Abstract
We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.
Highlights
Introduction to methodology and encoding rulesJ Chem Inf Comput Sci
A working group at the National Evolutionary Synthesis Center (NESCent,53) initiated a project to address this[54] and to establish a database of reference fossils with a web service API55. To evaluate whether this new resource can be usefully applied in the analysis of molecular data we developed a proof-of-concept pipeline[55] that includes a reconciliation between fossil taxa from the FossilCalibrations database and extant taxa from in the TreeFam orthology database
We found that LODQA could generate effective SPARQL queries for some natural language questions like “Which genes are involved in calcium binding?” The LODQA interface to Bio2RDF is publicly available[155], while the LODQA interface to DisGeNET is discontinued due to major revisions to DisGeNET
Summary
Introduction to methodology and encoding rulesJ Chem Inf Comput Sci. American Chemical Society, 1988 [cited 2016 Nov 30]; 28(1): 31–6. The past few years have yielded considerable progress in the development and application of fundamental digital technologies that support research in the life sciences[2], including ontologies and Linked Open Data (LOD), semantic web services, natural language processing, and tooling for workflows and virtualization. While these technologies are useful for life sciences research, key to their long-term success lies in community agreements that foster standardization and interoperability[2]. BH15 involved 80 individuals from 12 countries and a wide variety of backgrounds, including computer programmers, bioinformaticians, biocurators, ontologists, biological scientists, systems biologists, data scientists, and linguists
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