Genephony: Knowledge Management Tool For Genome-Wide Research
As the life sciences increasingly become knowledge-intensive disciplines, every effort aimed at facilitating the production, organization and dissemination of new knowledge is bound to have a profound effect on the speed, accuracy and effectiveness of scientific research, and of genome-wide, hypothesis free research in particular. Data and information production in this new era is measured on extraordinarily large scales: just in the field of sequencing, massively parallel DNA sequencing systems have increased our sequencing capacity to hundreds of millions of base-pairs per process run. Microarray technology for gene expression or genotype analysis is undergoing a similar evolution, with modern platforms now reaching one million simultaneous measurements. Parallel advances are taking place in proteomics, transcriptomics and metabolomics. This is having a profound effect on genomics-based research throughout the full range of biological science: whole-genome studies that were once unfeasible are now within the possibilities of any medium-sized laboratory, the distinction between model and non-model organisms has been blurred, and it is now possible to directly sequence entire collections of microbes, and viruses.
Genephony is an online tool aimed at researchers who need an easy, practical way to annotate, integrate and explore genomic knowledge and data resulting from large-scale experiments. The system is robust, efficient and extremely easy to use: it automatically determines which operations are applicable on each dataset, and presents them to the user in a detailed, readable form. Identifiers are automatically recognized and converted in order to establish relationships between different datasets. Interval operations are available for all objects that represent regions on chromosomes (e.g. transcripts, binding sites). Very complex sequences of data manipulations can thus be performed in just a few steps, and no knowledge of the structure of the underlying database is required.
Compared to similar systems such as Galaxy , DAVID , or BioMart , Genephony offers a more explicit and general representation of biomedical object types and of the relationships among them (as opposed to Galaxy’s flat-file model or DAVID’s gene-set centric view), a flexible workflow model that does not constrain the user on a predefined analysis or annotation path, leaving him/her free to generate and combine datasets in an exploratory way, and powerful data reuse and interoperability features. Moreover, Genephony does not enforce a limit on the size of the datasets the user can use, thus making it possible to operate on the entire contents of a set at once regardless of its dimensions.
Genephony does not currently offer graphical output capabilities, since its main focus is on knowledge and information management, but it provides flexible ways of exporting the contents of its datasets in standard formats for use in external visualization and data manipulation tools such as the UCSC Genome Browser and Galaxy. Although it is not an analysis tool, its rich knowledge base makes it suitable for scenarios ranging from basic genomic data annotation to translational research applications aimed at establishing links between the genomic level and medically relevant phenotypes.
The manipulation and interpretation of very large datasets represents a significant bottleneck for researchers who are not experts in database technology and programming. By providing them with effective tools to perform these increasingly common tasks, Genephony has the potential to accelerate the process of turning experimental data into verifiable hypotheses and biomedically relevant findings. Genephony could also be used as a platform for the dissemination of domain-specific knowledge, since its modular nature facilitates the creation of customized knowledge bases. It can therefore be helpful in making biomedical information available and accessible outside the boundaries of research community, resulting in an added benefit for the general public.
If you enjoyed this post, please consider to leave a comment or subscribe to the feed and get future articles delivered to your feed reader.