The Planarian Anatomy Ontology

What is the Planarian Anatomy Ontology?

The Planarian Anatomy (PLANA) Ontology aims to comprehensively describe Schmidtea mediterranea anatomical features, and relationships among them, throughout the life cycle of both the sexually and asexually reproducing biotypes.

This controlled vocabulary consists >450 terms, encompassing subcellular to systems level anatomical entities, life cycle stages and developmental processes. To facilitate cross-species comparisons, extant terms and definitions were imported from UBERON, an integrated cross-species ontology of anatomical features, and other open-source ontologies.

Each PLANA term has:

1. a definition
2. a reference to an external ontology database and/or primary literature
3. annotations that establish relationships among terms

To remain current, the PLANA Ontology is a dynamic, versioned entity. Members of the community are encouraged to become curators! Curators edit existing terms, create new terms, and add or modify relationships among terms. Information on term curation can be found here.

Why use the PLANA Ontology?

1. Adherence to a standard vocabulary improves communication among researchers.
2. A tool to understand planarian anatomy.
   • What structures exist?
   • How do anatomical features develop?
   • What does each term mean?
3. Use terms as tags to improve organization and searchability for imaging and expression analysis data.
   • Which in situs show definitive pharynx patterning?

Explore the PLANA Ontology

• EBI Ontology Lookup Service (OLS)
  
  • The OLS provides a nice interface for exploring ontology relationships by expanding and collapsing terms. Once a term of interest is located, "Graph View" provides an interactive tool for an alternate display of the term.
• WebVowl
  
  • WebVowl shows every term and all the relations among terms. The graph zooms in and out. To ensure viewing of the whole ontology, go to filter menu and set slider to 0 degrees of collapsing.
• Planosphere
  
  • The ontology is used in, and is accessible though, the Molecular Fate Mapping Atlas, Molecular Staging Resource, and the PLANA Ontology Terms page.

How to download PLANA Ontology

• OBOPhenotype GitHub Organization
  
  • Houses the source files for the Planarian Anatomy Ontology.
• Open Biological and Biomedical Ontology, (OBO) Foundry.
  
  • The OBO displays the current PLANA ontology from GItHub.

How do I contribute to the PLANA Ontology?

One of the biggest strengths of the Planarian Anatomy Ontology is that it is a dynamic and interactive repository that changes to reflect new published knowledge. To keep the PLANA ontology up-to-date please add new terms, and edit existing terms as follows:

• Use our webform to help submit terms to the source ontology
• Use the official PLANA GitHub Repository Form
• Do it yourself with the source files available at Github. Create a FORK, edit to contain new terms, and submit a pull request. Get a Tutorial (coming soon)
• Email us at planosphere@stowers.org with the following information
  1. Term Name
  2. Definition
  3. Publication Reference
  4. Contact Name
  5. Contact Email
  6. Further information about this term

We value your feedback and questions. Please contact us at planosphere@stowers.org