Paper that describes the Worm Phenotype Ontology

You might have come across the term ‘ontology’ in the biomedical literature or in a database. You might have knowingly or unknowingly used it to query data. An ontology consists of well-defined terms that describe entities (for example, the entity might be a gene) and the relationships between them. The goal of building an ontology is to reflect the current knowledge in a particular domain using a controlled vocabulary, to provide a guide for organizing new data, and to allow users to conduct queries. The Worm Phenotype Ontology (WPO) is a hierarchically structured, controlled vocabulary of terms that can be used to standardize phenotype descriptions in C. elegans. Although the WPO was created in order to help manage and disseminate C. elegans phenotypic data, it is not exclusively limited to C. elegans biology, but rather devised to also incorporate phenotypes observed in related nematode species. The WPO will help facilitate data retrieval, and cross-species comparisons within the nematode community and in the larger scientific community, will permit data integration, and interoperability across different biological databases. We are actively developing the WPO to continue to fulfill the evolving needs of the scientific community and hope to engage researchers in this crucial endeavor. To know more, please visit this recent publication that describes the WPO: http://www.biomedcentral.com/1471-2105/12/32

Caenorhabditis sp. 3 PS1010 is now Caenorhabditis angaria.

A formal description of C. angaria has been published in the January 2010 issue of Nematology. Analysis of its phylogenetic position within the Caenorhabditis genus has defined a new species group (the Drosophilae group) of equal status, but separate from, the more familiar Elegans group containing C. elegans, C. briggsae, C. remanei, and other elegans look-alikes. Meanwhile, the genome of C. angaria (as determined by next-generation Illumina sequencing and RNA-seq scaffolding) has been published in the December 2010 issue of Genome Research, along with a detailed analysis of its ~23,000 protein-coding genes (available through the WormBase Genome Browser) and ~2,700 elements of conserved non-coding DNA. This is the first genome to be published for a member of the Drosophilae group, with DNA divergence between C. angaria and C. elegans similar to that between mammals and birds.

Full list of modENCODE C. elegans papers

Here’s a quick list of recently published modENCODE C. elegans papers:

Science
Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project.
Science 24 December 2010: Vol. 330 no. 6012 pp. 1775-1787
DOI: 10.1126/science.1196914

Genome Research
Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans
Genome Res. Published in Advance December 22, 2010
doi:10.1101/gr.113050.110

A global analysis of C. elegans trans-splicing
Genome Res. Published in Advance December 22, 2010
doi:10.1101/gr.113811.110

Broad chromosomal domains of histone modification patterns in C. elegans
Genome Res. Published in Advance December 22, 2010
doi:10.1101/gr.115519.110

Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans
Genome Res. Published in Advance December 22, 2010
doi:10.1101/gr.114587.110

High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans
Genome Res. Published in Advance December 22, 2010
doi:10.1101/gr.115931.110

Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome
Genome Res. Published in Advance December 22, 2010
doi:10.1101/gr.108845.110

Genome-wide analysis of alternative splicing in Caenorhabditis elegans
Genome Res. gr.114645.110 Published in Advance December 22, 2010
doi:10.1101/gr.114645.110

A Spatial and Temporal Map of C. elegans Gene Expression
Genome Res. gr.114595.110 Published in Advance December 22, 2010
doi:10.1101/gr.114595.110

Prediction and characterization of non-coding RNAs in C. elegans by integrating conservation, secondary structure and high throughput sequencing and array data
Genome Res. gr.110189.110 Published in Advance December 22, 2010
doi:10.1101/gr.110189.110