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| #summary A guide for editors of the ontologies hosted by this project. Start here!
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| | TODO |
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| = Introduction = | | == Protege Setup == |
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| This page is intended as a guide for editing the suite of ontologies hosted on this site.
| | See: http://code.google.com/p/caro2/wiki/Getting_started |
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| = Protege setup =
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| The following assumes Protege version 4.1, [http://obi-ontology.org/page/Tutorials#Protege4 OBI version].
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| == Names and IDs ==
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| Terms in the ontologies we use have separate names and IDs. The IDs are URIs with a syntax described below. The names are annotation values. Working with these ontologies in Protege 4.1 requires some tweaks to the default settings so that names are displayed rather than the short forms of IDs.
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| Open preferences and go to the renderer tab.
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| Choose render entities using annotation values.
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| [https://arthropod-anatomy-ontology.googlecode.com/svn/trunk/images/entity_rendering.png]
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| === Managing display of Long and short names ===
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| When working with multiple ontologies, we need both long names that are unique within the larger context of multiple ontologies. But these names are sometimes ungainly in the context of a single ontology. So, it is useful to also have short names that are unique only within their own ontology.
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| e.g. in insect anatomy: short name 'sensillum' long name 'insect sensillum'
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| We use rdf:label for short names and IAO_0000589 = 'OBO foundry unique label' for long names.
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| To manage display of these.
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| Open preferences and go to the renderer tab.
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| Click the annotations button in this tab:
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| [https://arthropod-anatomy-ontology.googlecode.com/svn/trunk/images/entity_rendering.png]
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| Set the annotation renderer as follows:
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| [https://caro2.googlecode.com/svn/wiki/annotation_setup.jpg]
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| Note - Protege 4.1 can be a bit finicky about this setup. It sometimes requires restarting or reloading ontologies to work.
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| === Managing IDs ===
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| IDs follow the specs outlined here:
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| http://www.obofoundry.org/id-policy.shtml
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| To set in Protege:
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| Preferences -> New Entities ->
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| Specified URI -> http://purl.obolibrary.org/obo/
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| [https://arthropod-anatomy-ontology.googlecode.com/svn/trunk/images/URI_specs.png]
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| Auto ID ->
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| numeric (iterative)
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| start and end - ranges to be distributed between editors. See [IdRangeLog]
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| Digit count: 7
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| prefix (see list of prefixes by ontology below)
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| [https://arthropod-anatomy-ontology.googlecode.com/svn/trunk/images/ID_specs.png]
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| == Working with multiple, interlinked ontologies ==
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| === Checkout and managing imports ===
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| Checkout of full repository currently => all the files you need to import in a single directory. This is likely to change in future as the repository evolves and if/when we want imports to resolve to copies held in other repositories. At this point we will need a standard Protege imports library xml.
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| === Editing multiple ontologies in one session ===
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| This is possible, although can easily lead to accidentally saving edits to the wrong file. If you attempt this:
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| 1. Choose the ontology you want to edit from the list at the top of the Protege window:
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| [https://arthropod-anatomy-ontology.googlecode.com/svn/trunk/images/ont_pick_list_closed.png]
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| [https://arthropod-anatomy-ontology.googlecode.com/svn/trunk/images/ont_pick_list_open.png
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| 2. Make sure your ID prefs are set for the ontology you are editing !
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| = Relations (object properties) =
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| Relations used in this project are currently maintained in caro_2.owl. IDs and full definitions for relations come from [https://obo-relations.googlecode.com/svn/trunk/src/ontology/ro.owl ro.owl]. This is likely to change in the near future so that relations and relevant imported terms are mireoted in from ro.owl.
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