GMOD
InsectaCentral
Contents
Overview
The InsectaCentral database is a unique insect transcriptome database built by GMOD components. The database schema is driven by Chado, Bio::DB::SeqFeature::Store and the Drupal modules of GMOD-DBSF. The software developed for this project aim to be species neutral and when released anyone can make a Central database.
Aim
InsectaCentral is a central repository of Insect transcriptomes, produced using traditional capillary (Sanger) sequencing or 454 Next Generation pyrosequencing (NGS). Our aim is to allow the thousands of researchers working on species without a huge Genome Consortium and rolling database funding to make use of their own and the community’s data in a streamlined, efficient and standardized fashion. Support for other data types is being implemented.
Data Origin
Data are acquired from NCBI’s dbEST, Short Read Archive and GenBank. We also process private datasets, from our laboratory or collaborators,
We process them using est2assembly and stored in GMOD’s chado database. We use this data warehouse to allow you to search using pre-annotated information and you can explore each gene/protein object using GBrowse, driven by BioPerl’s Bio::SeqFeature database.
Quality
We provide deep annotation using BLAST similarity analysis to many databases, Electronic Inference Annotation of GO, EC and KEGG terms and also provide InterProScan domains. This process requires trememdous computational power, so re-annotation is done sparingly. In addition, as there is no dedicated funding, we do not manually curate any of the datasets but we would do so should the opportunity arise. Likewise, as we do not have a head curator, we cannot implement a Community Annotation System even though we would very much like to. Should you be interested in supporting us to help you, then a simple email will set things in motion.
Content
The database is being constantly expanded as analysis of data progresses and support for new data types is implemented.
The current public release is: beta
Roadmap
- Alpha
EST datasets funded by/collaborated with RFC lab; EST datasets of special interest; in-depth annotation - Beta
Molecular markers; All Insecta transcriptomes; documentation - 1.0 Implementation of a community curation system;Tutorials; Solexa digital transcriptomics; preparation of manuscript
- 1.5 Homeless insect genomes + DAS genomes of interest
- 2.0 Geographical and population data of Insects in collaboration with the Atlas of Living Australia.
Wishlist
- GBrowse 2.x
- Head curator to supervise community gene models
Software
Once the software is ready for public release it’s source will be offered for laboratories to create InsectaCentral clones for use with any laboratory’s private data. The processing of the data is accomplished with est2assembly, which is already available.
The current public release is: beta
Roadmap
- Alpha
Most of ButterflyBase’s user interface; support for Sanger/454 EST data, SNP markers, BLASTs, ontology-based annotation; support for public + secure (private) data; Chado database engine; SeqFeature/Gbrowse driven exploration; iceBLAST interface - Beta
Support for sample library information; extended user interface; documentation; Drupalization of an extended BLAST interface; curation module - 1.0 Support for digital transcriptomics; Walkthrough/tutorials; Further Drupal standardization; preparation of manuscript
- 2.0 Support for geographical and population data; interface with Google Earth/Atlas of Living Australia; support for basic phylogenetic information
Wishlist
- Sun Grid Engine support
License
This software is GPLv2+ licensed as part of the Drupal package. It is currently supported by Alexie Papanicolaou while at CSIRO, the Australian Commonwealth Scientific and Research Organization (http://www.csiro.au).