=Paper=
{{Paper
|id=Vol-1327/4
|storemode=property
|title=Modeling a Microbial Community and Biodiversity Assay with OBI and PCO OBO Foundry Ontologies: the Interoperability Gains of a Modular Approach
|pdfUrl=https://ceur-ws.org/Vol-1327/icbo2014_paper_20.pdf
|volume=Vol-1327
|dblpUrl=https://dblp.org/rec/conf/icbo/Rocca-SerraWPGZ14
}}
==Modeling a Microbial Community and Biodiversity Assay with OBI and PCO OBO Foundry Ontologies: the Interoperability Gains of a Modular Approach==
<pdf width="1500px">https://ceur-ws.org/Vol-1327/icbo2014_paper_20.pdf</pdf>
<pre>
                                 ICBO 2014 Proceedings



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

Philippe Rocca-Serra1, Ramona Walls2, Jacob Parnell3, Rachel Gallery4, Jie Zheng5, Susanna
                   Assunta Sansone1 and Alejandra Gonzalez-Beltran1

    1. Oxford e-Research Centre, University of Oxford, OX1 3QG, Oxford, United
       Kingdom
    2. The iPlant Collaborative, University of Arizona, Thomas J. Keating Bioresearch
       Building, 1657 East Helen St., Tucson, AZ 85721, USA.
    3. NEON, Inc., 1685 38th St., Ste. 100, Boulder, CO 80301, USA.
    4. University of Arizona, 1311 E. 4th St. Tucson, AZ 85721, USA.
    5. Department of Genetics and Institute of Biomedical Informatics, Perelman School of
       Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA

   Abstract— 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, 16S ribosomal RNA gene
surveys are used to probe bacterial communities while Internal Transcribed Spacer (ITS)
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 semantic of a checklist is 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 (RDF) that
is consistent with community agreed-upon knowledge representation patterns found in the
Ontology for Biomedical Investigations (OBI).

   Keywords— microbial diversity, targeted gene survey, ontology, assay, OBO Foundry, ISA
framework




                                             64

</pre>