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

4. Reuse of phylogenies is
nonetheless rare
“Most attempts at
phylogenetic data reuse seem
to end in disappointment.”

5. Part of the challenge is
digital access
{<4% of published phylogenies

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. OMICS, 2006
“If inadequately documented, however,
even the most carefully constructed
phylogenetic analysis will languish in
the pages of a journal.”

8. Standards need
normative documents
Normative
Other
implentations
MIAME
MAGE-ML
MAGE-TAB
SOFT (GEO)
MIGS/MIMS/
MIMARKS
GCDML
Structured
Comments
(NCBI)
MIAPA ❌

9. Steps towards a Minimum
Information About a Phylogenetic
Analysis (MIAPA) Standard
2011 TDWG Conference

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. 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. 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. MIAPA Checklist: Example Topology
Already
(mostly)
provided by
CDAO

14. Reused terms with usage
recommendations

15. Data provenance
PROV Model

16. Data provenance
PROV Model

17. Data annotation using
the MIAPA Ontology

18. Data annotation using
the MIAPA Ontology
Annotated a total
of 10 published
phylogenies
See http://
github.com/miapa/
miapa

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. Incentivizing better metadata
T O B C A T
MIAPA

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