Difference between revisions of "App/ontology"
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Revision as of 11:21, 13 October 2009
Contents |
Overview
Ontologies in mx are very simple. They consist of user definable terms, relationship types, and relationships among terms. Terms can be tagged. References can be tied directly to terms through definitions, or through tags. Images can be attached to terms using figures.
Use
Welcome Screen
When you see this screen you are ready to begin! There are five tabs across the top:
- Ontology - this is the default screen (the one you see here)
- OTUs - the taxa to which morphological concepts apply
- Refs - where are references, keywords, tags, and serials are added and edited
- Images - images are uploaded here and can be tied to terms. We may be using Morphbank for this function, though we can discuss it further.
- Tags - the master list of tags for your perusal.
There are also links on the right for adding a term, listing all the terms and viewing the latest edits (check under "more options," where you will also find options to dump the ontology as an OBO flat file).
Search for Term
Before you enter a term you should see if it is already in the database. As you type into the search box the terms will automatically appear. If you see what you are looking for click that term and the press 'Show.' The results in the drop down include: name of term, 2. internal mx id, 2. xref (if applied), 3. term curator and year.
Add a Term
Adding terms is also fairly easy:
- Keystroke the word(s) (all lowercase unless a capital is warranted, e.g., for proper names like Waterston's organ)
- Add a definition in genus-differentia format that starts with a capital letter and ends with a period.
- Add OBO dbxref if from another ontology at OBO Foundary.
- Tie the term to the reference from which the definition was copied verbatim or from which the concept was derived. Curators are added to the references so they appear in the search (see example image)
- Tie it to the highest taxon for which this term applies
- Choose the language if not English.
Batch Upload
You can also batch load a list of terms you have in simple text.
General information
There is some information on how the ontology is being used here at the Hymenoptera Ontology wiki. A public example of the ontology in use can be found here.
Configuration
You can use an ontology created in your own project, or one created in another project that you (the creator) are a member of. If you want to use another project's click on 'settings' for your project, then 'edit'. At the bottom choose the project under 'Default Public Ontology'.
In App usage
Aside from the ontology tab there are various places the ontology can be applied or used in your project. Character descriptions can be marked-up after doing character->show, and clicking on the 'markup description'.