Modeling a microbial community and biodiversity assay with OBI and PCO: the gains of a modular approach ICBO2014, in Houston Oct 6-9 Philippe Rocca-Serra, Ramona Walls, Jacob Parnell, Rachel Gallery, Jie Zheng, Susanna Assunta Sansone and Alejandra Gonzalez-Beltran
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Modeling a Microbial Community and Biodiversity Assay with OBI and PCO OBO Foundry Ontologies: The Interoperability Gains of a Modular Approach
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Modeling a microbial community
and biodiversity assay with OBI
and PCO: the gains of a modular
approach
ICBO2014, in Houston Oct 6-9Philippe Rocca-Serra, Ramona Walls, Jacob Parnell, Rachel Gallery, Jie
Zheng, Susanna Assunta Sansone and Alejandra Gonzalez-Beltran
• ‘sequence analysis data transformation’ (OBI_0200187) has_specified_output some ‘data item’ (IAO_0000027) and is about ‘population quality’ (PCO_0000003)
Conclusions
• We have clarified the OWL representation of
several assays commonly used in biodiversity
studies.
• We have outlined good practice for serializing
biodiversity experimental process both using ISA,
SRA and RDF format
• We have shown how synergies obtained from
resources of the OBO Foundry can greatly benefit
fast development of fit for purpose tabular data
collection templates which greatly help compliance
with annotation standard guidelines.
Why does it matter?
• Correct sample size assessment
• Assessing independence of samples and
sampling events.
• Is it really possible to ascertain identity of
samples by solely relying a metadata?
• How can such uncertainties affect
downstream analysis / meta analysis?
Future directions
• Sample Collection Protocols and
Procedures as applied in biodiversity
studies (field studies, “Marine macrofauna
grab sampling method” and so forth)
• Clarify the reporting of actual results
• Keeping working with PCO and OBO
Foundry related efforts.
Acknowledgements
• Dr. Ramona Walls (iPlant, Uni of Arizona)
• Pr. Paula Mabee (Uni South Dakota)
• RCN: Phenotype Ontology Research Coordination Network , National Science Foundation (NSF-DEB-0956049), (2010 - 2015)