The Planarian Anatomy Ontology: A resource to connect data within and across experimental platforms

Abstract

As the planarian Schmidtea mediterranea (Smed) gains popularity as a research organism, the need for standard anatomical nomenclature is increasingly apparent. A controlled vocabulary streamlines data annotation, improves data organization, and enhances cross-platform and cross-species searchability. We created the Planarian Anatomy Ontology (PLANA), an extendable framework of defined Smed anatomical terms organized using relationships. The most current version contains over 800 terms that describe Smed anatomy from subcellular to system-level across all life cycle stages, in intact animals, and regenerating body fragments. Terms from other anatomy ontologies were imported into PLANA to promote ontology interoperability and comparative anatomy studies. To demonstrate the utility of PLANA for data curation, we created web-based resources for planarian embryogenesis, including a staging series and molecular fate mapping atlas, as well as a searchable Planarian Anatomy Gene Expression database, which integrates a variety of published gene expression data and allows retrieval of information of all published sequences associated with specific planarian anatomical regions. Finally, we report methods for continued curation of PLANA, providing a path for expansion and evolution of this community resource.

Identification of rare, transient post-mitotic cell states that are induced by injury and required for whole-body regeneration in Schmidtea mediterranea

“…The most significant 20 – 40 transcripts enriched in each global cluster were mapped to dd_Smed_v6 or dd_Smed_v4 using the same mapper and their expression and tissue specificity was characterized in published planarian single-cell datasets ( 23 , 24 ). Most global clusters were easily assigned to a previously described tissue lineage due to a shared gene expression profile and, in many cases, a cluster could be matched 1-to-1 to a cluster or subcluster in a previously published dataset or to a planarian ontology term ( 72 , Table S15 ).…”

Formalizing Phenotypes of Regeneration

“…8. Scan the caption and expression pattern to automatically assign ontology terms from the Planarian Anatomy Ontology [27] to the gene expression pattern by clicking Scan Caption and Scan Expression (see Note 25).…”

“…Predefined expression patterns for organs are also available for the user to select, which transfers directly to the current standard morphology. In addition, the tool automatically assigns gene ontology terms from the Planarian Anatomy Ontology [27] by scanning the spatial locations of the gene expression in the reference morphology as well as searching for keywords in the entered captions and descriptions.…”