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Tree Annotation Summary. Andrea, Arlin , Enrico, Hillmar , Joachim, Ramona. Overall Workflow. Select a sample of trees (10 trees) Develop a MIAPA-checklist annotation form Exercise of annotating sample studies using MIAPA checklist Develop a MIAPA ontology

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tree annotation summary

Tree Annotation Summary

Andrea, Arlin, Enrico, Hillmar, Joachim, Ramona

overall workflow
Overall Workflow
  • Select a sample of trees (10 trees)
  • Develop a MIAPA-checklist annotation form
  • Exercise of annotating sample studies using MIAPA checklist
  • Develop a MIAPA ontology
  • Develop ontology-based annotations of sample trees
  • Import Trees and Annotations in TreeStore and run queries
sample datasets
Sample Datasets
  • Supertree of mammals from Bininda-Emonds, et al 2007
  • Angiosperm phylogeny group (APG) tree of APGIII
  • Peters, et al hymenoptera tree
  • Tree of Life Web Project Structure
  • Angiosperm phylogeny from Smith et al. 2011
  • Tree of 720 taxa from The Genomic Encyclopedia of Bacteria and Archaea (GEBA)
  • Avian phylogeny of Jetz, et al. 2012
  • All-species living (microbial) tree of life based on SSU rRNA
  • Tree of all Eukaryotes in Genbank from Goloboff et al. 2009
  • NCBI taxonomy tree
sample datasets1
Sample Datasets
  • For each sample
    • Actual data (Newick, NEXUS)
    • Publication
    • Supplemental Publication Materials
miapa checklist form and application
MIAPA Checklist Form and Application
  • Googledoc form
  • Generate Spreadsheet
    • Pull-down menus
    • Free-text boxes
  • Based on MIAPA draft checklist from the TDWG 2011 workshop
  • Annotation of 10 sample studies
  • Identified
    • Improvements of checklist
    • Directions for MIAPA Ontology
miapa ontology
MIAPA Ontology
  • OWL
  • Imports several ontologies
    • CDAO
    • BIBO
    • PROV
    • IAO
  • https://github.com/miapa/miapa/blob/master/ontology/miapa.owl
ontology based annotations of sample studies
Ontology-based Annotations of Sample Studies
  • Bibliography
    • BIBO
    • Export from Zotero

<bib:Articlerdf:about="#item_3">

<z:itemType>journalArticle</z:itemType>

<dcterms:isPartOf>

<bib:Journal>

<dc:title>Nature</dc:title>

<prism:volume>446</prism:volume>

<prism:number>7135</prism:number>

</bib:Journal>

</dcterms:isPartOf>

<bib:authors>

<rdf:Seq>

<rdf:li>

<foaf:Person>

<foaf:surname>Bininda-Emonds</foaf:surname>

<foaf:givenname>O. R.</foaf:givenname>

</foaf:Person>

</rdf:li>

<rdf:li>

<foaf:Person>

<foaf:surname>Cardillo</foaf:surname>

<foaf:givenname>M.</foaf:givenname>

</foaf:Person>

</rdf:li>

ontology based annotations of sample studies1
Ontology-based Annotations of Sample Studies
  • Protégé-based Annotation of methods used
  • Derived from preliminary annotation using checklist
ontology based annotation of sample studies
Ontology-based Annotation of Sample Studies
  • Identified
    • Need for an interface for the generation of semantic descriptions (GSOC?)
    • Need for modifications of MIAPA ontology
    • Need for modifications of CDAO ontology