How should we deal with digital digital data?
discrete, qualitative
information from literature
Why are we doing this?
1. generate knowledgebase of limb phenotypes
2. query database for specific information
3. ask summary questions using database
1. generate knowledgebase of limb phenotypes
phenotypes in taxa
phenotypes across genes
1. generate knowledgebase of limb phenotypes
a primary use case:
connect genes implicated in phenotypes
of model organisms with phenotypic
diversity observed across the Tree of Life
1. generate knowledgebase of limb phenotypes
5 toes
4 fingers
phenotypes within a model taxon
the frog Xenopus
Scadding & Maden 1986
1. generate knowledgebase of limb phenotypes
phenotypes across Tree of Life
Hugi et al. 2012
2. query database for specific information
query phenotypes for an anatomical entity in a taxon
2. query database for specific information
query phenotypes for an anatomical entity in a taxon
example: how many phalanges are in Digit II of H. peronii?
Hugi et al. 2012
3. ask summary questions using database
query phenotypes across taxa:
example: what are the shape phenotypes of ultimate phalanx in Digit IV?
salamander feet
Hemidactylium
Ambystoma (axolotl)
Ambystoma
experimental
Alberch & Gale 1985
3. ask summary questions using database
query phenotypes across taxa:
example: what are the shape phenotypes of ultimate phalanx in Digit IV?
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3. ask summary questions using database
query phenotypes across taxa:
example: what are the shape phenotypes of ultimate phalanx in Digit IV?
3. ask summary questions using database
query phenotypes across taxa:
example: what are the shape phenotypes of ultimate phalanx in Digit IV?
Descriptive morphology
Evo-devo
I II III IV
II III IV V
Other evo-devo I II III IV V
the frog hand:
How should we deal with digital digital data?
Must focus on utility:
what would you expect when you query phenotypes?
what do you want to see?
what do you not want to see?