Alejandra Gonzalez-Beltran

Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach

The advent of affordable sequencing technology provides for a new generation of explorers who probe the world’s microbial diversity. Projects such as Tara Oceans, Moorea Biocode Project and Gut Microbiome rely on sequencing technologies to probe community diversity. Either targeted gene surveys (also known as community surveys) or complete metagenomes are evaluated. The former, being the less costly of the two methods, relies on the identification of specific genomic regions, which can be used as a proxy to estimate genetic distance between related species in a Phylum. For instance, 16u2009S ribosomal RNA gene surveys are used to probe bacterial communities while internal transcribed spacer surveys, for example, can be used for probing fungal communities. With the explosion of projects and frenzy to explore new domains of life, scientists in the field have issued guidelines to report minimal information (following a checklist), ensuring that information is contextualized in a meaningful way. Yet the semantics of a checklist are not explicit. We demonstrate here how a tabular template can be used to collect information on microbial diversity using an explicit representation in the Resource Description Framework that is consistent with community agreed-upon knowledge representation patterns found in the Ontology for Biomedical Investigations.

Investigation-Study-Assay, a toolkit for standardizing data capture and sharing

Abstract: This chapter introduces the problems experimentalists in all sectors face in utilizing third party data sets given the unhelpful wealth of formats and terminologies and the consequent mountain of technical frameworks needed to achieve data interoperability. We argue on the importance of a complementary set of open standards, the challenges we must overcome and the role the BioSharing effort is set to play. As an example of progress, we present the open source ISA software solution in action during the curation of the InnoMed PredTox data set, along with its growing active developer and user community, including academia and industrial sectors, such as The Novartis Institutes for BioMedical Research and Janssen Research & Development.