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The MIAPA ontology: An annotation ontology for validating minimum metadata reporting for phylogenetic analyses

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The MIAPA ontology: An
annotation ontology for validating
minimum metadata reporting for
phylogenetic analyses
Hilmar Lapp...

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Phylogenetic trees are published
at a rapidly increasing rate
Abby et al (2012) PNAS
Bininda-Emonds et al (2007)
Betancur ...

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Phylogenies are key to
many biological questions
Edwards & Smith 2010
Jetz et al 2012
Emerson & Gillespie, 2008

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The MIAPA ontology: An annotation ontology for validating minimum metadata reporting for phylogenetic analyses

  1. 1. The MIAPA ontology: An annotation ontology for validating minimum metadata reporting for phylogenetic analyses Hilmar Lapp, Joachim Baran, Enrico Pontelli, Arlin Stoltzfus, Ramona Walls 2013 iEvoBio Conference Snowbird, UT
  2. 2. Phylogenetic trees are published at a rapidly increasing rate Abby et al (2012) PNAS Bininda-Emonds et al (2007) Betancur et al 2013 Smith et al 2011
  3. 3. Phylogenies are key to many biological questions Edwards & Smith 2010 Jetz et al 2012 Emerson & Gillespie, 2008
  4. 4. Reuse of phylogenies is nonetheless rare “Most attempts at phylogenetic data reuse seem to end in disappointment.”
  5. 5. Part of the challenge is digital access {<4% of published phylogenies
  6. 6. The other challenge: Determining fitness for purpose •What kind of tree is it? •Does it have branch lengths? Support values? •From what kind of matrix or alignment? •How was the alignment created, how the tree?
  7. 7. OMICS, 2006 “If inadequately documented, however, even the most carefully constructed phylogenetic analysis will languish in the pages of a journal.”
  8. 8. Standards need normative documents Normative Other implentations MIAME MAGE-ML MAGE-TAB SOFT (GEO) MIGS/MIMS/ MIMARKS GCDML Structured Comments (NCBI) MIAPA ❌
  9. 9. Steps towards a Minimum Information About a Phylogenetic Analysis (MIAPA) Standard 2011 TDWG Conference
  10. 10. Draft MIAPA checklist • Topology: including identifier; type of tree, topology, and consensus • OTUs: Terminal nodes with appropriate labels and referenced to meaningful external identifier(s) • Branch lengths and branch support, unless not applicable to analysis method. • Character matrix: aligned data matrix that is the basis for the tree, with data type; accession numbers of the sequences; mapping from rows to a tip of the topology • Alignment method • Tree inference method Now on Github: http://github.com/miapa/miapa
  11. 11. MIAPA Ontology • Initiated at the Phylotastic II hackathon in Tucson (Feb 2013) • Developed in OWL • Designed to follow OBO Foundry best practices • Open: CC0, http://github.com/miapa/miapa • Mailing list: miapa-discuss@googlegroups.com • OBO ID policy: http://purl.obolibrary.org/obo/ MIAPA_NNNNNNN for term IDs
  12. 12. MIAPA Ontology • Application Ontology: Reuses most terms and properties from existing ontologies • Comparative Data Analysis Ontology (CDAO) • Information Artifact Ontology (IAO) • Software Ontology (SWO + EDAM) • W3C Provenance Ontology (PROV) • In addition, some properties from Darwin Core (DwC), Semantic Darwin Core (DSW), and Dublin Core (DC)
  13. 13. MIAPA Checklist: Example Topology Already (mostly) provided by CDAO
  14. 14. Reused terms with usage recommendations
  15. 15. Data provenance PROV Model
  16. 16. Data provenance PROV Model
  17. 17. Data annotation using the MIAPA Ontology
  18. 18. Data annotation using the MIAPA Ontology Annotated a total of 10 published phylogenies See http:// github.com/miapa/ miapa
  19. 19. Phylogenetic Tree and Data RDF Triplestore RDF, using CDAO RDFization MIAPA Expert KnowledgeManual Annotation RDF, using CDAO and MIAPA Automatic Annotation Extract & Transform MIAPA information Actor SPARQL Queries MIAPA annotations can facilitate data integration
  20. 20. Incentivizing better metadata T O B C A T MIAPA
  21. 21. Acknowledgements • Jim Leebens-Mack and other authors of the 2006 publication • Maryam Panahiazar for earlier work on ontology support for MIAPA • Nico Cellinese and participants of the 2011 TDWG Workshop on MIAPA • HIP Leadership Team (organizers of the 2013 Phylotastic Hackathon in Tucson) • Andrea Thomer, co-conspirator at the Tucson hackathon • Phylotastic Hackathon sponsors: NESCent, Biodiversity Synthesis Center, iPlant Collaborative

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