The MIAPA ontology: Anannotation ontology for validatingminimum metadata reporting forphylogenetic analysesHilmar Lapp, Jo...
Phylogenetic trees are publishedat a rapidly increasing rateAbby et al (2012) PNASBininda-Emonds et al (2007)Betancur et a...
Phylogenies are key tomany biological questionsEdwards & Smith 2010Jetz et al 2012Emerson & Gillespie, 2008
Reuse of phylogenies isnonetheless rare“Most attempts atphylogenetic data reuse seemto end in disappointment.”
Part of the challenge isdigital access{<4% of published phylogenies
The other challenge:Determining fitness for purpose•What kind of treeis it?•Does it havebranch lengths?Support values?•From...
OMICS, 2006“If inadequately documented, however,even the most carefully constructedphylogenetic analysis will languish int...
Standards neednormative documentsNormativeOtherimplentationsMIAMEMAGE-MLMAGE-TABSOFT (GEO)MIGS/MIMS/MIMARKSGCDMLStructured...
Steps towards a MinimumInformation About a PhylogeneticAnalysis (MIAPA) Standard2011 TDWG Conference
Draft MIAPA checklist• Topology: including identifier; type of tree, topology, andconsensus• OTUs: Terminal nodes with appr...
MIAPA Ontology• Initiated at the Phylotastic II hackathon inTucson (Feb 2013)• Developed in OWL• Designed to follow OBO Fo...
MIAPA Ontology• Application Ontology: Reuses most terms andproperties from existing ontologies• Comparative Data Analysis ...
MIAPA Checklist: Example TopologyAlready(mostly)provided byCDAO
Reused terms with usagerecommendations
Data provenancePROV Model
Data provenancePROV Model
Data annotation usingthe MIAPA Ontology
Data annotation usingthe MIAPA OntologyAnnotated a totalof 10 publishedphylogeniesSee http://github.com/miapa/miapa
Phylogenetic Tree and DataRDF TriplestoreRDF, using CDAORDFizationMIAPAExpert KnowledgeManualAnnotationRDF, using CDAO and...
Incentivizing better metadataT O B C A TMIAPA
Acknowledgements• Jim Leebens-Mack and other authors of the 2006publication• Maryam Panahiazar for earlier work on ontolog...
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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

  1. 1. The MIAPA ontology: Anannotation ontology for validatingminimum metadata reporting forphylogenetic analysesHilmar Lapp, Joachim Baran, Enrico Pontelli,Arlin Stoltzfus, Ramona Walls2013 iEvoBio ConferenceSnowbird, UT
  2. 2. Phylogenetic trees are publishedat a rapidly increasing rateAbby et al (2012) PNASBininda-Emonds et al (2007)Betancur et al 2013Smith et al 2011
  3. 3. Phylogenies are key tomany biological questionsEdwards & Smith 2010Jetz et al 2012Emerson & Gillespie, 2008
  4. 4. Reuse of phylogenies isnonetheless rare“Most attempts atphylogenetic data reuse seemto end in disappointment.”
  5. 5. Part of the challenge isdigital access{<4% of published phylogenies
  6. 6. The other challenge:Determining fitness for purpose•What kind of treeis it?•Does it havebranch lengths?Support values?•From what kind ofmatrix oralignment?•How was thealignment created,how the tree?
  7. 7. OMICS, 2006“If inadequately documented, however,even the most carefully constructedphylogenetic analysis will languish inthe pages of a journal.”
  8. 8. Standards neednormative documentsNormativeOtherimplentationsMIAMEMAGE-MLMAGE-TABSOFT (GEO)MIGS/MIMS/MIMARKSGCDMLStructuredComments(NCBI)MIAPA ❌
  9. 9. Steps towards a MinimumInformation About a PhylogeneticAnalysis (MIAPA) Standard2011 TDWG Conference
  10. 10. Draft MIAPA checklist• Topology: including identifier; type of tree, topology, andconsensus• OTUs: Terminal nodes with appropriate labels andreferenced to meaningful external identifier(s)• Branch lengths and branch support, unless notapplicable to analysis method.• Character matrix: aligned data matrix that is the basisfor the tree, with data type; accession numbers of thesequences; 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 inTucson (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 andproperties 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), andDublin Core (DC)
  13. 13. MIAPA Checklist: Example TopologyAlready(mostly)provided byCDAO
  14. 14. Reused terms with usagerecommendations
  15. 15. Data provenancePROV Model
  16. 16. Data provenancePROV Model
  17. 17. Data annotation usingthe MIAPA Ontology
  18. 18. Data annotation usingthe MIAPA OntologyAnnotated a totalof 10 publishedphylogeniesSee http://github.com/miapa/miapa
  19. 19. Phylogenetic Tree and DataRDF TriplestoreRDF, using CDAORDFizationMIAPAExpert KnowledgeManualAnnotationRDF, using CDAO and MIAPAAutomaticAnnotationExtract &TransformMIAPAinformationActorSPARQLQueriesMIAPA annotations canfacilitate data integration
  20. 20. Incentivizing better metadataT O B C A TMIAPA
  21. 21. Acknowledgements• Jim Leebens-Mack and other authors of the 2006publication• Maryam Panahiazar for earlier work on ontologysupport for MIAPA• Nico Cellinese and participants of the 2011 TDWGWorkshop on MIAPA• HIP Leadership Team (organizers of the 2013Phylotastic Hackathon in Tucson)• Andrea Thomer, co-conspirator at the Tucson hackathon• Phylotastic Hackathon sponsors: NESCent, BiodiversitySynthesis Center, iPlant Collaborative

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