scale projects that reuse it, including Ensembl Genomes, Gramene (45), WormBase and WormBase ParaSite (46), VectorBase (47), PomBase (48) and AvianBase (49).”
Insecticide Resistance in African Anopheles Mosquitoes: A Worsening Situation that Needs Urgent Action to Maintain Malaria Control. (2016, methodology): “Two global databases have been established (IR Mapper [21] and VectorBase [22]), with the WHO also planning to establish their own global database [20].”
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds (2016, methodology): “gambiae genome assembly AgamP4 and the AaegL2 and CpipJ2 draft genomes available from VectorBase (28, 39).”
agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update (2017, background): “In addition, Fish, Bird, Amphibia, Insecta and Mammalia were categorized under animal (19,45).”
UniProt: the universal protein knowledgebase in 2021 (2020, background): “The majority of these proteomes continue to be based on the translation of genome sequence sub-missions to the INSDC source databases––ENA, GenBank and the DDBJ (4)––supplemented by genomes sequenced and / or annotated by groups such as Ensembl (5), NCBI RefSeq (6), Vectorbase (7) and WormBase ParaS”
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center (2021, methodology): “The underlying architecture of VEuPathDB couples the Genomics Unified Schema (GUS) (3) and the highly flexible Strategies Web Development Kit (WDK) (4) from EuPathDB with VectorBase’s efficient bioinformatic pre-processing workflows and pipelines processed through the European Bioinformatics Institu”