title: Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach.
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, 16 S 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.
authors: Oxford e-Research Centre, University of Oxford, OX1 3QG, Oxford, UK, The iPlant Collaborative, University of Arizona, Thomas J. Keating Bioresearch Building, 1657 East Helen St., Tucson, AZ 85721, USA, NEON, Inc. 1685 38th St., Ste. 100, Boulder, CO 80301, USA, University of Arizona, 1311 E. 4th St. Tucson, AZ 85721, USA and Department of Genetics and Institute of Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA philippe.rocca-serra@oerc.ox.ac.uk.
authors: Philippe
authors: P
authors: Rocca-Serra
authors: Oxford e-Research Centre, University of Oxford, OX1 3QG, Oxford, UK, The iPlant Collaborative, University of Arizona, Thomas J. Keating Bioresearch Building, 1657 East Helen St., Tucson, AZ 85721, USA, NEON, Inc. 1685 38th St., Ste. 100, Boulder, CO 80301, USA, University of Arizona, 1311 E. 4th St. Tucson, AZ 85721, USA and Department of Genetics and Institute of Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors: Ramona
authors: R
authors: Walls
authors: Oxford e-Research Centre, University of Oxford, OX1 3QG, Oxford, UK, The iPlant Collaborative, University of Arizona, Thomas J. Keating Bioresearch Building, 1657 East Helen St., Tucson, AZ 85721, USA, NEON, Inc. 1685 38th St., Ste. 100, Boulder, CO 80301, USA, University of Arizona, 1311 E. 4th St. Tucson, AZ 85721, USA and Department of Genetics and Institute of Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors: Jacob
authors: J
authors: Parnell
authors: Oxford e-Research Centre, University of Oxford, OX1 3QG, Oxford, UK, The iPlant Collaborative, University of Arizona, Thomas J. Keating Bioresearch Building, 1657 East Helen St., Tucson, AZ 85721, USA, NEON, Inc. 1685 38th St., Ste. 100, Boulder, CO 80301, USA, University of Arizona, 1311 E. 4th St. Tucson, AZ 85721, USA and Department of Genetics and Institute of Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors: Rachel
authors: R
authors: Gallery
authors: Oxford e-Research Centre, University of Oxford, OX1 3QG, Oxford, UK, The iPlant Collaborative, University of Arizona, Thomas J. Keating Bioresearch Building, 1657 East Helen St., Tucson, AZ 85721, USA, NEON, Inc. 1685 38th St., Ste. 100, Boulder, CO 80301, USA, University of Arizona, 1311 E. 4th St. Tucson, AZ 85721, USA and Department of Genetics and Institute of Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors: Jie
authors: J
authors: Zheng
authors: Oxford e-Research Centre, University of Oxford, OX1 3QG, Oxford, UK, The iPlant Collaborative, University of Arizona, Thomas J. Keating Bioresearch Building, 1657 East Helen St., Tucson, AZ 85721, USA, NEON, Inc. 1685 38th St., Ste. 100, Boulder, CO 80301, USA, University of Arizona, 1311 E. 4th St. Tucson, AZ 85721, USA and Department of Genetics and Institute of Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors: Susanna-Assunta
authors: SA
authors: Sansone
authors: Oxford e-Research Centre, University of Oxford, OX1 3QG, Oxford, UK, The iPlant Collaborative, University of Arizona, Thomas J. Keating Bioresearch Building, 1657 East Helen St., Tucson, AZ 85721, USA, NEON, Inc. 1685 38th St., Ste. 100, Boulder, CO 80301, USA, University of Arizona, 1311 E. 4th St. Tucson, AZ 85721, USA and Department of Genetics and Institute of Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors: Alejandra
authors: A
authors: Gonzalez-Beltran
mesh_terms: D044822:Biodiversity; D063990:Gene Ontology; D005798:Genes, Bacterial; D020459:Genes, rRNA; D059013:Microbial Consortia / Q000502:physiology*; D008954:Models, Biological; D012336:RNA, Ribosomal, 16S / Q000235:genetics*
chemical_list: D012336:RNA, Ribosomal, 16S
references: Nat Genet. 2012 Jan 27;44(2):121-6
references: 22281772
references: Nat Biotechnol. 2011 May;29(5):415-20
references: 21552244
references: Genome Res. 2013 Oct;23(10):1704-14
references: 23861384
references: Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14691-6
references: 20679230
references: Stand Genomic Sci. 2010 Dec 25;3(3):243-8
references: 21304727
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D28-31
references: 20972220
references: J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S7
references: 20626927
references: Proc Biol Sci. 2003 Aug 7;270 Suppl 1:S96-9
references: 12952648
references: Nat Biotechnol. 2007 Nov;25(11):1251-5
references: 17989687
references: Appl Environ Microbiol. 2009 Dec;75(23):7537-41
references: 19801464
references: PLoS One. 2014 Mar 03;9(3):e89606
references: 24595056
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D13-21
references: 18045790
references: Nat Methods. 2008 Oct;5(10):887-93
references: 18794863