Morphology and ontology efforts by the Lepidoptera AToL

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Morphology and ontology efforts by the
Lepidoptera AToL

• Cynthia Parr
• University of Maryland
• Susan Weller
• University of Minnesota

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Molecular phylogenetics
Fossils
Resolution of branching at superfamily and family
level using 5 to 26 nuclear genes and 350 to 500
taxa.
Compilation of information on all known
lepidopteran fossils images, description,
references
Cyberinfrastructure Initiative
Morphology initiative

SesameTriple Store
Current knowledge Initiative
25 parallel ontologies for superfamilies, To be
merged via 1) jamboree 2) semantic integration
(machine reasoning) aided by molecular tree.
Will relate to HymATOL and Flybase terms.
Lepidopterist community describes systematics and
life history using text, images, datasets, and
structured data extending ETHAN ontology.
Ditrysia is-A Heteroneura Heteroneura
Has-Character X X is-A AntennalCharacter
LepTree
Tree of Life
EOL
OWL-DL RDF
For different human audiences
For computer agents
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1000(?) morphological terms x 26 superfamilies
etc.
Do anatomical terms refer to the same structures
. . .
Jamboree Given tree and collaborative human
examination of evidence? Semantic Integration
Given tree and knowledge of how each is described
relative to other ontologioes
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Morphology Initiative

• 9 symposia and workshops in 3 yrs
• 50-200 participants from Australia, Taiwan,
  Japan, USSR), Western and Eastern Europe, Canada,
  and Latin America (Mexico, Costa Rica, Brazil,
  Peru).
• Initial compilation/reconciliation of genitalic
  terms for male genitalia (95) female genitalia
  (44), larvae next!
• Annotation through Minijamboree, Jamboree

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From spreadsheets to . . .a simple editing
interface and display
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Taxon template describes morphological detail for
taxa
Glossary definitions show up on mouseover
throughout site
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Image annotation needs

• Launch app from an image on our website
• Define a polygon region
• Drag ontology terms relevant to region

• Display annotations and images to others back on
  our site (with detailed definitions)
• Allow comments and re-annotations
• Eventually, use machine reasoning to identify
  equivalent or related terms across glossaries

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Re-engineering

• Other modules also populating ontologies people,
  projects, references
• Each module hacked to do this
• Instead we are now making a generic RDF
  Import/Export module for Drupal
• Provide more flexibility and ability to manage
  additional kinds of relationships and new
  ontologies

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Questions for discussion

• What are the shared goals for morphologists?
• Communication goals
• Research goals
• Other goals (e.g. for ontologists)?
• What do ontologies really give us?
• Barriers to adoption of tools?

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Some architecture
Tolweb.org
LepTree.net
LepTaxonTree
Morphological glossary
Tree of Life page
Taxon Page
References
Taxon page template
TreeGrow
For setting up the tree structure
Adding text, values, and keywords for both Taxon
pages and Tree of life pages
Enter text and cross-linking that defines
morphological terminology (note, one glossary
also used for template)
Enter references for shared references bank,
Taxon Pages and TOL pages