Bgee now provides a tool for doing enrichment of gene sets using anatomical expression annotated to Bgee
This release incoporates multiple improved textual definitions, with wikipedia definitions being replaced either with more ontological resources such as the mammalian phenotype ontology, or rewritten de novo. The alignment with the embryonic mouse anatomy ontology has been updated and improved. Multiple other improvements and new terms, in particular in neuroanatomical and urogenital parts of the ontology.
The Encyclopedia of DNA elements (ENCODE) project identifies properties of regions of the genome such as chromatin structure, protein-binding and methylation. Many of these properties are specific to cell types and tissues, so the ENCODE project uses ontologies to organize and query this information...
Presentation from GIGA2 meeting
The new version of Bgee has data from 17 species, all annotated using Uberon anatomical structures
JBMS Paper: Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology
Spatial terminology is used in anatomy to indicate precise, relative positions of structures in an organism. While these terms are often standardized within specific fields of biology, they can differ dramatically across taxa. The Biological Spatial Ontology standardizes the description of spatial and topological relationships across taxa to enable the discovery of comparable phenotypes.
JBMS Paper: Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon
Our paper on the unification of multiple vertebrate anatomy ontologies has been published in JBMS
This paper describes the development of the renal portion of the Gene Ontology and subsequent annotation and analysis
This release includes some improvements to the representation of buccinator, orbicularis oris and digastric muscles, based on the Mammalian Feeding ontology FEED. A number of improvements were made to the skeletal system, continued implementation a standard pattern for endocondral bones with particular attention to the ribs and vertebrae. A number of new classes for a variety of systems have been added, including term requests for ENCODE. This release also marks the debut of the platypus bill.