Figure 1.
NeXML fragments demonstrating embedded Phenex annotations.
A. A taxon. B. A character and character state.
Table 1.
Metadata identifiers and XML elements used by Phenex to embed annotations with NeXML documents.
Figure 2.
Correspondence between Entity-Quality statements and evolutionary characters.
A. Comparison of the structure of phenotypic descriptions using character-character state vs. Entity-Quality ( = ‘Phenotype’) syntaxes. B. The defined relationship between an attribute quality type (shape) and a value quality type (triangular) within the Phenotype and Trait Ontology (PATO).
Figure 3.
Phenex screenshot of window configured with panels for browsing and searching of ontology terms and relationships.
Note that users can configure the position and size of each panel on the fly. See text for interface details of each panel; the window shows data from a publication [31] curated by the Phenoscape project.
Figure 4.
Phenex screenshot of window configured with panels for editing of taxon lists, voucher specimens, and publication information.
Figure 5.
Phenex screenshot of window configured with panels for editing of character and character states data, phenotypes (i.e. EQ statements), and character-by-taxon matrix.
Figure 6.
An example of lexigraphically dissimilar phenotype descriptions from two publications [32], [33] that are semantically similar in that they pertain to the same anatomical structure.
The ‘dorsal arrector’ and the ‘posterior pectoral-spine serrae’ are both parts of the pectoral fin, which is immediately apparent to both humans and computers from the structure of the anatomy ontology. Some of the data relationships shown, such as PHENOSCAPE:exhibits and those from CDAO (Comparative Data Analysis Ontology, [30]), are not explicit in Phenex. Instead, these are generated by the interpretation of NeXML documents within the Phenoscape Knowledgebase data loading software.