Release VB-2012-12

Overview

As part of a ongoing development, and feedback from multiple constituents, we have upgraded the VectorBase site. The prior version of the website is available at https://classic.vectorbase.org and still has some legacy data of interest. To help you get acclimated with the new site, here are six specific changes:

  • We have redesigned the homepage to highlight data, tools and resources, FAQs and community interactions. We also anticipate user-focused customization (e.g., accessing previous analyses) in later versions of this site.
  • The BLAST tool has been improved based on prior feedback and is available under the “Tools” tab.
  • Computing resources increased by 100% for BLAST, ClustalW, and HMMER jobs.
  • The search box in the upper right corner of all VectorBase pages can access a new unified search framework. Data is faceted and queries can be filterable by species or type. For more information follow this link and found the Search tutorial.
  • We have extended the organisms page. This has allowed us to group genomes in a scalable manner while also highlighting and archiving strain, assembly and gene build history.
  • The old help pages/wiki have been reallocated into new content under “Help” and “Community” tabs to consolidate these important documents into a single site and to facilitate search access.

You can also take a tour of the new site

Other highlights of the December release of VectorBase (VB-2012-12) include:

  • First release of dengue ontology (IDODEN)
  • Anopheles darlingi included in VectorBase compara & mart resources
  • An update to gene symbols and synonyms for mosquito species adding or modifying 830 loci

We are interested in feedback about these changes using the Contact Us page or mail the the helpdesk.

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
Phlebotomus papatasi Israel PpapI1 AJVK00000000 Repeats, SNAP

Variation Data

No new data for this release.

Expression Data

No new data for this release.

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 2012-11-26
Anopheles Anopheles gambiae Anopheline mitochondrial genes 2012-11-26
Culex Culex quinquefasciatus Culicine mitochondrial genes 2012-11-26
Ixodidae and Argasidae Ixodes scapularis Ixodida mitochondrial genes 2012-11-26

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 2.0 The gene ontology.
IDODEN 0.01 Alpha 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 1.2.4 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.

Ontology browser

The Controlled Vocabulary/Ontology browser has been upgraded. Most noteworthy changes:

  • it is now possible to search for terms using synonyms
  • Term synonyms are now listed along with the rest of the term's details
  • OBO flat files can be downloaded by using the links on the main page of the CV browser

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: 
Friday, December 14, 2012