WormBase release WS247

Orthology update

* Data from Inparanoid was updated to version 8
* Orthology data for all core nemtatodes and model organisms was imported from WormBase Parasite release 1
* OMA and TreeFam data was removed in preparation for an update (TreeFam accessions will remain as database crossreferences)

Expression and Picture update

* A large set of expression graphs for other nematodes produced by Yanai’s has been added

RNASeq data

The RNASeq data will become richer in WS247.

There will also be “control” mean and median FPKM values derived from the data which does not have a specific experimental condition applied.

New/updated reference genomes

This release we see a rebuild of C. elegans, B. malayi and O. volvulus. Various data classes and curational activites have been undertaken on these species since the release of WS246

New Features for WS246

Human Disease Data Update

As part of WormBase efforts to curate genes that are potential models for inherited human diseases, 867 genes have been predicted as potential disease genes. In addition curation efforts added publications on experiments using C.elegans genes to investigate human genetic diseases to 181 genes. And 244 genes have been identified from publications as being relevant to research in that field.

WormBase curates human disease relevance data by designating genes as ‘Experimental models’ for a specific human disease based on experimental data published in the literature. In addition to manual curation, an automated data pipeline designates genes as ‘Potential models’ based on orthology with the human gene. Detailed text descriptions called ‘Human disease relevance’ descriptions describe how the elegans gene is a genetic model for the human disease. All human disease relevant data can be found in the ‘Human Diseases’ widget and in the ‘Overview’ section on gene pages.

WS237 released

It has become necessary for us to modify the structure of the “releases” branch FTP site. The reason for this is that we are now required to represent potentially multiple alternative reference genomes sequences for a single nematode species (e.g. Ascaris suum).

In many cases, these references will originate from different strains, but that may not always be the case. We have therefore chosen to differentiate between alternative reference genomes for a single species by including the NCBI BioProject accession (http://www.ncbi.nlm.nih.gov/bioproject) in the directory path and files names. Alternative genome sequencing efforts for the same species will each be assigned their own unique NCBI BioProject accession.