Biology subjects

Orchard, S.

Publications and source records attributed to Orchard, S..

5 recordsLinked to original sources

bioRxiv2018

CausalTab: PSI-MITAB 2.8 updated format for signaling data representation and dissemination

Combining multiple layers of information underlying biological complexity into a structured framework, and in particular deciphering the molecular mechanisms behind cellular phenotypes, represent two challenges in systems biology. A key task is the formalisation of such information in models describing how biological entities interact to mediate the response to external and internal signals. Several databases with signaling information, such as SIGNOR, SignaLink and IntAct, focus on capturing, organising and displaying signaling interactions by representing them as binary, causal relationships between biological entities. The curation efforts that build these individual databases demand a concerted effort to ensure interoperability among resources, through the development of a standardized exchange format, ontologies and controlled vocabularies supporting the domain of causal interactions. Aware of the enormous benefits of standardization efforts in the molecular interaction research field, representatives of the signalling network community agreed to extend the PSI-MI controlled vocabulary to include additional terms representing aspects of causal interactions. Here, we present a common standard for the representation and dissemination of signaling information: the PSI Causal Interaction tabular format (CausalTAB) which is an extension of the existing PSI-MI tab-delimited format, now designated MITAB2.8. We define the new term \"causal interaction\", and related child terms, which are children of the PSI-MI \"molecular interaction\" term. The new vocabulary terms in this extended PSI-MI format will enable systems biologists to model large-scale signaling networks more precisely and with higher coverage than before.

systems biology↗

bioRxiv2018

Capturing variation impact on molecular interactions: the IMEx Consortium mutations data set

The current wealth of genomic variation data identified at the nucleotide level has provided us with the challenge of understanding by which mechanisms amino acid variation affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in the development of disease. Physical interactions between molecules are the linking steps underlying most, if not all, cellular processes. Understanding the effects that amino acid variation of a molecules sequence has on its molecular interactions is a key step towards connecting a full mechanistic characterization of nonsynonymous variation to cellular phenotype. Here we present an open access resource created by IMEx database curators over 14 years, featuring 28,000 annotations fully describing the effect of individual point sequence changes on physical protein interactions. We describe how this resource was built, the formats in which the data content is provided and offer a descriptive analysis of the data set. The data set is publicly available through the IntAct website at www.ebi.ac.uk/intact/resources/datasets#mutationDs and is being enhanced with every monthly release.

bioinformatics↗

bioRxiv2018

Protected area effectiveness for fish spawning habitat in relation to earthquake-induced landscape change

We studied the effectiveness of conservation planning methods for Galaxias maculatus, a riparian spawning fish, following earthquake-induced habitat shift in the Canterbury region of New Zealand. Mapping and GIS overlay techniques were used to evaluate three protection mechanisms in operative or proposed plans in two study catchments over two years. Method 1 utilised a network of small protected areas around known spawning sites. It was the least resilient to change with only 3.9% of post-quake habitat remaining protected in the worst performing scenario. Method 2, based on mapped reaches of potential habitat, remained effective in one catchment (98%) but not in the other (52.5%). Method 3, based on a habitat model, achieved near 100% protection in both catchments but used planning areas far larger than the area of habitat actually used. This example illustrates resilience considerations for protected area design. Redundancy can help maintain effectiveness in face of dynamics and may be a pragmatic choice if planning area boundaries lack in-built adaptive capacity or require lengthy processes for amendment. However, an adaptive planning area coupled with monitoring offers high effectiveness from a smaller protected area. Incorporating elements of both strategies provides a promising conceptual basis for adaptation to major perturbations or responding to slow change.

ecology↗

bioRxiv2017

Earthquake-induced habitat migration in a riparian spawning fish: implications for conservation management

Galaxias maculatus is a riparian spawning fish that supports an important recreational fishery in New Zealand with spawning habitat requirements strongly structured by salinity gradients at rivermouths. This study reports changes to the spawning habitat following a series of large earthquakes that resulted in widespread deformation of ground surfaces in the vicinity of waterways. Assessments of habitat recovery focussed on two rivers systems, the Avon and Heathcote, with pre-disturbance data available over a 20 year period. Recovery dynamics were assessed by field survey and mapping of spawning habitat prior to and on seven occasions after the disturbance event. Riparian land-use and management patterns were mapped and analysed using overlay methods in GIS. Habitat migration of up to 2 km occurred in comparison to all previous records and several anthropogenic land uses have become threats due to changed patterns of co-occurrence. Incompatible activities now affect more than half of the spawning habitat in both rivers, particularly in areas managed for flood control purposes and recreational use. The results are an example of landscape scale responses to salinity and water level changes driven by tectonic dynamics. These dynamics are not the source of the stress per se, rather, they have increased exposure to pre-existing stressors. The case illustrates important principles for managing subtle, yet widespread, change. Adaptive conservation methods and investments in information are priorities for avoiding management failure following environmental change.

ecology↗

bioRxiv2017

Best Practice Data Life Cycle Approaches for the Life Sciences

Throughout history, the life sciences have been revolutionised by technological advances; in our era this is manifested by advances in instrumentation for data generation, and consequently researchers now routinely handle large amounts of heterogeneous data in digital formats. The simultaneous transitions towards biology as a data science and towards a life cycle view of research data pose new challenges. Researchers face a bewildering landscape of data management requirements, recommendations and regulations, without necessarily being able to access data management training or possessing a clear understanding of practical approaches that can assist in data management in their particular research domain.\n\nHere we provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on omics datasets and computer-based data processing and analysis. We discuss the different stages of the data life cycle and provide practical suggestions for useful tools and resources to improve data management practices.

bioinformatics↗