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Measurement-Based phenotype data models.

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posted on 24.11.2020, 18:23 by Anne E. Thessen, Ramona L. Walls, Lars Vogt, Jessica Singer, Robert Warren, Pier Luigi Buttigieg, James P. Balhoff, Christopher J. Mungall, Deborah L. McGuinness, Brian J. Stucky, Matthew J. Yoder, Melissa A. Haendel

(A) Semantic Morph·D·Base. Pink-bordered boxes: instances; yellow-bordered boxes: classes; gray-bordered boxes: literals (labels or values); boxes with dashed borders: named graphs. (B) TaxonWorks. The underlying goal is to let scientists assert phenotype observations as required for their research. Assertions are persisted in Descriptor–Observation format where subclasses of descriptor (e.g., qualitative, quantitative, statistical, gene, free-text, and media) classify/define observations. Descriptor types anticipate downstream serialization into computable formats, semantic or otherwise. Phenotype assertions are at the class (= Taxon concept, an “OTU” in TaxonWorks) or instance (= Collection object) level (“Entity”). Ultimately, both levels will permit anatomical part assertions. While the approach includes improvements to the overall semantics, it still lacks specifics used in other models (e.g., Fig 5A and 5C); however, the typed descriptor approach provides a flexible software design, whereby incremental improvements to semantics are possible. All data are highly annotatable. Dashed boxes are features in progress. (C) Global Plant Phenological Database. Rounded rectangles represent classes, and hexagons represent instances. The original data set (bottom of figure) indicates that there is an instance of the class/phenophase “open flower presence,” which is a quality of an instance of “whole plant” from the PO. Because the value of the instance of measurement datum is >0, the ontology infers that open flowers are present. Due to the subsumption hierarchy of the PO (left side of figure), the ontology can also infer that nonsenesced flowers, flowers, and plant structures are present. IAO, Information Artifact Ontology; PATO, Phenotype and Trait Ontology; PO, Plant Ontology; OBI, Ontology for Biomedical Investigations; OTU, Operational Taxonomic Unit; RDF, Resource Description Framework; RO, Relations Ontology; UO, Unit Ontology.