Readme file for the folder /POC/branches/beta/ontology/OBO_format

This folder contains the beta versions of the Plant Ontology files for the upcoming release.  Note that these files also contain the Spanish and Japansese translations of the PO terms.  This may cause issues for some browsers as a result of the special characters.  When preparing association files for the database release users should use these files, not the files in the Live tag or the developer's files.

Note that the Plant Ontology is now provided as a single file (plant_ontology.obo), which contains both the Plant Anatomy Ontology branch and the Plant Growth and Development Stage Ontology branch. All editing is done on the plant_ontology.obo file. New versions of po_anatomy.obo and po_temporal.obo are created only with new releases.

Folders in this file:

plant_ontology.obo: This is the main file, containing both the Plant Anatomy Ontology branch and the Plant Growth and Development Stage Ontology branch and it contains all relations, including those relations between the PAO and the PGDSO. Relations that are inferred based on intersection_of relation are not asserted. 

plant_ontology_assert.obo: Corresponds to plant_ontology.obo, but with all of the relations that can be inferred from intersection_of relations asserted. This file is created using the "Assert implied links" panel in OboEdit.

plant_ontology_assert_basic.obo: Corresponds to plant_ontology_assert.obo, but with only is_a and part_of relations. All relations that can be inferred based on intersection_of relations have been asserted. The relations adjacent_to, derives_from, develops_from, has_part, participates_in, and disjoint_from have been removed. This file is created using "link filtering" (advanced save options) in OboEdit.

po_anatomy.obo: This file is updated with each release, by saving only terms from plant_ontology_assert_basic.obo with the namespace "anatomy" and removing all relations between the PAO and the PGDSO, including intersection_of relations.  Note that this file contains only the is_a and part_of relations.

po_temporal.obo: This file is updated with each release, by saving only terms from plant_ontology_assert_basic.obo with the namespace "plant growth and development stage" and removing all relations between the PAO and the PGDSO, including intersection_of relations. Note that this file contains only the is_a and part_of relations.