VBO - A Tool for Bridging Vertebrate Anatomy Ontologies
Lead Research Organisation:
European Bioinformatics Institute
Department Name: Microarray Group
Abstract
Anatomy is a central concept to the biomedical sciences. For multicellular animals the differentiation of cells into different structures and cell types, their arrangement in space - their Anatomy - defines the organism. Biologists need formal, unambiguous ways to describe Anatomy, and whilst the familiar Latin terms to describe our arms, legs, fingers and blood vessels for example have stood us in good stead for centuries, we are now in a position where the amount of data being collected on, for example, where genes are expressed, needs to be annotated in ways that a computer can understand. An approach to this, now widely used, is to make an 'ontology' which is a tree-like arrangement of anatomical terms in a common-sense hierarchy. The 'big toe' is a part of the 'foot' which is a part of the 'leg' etc. Such ontologies have been made for several species such as human and mouse. However, as there are differences in anatomy between species such single species anatomy ontologies are not re-usable, even between closely related species. This project addresses this problem by developing a system whereby we can link the anatomical descriptions of structures in humans, mice, fish and birds through the common evolutionary ancestor of the structure. Thus we can link the bird's wing, the mouse's paw and the fish's fin through their common evolutionary ancestral structure. Molecular biology tells us that this is a true linkage and that genes responsible for the development of all of these structures have a great deal in common and in many cases are orthologs. By developing this computable description of detailed cross-species anatomy we will enable scientists currently collecting large amounts of data on gene expression, abnormal morphology and biological processes in different tissues to compare their data computationally with that being collected by other scientists working in different vertebrate species. This will allow the discovery of new information about the function of genes and the interaction of gene products in the organism and ultimately inform us about the way that humans and other species are similar, or different. Computational comparison is needed as modern technologies allow scientists to compare gene expression - where and when a gene is active, for thousands of genes at a time.
Technical Summary
The VBO ( Vertebrate anatomy Bridging Ontology) project will deliver a vertebrate cross-species anatomy ontology developed using a novel approach; that of the Most Recent Common evolutionary Ancestor (MRCA). This cross-species anatomy ontology will fill a critical gap in data annotation for systems biology, functional genomics and high throughput data gathering by allowing computational cross-species integration of data between the key model vertebrate organisms. Cross-species integration of such data along the anatomical axis is currently not possible due to the lack of a public domain cross-species anatomy ontology which is implementable by existing data resources. This is a serious problem as, for example, the wealth of data from comparative genomics is not aligned anatomically in any meaningful way and cross-species gene expression data cannot be accurately queried by anatomical location. The novel approach used for its construction will allow for application to species without explicitly derived anatomy ontologies and extension to new organisms. Development of VBO will allow leveraging of the data in the public domain and provide added value through integration and comparative analysis of datasets derived from multiple species. In addition, the new paradigm it exploits will support generation of new computational approaches to data integration by the knowledge management community, an area where ontology development is burgeoning. This is a community project and will gather input from a range of potential users and domain experts. The Project brings together biologists and computer scientists working with the biology and informatics of the major vertebrate model organisms, and builds on a UK strength in this area. It will engage with the wider user community through two workshop meetings and an extensive web presence. All project resources will be made publicly available via Open BioMedical Ontologies (OBO) and relevant databases.
Publications
Zheng-Bradley X
(2010)
Large scale comparison of global gene expression patterns in human and mouse.
in Genome biology
Xue V
(2012)
MageComet--web application for harmonizing existing large-scale experiment descriptions.
in Bioinformatics (Oxford, England)
Travillian RS
(2011)
Anatomy ontologies and potential users: bridging the gap.
in Journal of biomedical semantics
Su J
(2015)
A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging.
in Skeletal muscle
Shankar R
(2010)
Annotare--a tool for annotating high-throughput biomedical investigations and resulting data.
in Bioinformatics (Oxford, England)
Sarkans U
(2021)
REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology.
in Nature methods
Petryszak R
(2016)
Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.
in Nucleic acids research
Petryszak R
(2014)
Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.
in Nucleic acids research
Hartley M
(2022)
The BioImage Archive - Building a Home for Life-Sciences Microscopy Data.
in Journal of molecular biology
Gostev M
(2012)
The BioSample Database (BioSD) at the European Bioinformatics Institute.
in Nucleic acids research
Description | A harmonized ontology for describing vertebrate anatomy integrated in other ontologies |
Exploitation Route | The developed ontology is widely used to annotated genomics and bioinformatics data by many groups around the world |
Sectors | Digital/Communication/Information Technologies (including Software),Pharmaceuticals and Medical Biotechnology |
URL | http://www.ebi.ac.uk/efo/ |
Description | The developed ontology is used in Gene Expression Atlas at EBI and in the work of the Centre for Theraupetic Target Validation of the GSK, Sanger Institute and EBI |
First Year Of Impact | 2013 |
Sector | Digital/Communication/Information Technologies (including Software),Education,Pharmaceuticals and Medical Biotechnology |
Impact Types | Policy & public services |