The Planarian Anatomy Ontology

The Planarian Anatomy Ontology: A partonomic standard vocabulary describing planarian anatomical features from embryogenesis to adulthood.


 

Overview

As the regenerative flatworm Schmidtea mediterranea gains popularity as a developmental research organism the need for standard nomenclature and a centralized repository of anatomical terms has become increasingly apparent. Utilization of a controlled vocabulary creates opportunities to catalogue genes and expression data for computational searches across research groups and cross-species comparisons, all while establishing a framework for integration of new terms. We created a Planarian Anatomy Ontology containing 327 terms and definitions for cellular organelles, cell types, tissues, organ systems, anatomical entities, life cycle stages and developmental processes described in the literature. Where possible, extant terms and definitions from Uberon and other open source anatomy ontologies were imported into the ontology to strengthen cross-species queries. Partonomy relationships between terms have been established; for example, cholinergic neuron is a neuron and is part of the central nervous system. Moving forward, we are employing the depicted by relationship to link image(s) of anatomical features that will be viewable using advanced search criteria on planosphere.stowers.org. The latest version of the ontology is freely available at OBO Foundry. To support data integration and encourage contribution and curation by members of the community, we are creating the infrastructure necessary for individuals to contribute new terms, relationships and modifications for extant terms. Please see more information below about how to contribute new terms.

 

The Planarian Anatomy Ontology is a labor of love and work in progress. Any suggestions, issues, questions, as well as new term submission or correction are wanted and welcome. Please contact us at planosphere@stowers.org

 

Call for Experts

If you would like to be available for consultation for a specific areas of expertise in planarian anatomy please contact us and let us know your wheel house. For example, if you know and love the neoblast compartment, reproductive system, musculature, etc . Tell us about it. Help us make it right!

 

Browse Anatomy Ontology

OBOPhenotype GitHub Organization houses the source files for the Planarian Anatomy Ontology.
PLANA, the Planarian Anatomy Ontology, is member of the Open Biological and Biomedical Ontology, (OBO) Foundry. The OBO is a collective of ontology developers that are committed to collaboration and adherence to shared principles.
EBI Ontology Lookup Service (OLS) provides a nice interface for exploring the ontology relationships by expanding and collapsing terms. Once a term of interest is located, "Graph View" provides a interactive tool for an alternate display of the term.
WebVowl gives a view of each terms and all the relations. The graph can be zoomed in and out. To ensure viewing of the whole ontology, go to filter menu and set slider to 0 degrees of collapsing.

 

Contribute New Terms

There are three ways to contribute terms. Please select the method for which you are most comfortable.

  1. DIY: The source files can be downloaded from Github and edited and resubmitted to contain new terms. Get a Tutorial (coming soon)
  2. 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
  3. Use our webform to help submit terms to the source ontology