The Planarian Anatomy (PLANA) 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.

PLANA is a collection of classes curated from the literature and other organism anatomy ontologies to describe anatomical features, life cycle stages, and developmental processes in the regenerative flatworm Schmidtea mediterranea. 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. The preprint detailing PLANA construction can be found here

The latest version of the PLANA Ontology is available through the Open Biological and Biomedical Ontology Foundry (OBO). PLANA Ontology classes are searchable at the EMBL-EBI Ontology Lookup Service (OLS) and the PLANA Ontology Terms Page.

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 like we do here in our embryonic molecular staging resource, individual anatomical term pages, and in our Planarian Anatomy Gene Expression searches.
   

Explore the PLANA Ontology

You can explore the structure of PLANA at the following places:

• 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
  
  • Planosphere displays the classes and accompanying information from some of the tools that use PLANA (detailed below) on individual term pages
• The ontology is used in, and is accessible though these tools:
  
  • Within Planosphere:
    
    • Molecular Fate Mapping Atlas
    • Molecular Staging Resource
    • PLANA Ontology Terms Page
    • PAGE Searches
  • Outside Planosphere:
    
    • Roy et al., 2020

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 the official PLANA GitHub Repository Form
• 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