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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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Presentation at ICBO meeting 2014 in Houston:
Modelling Microbial Biodiversity Assay

Published in: Science
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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

  1. 1. 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
  2. 2. Biodiversity in the News • Grim headlines • True for many Vertebrates species • Mankind only now starts to build tools enabling true exploration of diversity
  3. 3. Exploring the world biodiversity • Game changing progress in sequencing technology – Illumina – Oxford Nanopore Minion http://dx.doi.org/10.5524/100102
  4. 4. Microbial Diversity
  5. 5. Biodiversity studies with molecular techniques • Shotgun sequencing: – Sequencing as much as possible (probing is limited by sequencing depth available, the rarer the species, the deeper the sequencing needs to be) • Targeted sequencing: – Reliance on a ‘marker gene’ whose variability will be used to estimate distance between species
  6. 6. ‘Barcode’ as in Multiplexed Libraries genomic DNA isolated from individual sample is -fragmented (shearing) -ligated to a unique short DNA tag (i.e called the barcode) -PCR amplification and sequencing -output of a single collection of reads which can be subsequently sorted using the DNA short-hand by computational mean – deconvolution process Credits: http://rdp.cme.msu.edu/wiki/index.php/Pyrosequencing_Help
  7. 7. ‘Barcode’ as in Barcode of Life Credits: http://www.barcodeoflife.org
  8. 8. Ambiguous Language • What is a barcode or what is a barcoding experiment? – Metaphors are impenetrable to computers. – Need to make representation unambiguous – Barcoding, meaning a technique for processing more samples in one go -> another word for multiplexing – Barcoding, meaning the creation of a unique profile as a means to identify types of living things
  9. 9. Heaps of sequence data for sure….but • What is the value in the absence of accompanying descriptors? • Essential annotation to ascertain identity and origin, sampling conditions and rationale
  10. 10. Helping Data Management • MIXS Guidelines checklist • SRA xml schema, Genbank records… • Tabular Templates for Data Collection • Wealth of RDF conversion tools – R2RML W3C data standards • Using the same xml and same guidelines, nevertheless ambiguities subsist
  11. 11. ISA templates for Microbial Diversity Studies • Integrating MIXS checklist in the ISA framework • Mapping MIXS entities into SRA XML schema – Properties of sample – Properties of sample processing – Properties of resulting libraries – Properties of data processing
  12. 12. Ambiguities: Barcoding • Library Experiment Sample unicity • Use Case: creation of libraries for Bacteria,Fungi,Eukaryota with specific genes (16sRNA, ITS, COI) • ISA conversion to ENA: – 1 sample -> 3 libraries • SRA/ENA submission: – 3 libraries -> 3 samples
  13. 13. Working with OBI, PCO,SO, CHEBI Drawn using CMAPtools: http://cmap.ihmc.us
  14. 14. Working with OBI, PCO,SO, CHEBI Drawn using CMAPtools: http://cmap.ihmc.us
  15. 15. OBI-PCO based representation • ‘targeted gene survey’ • has part some ‘library preparation’ (OBI_0000711) • ‘polymerase chain reaction’ (OBI_0000415) is_part_of ‘library preparation’ (OBI_0000711) • ‘polymerase chain reaction’(OBI_0000415) • has_specified_input some ‘forward pcr primer’ (OBI_0000722) • has_specified_input some ‘reverse pcr primer’ (OBI_0001951) • has_specified_input some ‘multiplexing sequence identifier’ • has_specified_input some ‘DNA extract’ (OBI_0001051) • ‘library preparation’ (OBI_0000711) ‘has_specified_output’ some ‘single fragment library’ (OBI_0000736) • ‘library preparation’ (OBI_0000711) precedes ‘DNA sequencing’(OBI_0000626) • ‘library sequence deconvolution’ is_preceded_by ‘DNA sequencing’(OBI_0000626) • ‘library sequence deconvolution’ is_followed_by ‘(OBI_0200187)’ • ‘sequence analysis data transformation’ (OBI_0200187) has_specified_output some ‘data item’ (IAO_0000027) and is about ‘population quality’ (PCO_0000003)
  16. 16. 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.
  17. 17. 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?
  18. 18. 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.
  19. 19. 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) • Dr. Jie Zheng and OBI companions • PCO coworkers and RCN workshop participants • ISA Team • You
  20. 20. Acknowledgements 2

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