Release VB-2013-02

Overview

We are pleased to announce the February release of VectorBase (VB-2013-02). Highlights of this release include:

  • New gene pinboard and annotation export features in Expression Maps
  • Ensembl genome browser updated to e! 69
  • New version of IDODEN ontology (Dengue)
  • Improved search results for expression and population biology samples
  • Added an ability to download mtDNA sequences by selecting them (based on user feedback)
  • BAC hybridization (Maria V. Sharakhova) and AnoXcel (Jose Ribero) searches from classic site now on new site in beta form
  • Over 100 new gene symbols were incorporated (especially for Ixodes scapularis)
  • Mitochondrial and CV Browser data updated
  • New organism page: Biomphalaria glabrata
  • Stable ID tracking for recent Aedes, Culex and Ixodes genesets
  • Correction of some stable IDs for Aedes, Culex and Ixodes genesets, old IDs are tracked
  • Nine new tutorials

Genomes

Released genomes, with gene predictions

Species Assembly Gene set GenBank WGS
Aedes aegypti Liverpool AaegL1 AaegL1.3 AAGE02000000
Anopheles darlingi Coari AdarC1 AdarC1.0 ADMH00000000
Anopheles gambiae PEST AgamP3 AgamP3.7 AAAB01000000
Culex quinquefasciatus JHB CpipJ1 CpipJ1.3 AAWU01000000
Ixodes scapularis Wikel IscaW1 IscaW1.2 ABJB01000000
Pediculus humanus USDA PhumU1 PhumU1.2 AAZO01000000
Pre-released genomes, with mapped data and gene predictions
Rhodnius prolixus CDC RproC1 RproC1.0 ACPB00000000
Glossina morsitans Yale GmorY1 GmorY1.0  
Anopheles stephensi Indian Wild Type AsteI1 AsteI1.0  

Pre-released genomes, with mapped data but no gene predictions

Species Assembly GenBank WGS Project Data available
Anopheles gambiae M AgamM1 ABKP00000000 Repeats, ESTs
Anopheles gambiae S AgamS1 ABKQ00000000 Repeats, ESTs
Lutzomyia longipalpis Jacobina LlonJ1 AJWK00000000 Repeats, SNAP, ESTs
Phlebotomus papatasi Israel PpapI1 AJVK00000000 Repeats, SNAP, ESTs

Variation Data

No new data for this release.

Expression Data

There is no new microarray expression data for this release, however the Expression Map interface has a new feature. It is now possible to export gene annotation information for the genes in one or more expression cluster with a few clicks of your mouse. Look for the "save gene IDs to pinboard" button in the cluster info popup windows.

Mitochondrial gene summaries for VectorBase genera

Links to Mitochondrial data for the 4 main genera are presented below for convenience.

Genus/genera Reference species Mitochondrial gene resource Last updated
Aedes Aedes aegypti Aedine mitochondrial genes 2013-02-01
Anopheles Anopheles gambiae Anopheline mitochondrial genes 2013-02-01
Culex Culex quinquefasciatus Culicine mitochondrial genes 2013-02-01
Ixodidae and Argasidae Ixodes scapularis Ixodida mitochondrial genes 2013-02-01

Ontologies

VectorBase supports seven ontologies developed by IMBB with members of the research community. These are available for browsing and download.

Ontology Version Description
GAZ 1.512 A controlled vocabulary of geographic locations.
GO 1.1437 The gene ontology.
IDODEN 0.2 Beta release of an an ontology that describes all aspects of Dengue. Clinical data, epidemiological data, biological data concerning vertebrate hosts, vectors and viruses as well as interventions and attempts to control the disease.
IDOMAL 1.2.5 An ontology to describe all aspects of malaria. Clinical data, epidemiological data, biological data concerning vertebrate hosts, vectors and parasites as well as interventions and attempts to control the disease.
MIRO 2.0 An ontology to describe mosquito populations, methods and mechanisms that are used to identify/monitor insecticide resistance.
TADS 1.21 An ontology to describe the anatomy of ticks.
TGMA 1.10 An ontology to describe the anatomy of mosquitoes.

Known issues

Biomart filtering on variation type is not working, this will be addressed for the next release.

Please report any problems to the helpdesk.

Release date: 
Wednesday, February 20, 2013