Data from: Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies

Dececchi TA, Balhoff JP, Lapp H, Mabee PM

Date Published: June 9, 2015

DOI: http://dx.doi.org/10.5061/dryad.rm907

 

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Title README
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Description README file
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Title supplementary_table_1
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Description Supplementary Materials Table 1. List of publications used in constructing the synthetic supermatrix. Focal group, number of taxa, and number of fin, limb, and girdle characters, states and phenotype annotations. Studies focused explicitly on the fin to limb transition are denoted by an asterisk.
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Title supplementary_table_2
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Description Supplementary Materials Table 2. Taxa (136) present in the variable-only synthetic supermatrix based on inferred data alone.
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Title supplementary_table_3
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Description Supplementary Materials Table 3. Conflicting characters. Characters with conflicting states in the variable-only supermatrix, listed by taxon. Conflict type (between direct assertions, direct vs. inferred, and inferred vs. inferred) indicated in right-most column.
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Title supplementary_table_4
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Description Supplementary Materials Table 4. Isomorphic characters. Clusters (93) of fully isomorphic characters across the variable-only synthetic supermatrix, arranged from high (10) to low (2).
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Title supplementary_table_5
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Description Supplementary Materials Table 5. Taxon sampling. The number of source matrices (right-most column) from which taxa (Vertebrate Taxonomy Ontology (VTO) identifier number, left-most column), at various taxonomic ranks, were sampled.
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Title supplementary_table_6
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Description Supplementary Materials Table 6. The number of published character states that entail the presence or absence for selected sets of anatomical entities and taxa.
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Title uberon_presences
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Description WL ontology containing a "presence class" corresponding to each anatomical structure from the Uberon anatomy ontology. Ontotrace code in `GeneratePresenceClasses.scala`
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Title sarcop-presence-absence-variable
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Description NEXUS-formatted translation of `sarcop-presence-absence-variable.xml
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Title sarcop-presence-absence-variable.xml
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Description NeXML character matrix retaining only variable columns from `sarcop-presence-absence-all.xml`
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Title sarcop-presence-absence-all.xml
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Description NeXML character matrix, generated using these input expressions to Ontotrace.
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When using this data, please cite the original publication:

Dececchi TA, Balhoff JP, Lapp H, Mabee PM (2015) Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies. Systematic Biology 64(6): 936-952. http://dx.doi.org/10.1093/sysbio/syv031

Additionally, please cite the Dryad data package:

Dececchi TA, Balhoff JP, Lapp H, Mabee PM (2015) Data from: Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.rm907
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