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TEMBLOR funded projects at the EBI (Archive Document)
DESPRAD
| Standards and repositories for gene expression experiments
Now that we have sequence information for entire genomes, understanding which genes are active in specific cells under different conditions is an important and reachable goal. DNA microarrays enable us to gather information on which messenger RNAs are present in biological samples taken under different conditions, and allow data on many thousands of genes to be collected simultaneously. For example, using microarrays it's possible to determine which genes are relatively active in brain cells compared with liver cells, in tissues at different stages of development, or in diseased versus healthy organs.
This information is of great value to biomedical researchers and should be freely shared, but there are substantial informatics challenges in collecting, organising and disseminating this information.
The aim of DESPRAD (Development and Establishment of Standards and Prototype Repository for DNA-Array Data) is to develop public repository of microarray data at the EBI, and the development of software to interpret the data...more
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IntAct
| Standards and resources for protein–protein interaction data
The aim of proteomics is not only to document which proteins are expressed in different cell types under different conditions, but also to understand the functions of all those proteins and how they interact with each other to build fully functioning cells and organisms. Cells carry out all of their functions through networks of protein-protein interactions, and disruptions to these networks are a major cause of disease. Cataloguing all protein-protein interactions will therefore be of enormous importance to both pure and applied biomedical research, but this task is far from trivial.
Interaction data are often noisy and incomplete, and different types of experiments to measure protein-protein interactions have varying levels of reliability. Large sets of protein-protein interaction data are already available, but they are scattered in different databases. They need to be brought together, compared and cross-validated. The IntAct project aims to define standards for the collection of protein-protein interaction data, and provide a database that's compliant with them. In the long term, IntAct will cooperate with other providers of protein-protein interaction data to provide a central, synchronised resource for protein-protein interactions...more
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Integr8
| An integrated layer for the exploitation of genomic and proteomic data
If biologists are to make the most of the wealth of genomic and post-genomic information that's now available, they will need to be able to search across different databases, hopping seamlessly from '-ome' to '-ome'. Integr8 is the glue that holds all the TEMBLOR projects together.
The resources that will be built by the DESPRAD, PDBe and IntAct projects will be combined with other important sources of genomic and proteomic information. Many of these resources are maintained at the EBI, including:
Integr8 will connect all this information to allow easy access for researchers, making the value of the composite much greater than the sum of its parts. Integr8 will link a defined set of objects, using individual genes (particularly those in completed genomes) as the unit upon which related information is hung.
Researchers will be able to perform text-, structure- and sequence-based searches to access gene sequences, their genomic context, transcripts, protein sequences and more.
Each transcript will be linked 'down' to the genomic sequence from which it is transcribed, and 'up' to the protein sequence into which it is translated. Each level will give direct access to the scientific knowledge about a given gene, transcript or protein. This will encompass information on:
- genetic regulatory elements
- gene expression
- protein expression
- gene product information
- protein families and domains
- protein-protein-interactions
- structural and ligand information
- molecular function
- biological role
- location of gene products
All this will be linked to the scientific literature and patent information, as well as to information on biological materials (in particular gene libraries, individual clones, high-density clone filters, DNA and protein filters, clone and DNA pools etc.).
Part of the integr8 project is the development of existing EBI resources.
These include ClusTr, InterPro and GO...more
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PDBe
| Storing and analysing the structures of large molecules
Structural biology has had an enormous impact on our understanding of biology and medicine. Three-dimensional structures give us mechanistic insight into how macromolecules work, and help to explain how their functions are disrupted by mutation or interaction with small molecules. We're now in a position to combine structural biology with genomics to solve every protein fold encoded by a genome.
As these efforts gain momentum, the demand for efficient access to sequence, structure and protein-family information is rising; biologists need standardised ways of viewing and describing 3-D structures so that they can share data effectively.
The PDBe TEMBLOR project, coordinated by The EBI's PDBe group, is improving the quality and consistency of structural information, and is developing a range of services that allow biologists to search and analyse structural data effectively...more
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The project is funded by the European Commission as the TEMBLOR,
contract-no. QLRI-CT-2001-00015 under the RTD programme
"Quality of Life and Management of Living Resources"
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