DOI: 10.5061/dryad.rm907
title: Data from: Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies

description: 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 noncomputer 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; kb.phenoscape.org), 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 639 variable characters scored for 1051 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, that is, 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.
description: READMEREADME
 filesupplementary_table_1Supplementary 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.supplementary_table_2Supplementary Materials Table 2. Taxa (136) present in the variable-only synthetic supermatrix based on inferred data alone.supplementary_table_3Supplementary 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.supplementary_table_4Supplementary Materials Table 4. Isomorphic characters. Clusters (93) of fully isomorphic characters across the variable-only synthetic supermatrix, arranged from high (10) to low (2).supplementary_table_5Supplementary 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.supplementary_table_6Supplementary Materials Table 6. The number of published character states that entail the presence or absence for selected sets of anatomical entities and taxa.uberon_presencesWL ontology containing a "presence class" corresponding to each anatomical structure from the Uberon anatomy ontology. Ontotrace code in `GeneratePresenceClasses.scala`sarcop-presence-absence-variableNEXUS-formatted translation of `sarcop-presence-absence-variable.xmlsarcop-presence-absence-variable.xmlNeXML character matrix retaining only variable columns from `sarcop-presence-absence-all.xml`sarcop-presence-absence-all.xmlNeXML character matrix, generated using these input expressions to Ontotrace.