The reality of larger and larger molecular databases and the need to integrate data scalably have presented a major challenge for the use of phenotypic data. Morphology is currently primarily described in discrete publications, entrenched in non-computer readable text, and requires enormous investments of time and resources to integrate across large numbers of taxa and studies. Here we present a new methodology, using ontology-based reasoning systems working with the Phenoscape Knowledgebase (KB), to automatically integrate large amounts of evolutionary character state descriptions into a synthetic character matrix of neomorphic (presence/absence) data. Using the KB, which includes more than 55 studies of sarcopterygian taxa, we generated a synthetic supermatrix of 1051 variable characters scored for 639 taxa resulting in over 145,000 populated cells. Of these characters, over 76% were made variable through the addition of inferred presence/absence states derived by machine reasoning over the formal semantics of the source ontologies. Inferred data reduced the missing data in the variable character-subset from 98.5% to 78.2%. Machine reasoning also enables the isolation of conflicts in the data, i.e., cells where both presence and absence are indicated; reports regarding conflicting data provenance can be generated automatically. Further, reasoning enables quantification and new visualizations of the data, here for example, allowing identification of character space that has been undersampled across the fin to limb transition. The approach and methods demonstrated here to compute synthetic presence/absence supermatrices are applicable to any taxonomic and phenotypic slice across the tree of life, providing the data are semantically annotated. Because such data can also be linked to model organism genetics through computational scoring of phenotypic similarity, they open a rich set of future research questions into phenotype to genome relationships.