Visualise health consequences of mutations in protein structures

PLan-Variants

This pilot web service bridges the disciplines of clinical genetics and structural biology by displaying the health consequences of mutations as annotations on a protein structure.

Unlocking data from mouse disease models: diabetes ontology

The BioMedBridges diabetes-specific ontology enables users to integrate mouse disease model and human data resources while taking into account the different temporal stages of human disease.

Supporting researchers sharing sensitive data: identifying requirements

Legal and Ethical Requirements Assessment Tool - LAT

Uncertainty about ethical and legal requirements with respect to sensitive data – such as personally identifiable data – is one of the most important barriers to data sharing. Aimed at researchers with limited or no background or experience with these formal requirements, this tool aims to clarify if and how sensitive data can be shared, or when additional actions or expert advice are needed.

Unlocking biomolecule volume data

Information on the structure of macromolecules is important for biology and medicine because the function of many important biological processes can be directly linked to macromolecular structure or changes therein. For example, structural information on how a drug is bound to a target may yield vital clues on how to optimize its structure to promote more efficient binding. The BioMedBridges shape-matching software - which will be incorporated into a web-based shape-matching service - will enable the wealth of low-resolution volume data in the EMDB and PDB resources to be searched based on their shape, providing entirely new perspectives on the relationships between structures.

Sharing protein engineering knowledge

PiMS

PiMS is a laboratory information management system for use in recombinant protein production laboratories; to manage the stages from the selected target protein to the production of soluble protein. PiMS development is part of a larger vision to provide a unified and extensible set of software tools for structural biology, offering seamless data transfer and a consistent user experience, from target selection to the interpretation of the structure.

Making sure standards are fit for purpose

The Metadata Model and Mapping Registry (MMMR) enables researchers to find a representative collection of meta-data artefacts (models, formats, minimal information guidelines, biobank data dictionaries, detailed clinical/research models) of use to the biomedical science community.

Unlocking small-molecule resources

The UniChem connectivity search function allows users to find not only exact matches of their chemical structure across 60 million related molecules from 21 data sources worldwide, but also identifies 'equivalent' structures that have the same atom connectivity while differing in stereochemistry or isotopic composition, or which exist in a different salt form. This functionality is particularly important in the development of new pharmaceuticals, where early candidate triage can save significant amounts of time and money.

Integrating phenotypic image annotations across species

CMPO is a species-neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. It is compatible with related ontology efforts, allowing for future cross-species integration of phenotypic data.

Imaging data management and interoperability

Bigr XNAT adds a custom REST interface to the open source platform XNAT, enabling data from medical imaging databases to be embedded into XNAT and vice versa. It creates a user-friendly data bridge for medical imaging trials that supports sharing and analysis of imaging and image-derived data and which supports centralised correlative analysis between image-derived data and other types of data such as clinical data (e.g. disease status, age) and genetic data.

Final version of the web-based shape-matching service

A software pipeline named SMaSB was previously developed to perform the volume/shape matching that underpins the set of tools being developed in WP9. These tools are novel in providing access to a growing class of structural biology data viz. volume data. The SMaSB software is primarily a set of Python codes which organise the metadata, control the data flow during volume/shape matching, and record the results. Third-party software is called to perform the compute-intensive steps in the pipeline. The first full version of SMaSB was released in December 2014, and reported in Deliverable 9.1. We now report on the associated web service (PDBeShape) which provides a user-friendly front-end to SMaSB results. It provides web access to a curated database of structural volumes, derived from deposited structures in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB), together with pre-processed alignments and scores. We have made the first version of the PDBeShape service publically available at http://wwwdev.ebi.ac.uk/pdbe/emdb/shape/welcome/. Here we give details on the current functionality of PDBeShape and the technical underpinning. More extensive documentation is provided on the web page.

Tools and resources