Difference between revisions of "App/ontology"

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== Use ==
 
== Use ==
  
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=== Welcome Screen ===
 
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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).<br />
 
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).<br />
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=== Search for Term ===
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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.
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Revision as of 11:01, 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

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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

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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.

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'.

API

A undocumented API exists for remote queries against the database (see the search action in the public controller in the source code), we're hoping to improve this and make it public soon.

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