Difference between revisions of "App/ontology"

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== Overview ==
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The mx database infrastructure includes an ontology building module that is easy to use and quite powerful. We're using mx as the backend of our [http://hymglossary.tamu.edu Hymenoptera Glossary]. Information on how to use it is included below.
  
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Ontologies in mx 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.
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----
  
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== Welcome Screen ==
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<table>
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[[Image:welcome.png]]
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<tr>
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<br />
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<td width="400">
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<p>
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[[App/ontology]] - Welcome Screen<br />
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When you see this screen you are ready to begin! There are five '''tabs''' across the top:
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The first screen you see when you log in and select the Hymenoptera Ontology project link.
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<ul>
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</td>
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<li>Ontology - this is the default screen (the one you see here)</li>
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<td>
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<li>OTUs - the taxa to which morphological concepts apply</li>
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[[ Image:welcomeSmall.png]]
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<li>Refs - where are references, keywords, tags, and serials are added and edited</li>
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</td>
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<li>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.</li>
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</tr>
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<li>Tags - the master list of tags for your perusal.</li>
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</table>
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</ul>
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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 />
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<br />
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<br />
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== Search for Term ==
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[[Image:search.png]]
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----
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<br />
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<br />
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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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<br />
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<br />
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== Add a Term ==
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<table>
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[[Image:AddTermv2.png]]
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<tr>
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<td width="400">
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[[App/ontology#Search for Term]] - Search for Term<br />
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Search for the term you want to enter to see if it is already there.
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</td>
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<td>
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[[Image:searchSmall.png]]
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</td>
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</tr>
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</table>
  
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Adding terms is also fairly easy:
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# Click on the 'new' link to add a term.
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# Keystroke the word(s) (all lowercase unless a capital is warranted, e.g., for proper names like Waterston's organ).
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# Add a definition in [[How we construct definitions|genus-differentia]] format that starts with a capital letter and ends with a period.
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# Add OBO dbxref if from another ontology at OBO Foundary.
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# 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).
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# Tie it to the highest taxon for which this term applies.
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# Choose the language if not English.
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<br />
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<br />
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== Add a Relationship ==
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<table>
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[[Image:RelateTerms.png]]
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<tr>
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<br />
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<td width="400">
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Once the term is added you'll need to add its relationship(s) to other terms. Previously added relationships will appear at the bottom of the page.
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[[App/ref#Searching]] - Search for Reference]]<br />
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<br />
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If you have a list of terms from a reference you'll want to make sure your reference is already in the database.
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<br />
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</td>
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<td>
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[[Image:litSearchSmall.png]]
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</td>
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</tr>
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</table>
  
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== Add Tags ==
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----
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[[Image:tag.png]]
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<br>
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Adding a tag ([[App/tag]]) is an easy way to comment on a particular term or to add alternative definitions and spellings (e.g., the plural spelling). There are a number of keywords already in the database: e.g., 'alternative definition' (for different verbal descriptions of the same concept - NOT entirely different definitions, which should have their own entries), 'plural' for plural spellings that are obvious, 'remove' (terms you think should go into other ontologies), 'comment.' Simply click the 'Tag' link under 'functions' on the left. The light red overlay will appear and you can tie a keyword, a reference, page numbers, and your comments to this term.
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<br />
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A list and explanation of [[ontology specific keywords]].
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<br />
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<br />
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== Mark Up Your Definitions ==
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<table>
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[[Image:mark.png]]
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<tr>
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<br />
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<td width="400">
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The 'markup definition' link highlights and links to terms in the definition that are already in the ontology
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[[App/ref#Adding_References]] - Add a Reference<br />
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<br />
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If your reference is not in the database already you'll want to add it before adding your term(s).
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<br />
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</td>
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<td>
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[[Image:AddLitSmall.png]]
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</td>
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</tr>
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</table>
  
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== Other Options ==
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----
  
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=== Batch Upload ===
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<table>
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[[Image:batch.png]]
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<tr>
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<br />
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<td width="400">
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You can also batch load a list of terms you have in simple text.<br />
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[[App/ontology#Add_a_Term]] - Add a Term<br />
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<br />
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If your term isn't in the database you can add it using this form.
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<br />
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</td>
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<td>
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[[Image:addTermSmall.png]]
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</td>
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</tr>
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</table>
  
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=== Manage the Ontology ===
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----
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[[Image:Manage ontology.png]]
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<br />
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<br />
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=== Navigate and Create within a Tree ===
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<table>
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[[Image:Tree ontology.png]]
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<tr>
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<br />
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<td width="400">
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<br />
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[[ App/ontology#Batch_Upload]] - Add Multiple Terms (Batch Mode)<br />
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If your terms aren't in the database you can add them using this form.
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</td>
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<td>
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[[Image:batchSmall.png]]
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</td>
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</tr>
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</table>
  
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=== Filter by Tags ===
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----
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[[Image:Tag filter.png]]
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<br />
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<table>
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<tr>
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<td width="400">
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[[App/ontology#show_term]] - Add a Relationship<br />
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After your term is added you'll want to enter its relationships (e.g., your term is "part of" or a "type of" something).
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</td>
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<td>
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[[Image:addrelSmall.png]]
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</td>
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</tr>
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</table>
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----
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<table>
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<tr>
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<td width="400">
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[[App/ontology#Add_Tags]] - Add Tags<br />
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You can "tag" your term with alternative spellings, alternative definitions (different wording for the same concept - NOT entirely different definitions, which should have their own entries), your own comments etc. using the tag function.
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</td>
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<td>
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[[Image:TagSmall.png]]
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</td>
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</tr>
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</table>
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----
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<table>
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<tr>
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<td width="400">
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[[App/tag]] - View/Edit Tags <br />
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If you made an error in your tag (e.g., wrong reference, page numbers, etc.) you can edit it.
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</td>
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<td>
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[[Image:tagsBrowseSmall.png]]
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</td>
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</tr>
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</table>
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----
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<table>
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<tr>
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<td width="400">
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[[App/keyword]] - View/Edit Keywords<br />
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Keywords are used in tags.
 
A list and explanation of [[ontology specific keywords]].
 
A list and explanation of [[ontology specific keywords]].
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<br />
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</td>
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<br />
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<td>
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[[Image:Keywords small.png]]
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</td>
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</tr>
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</table>
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----
  
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=== Filter by Personally Edited ===
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<table>
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[[Image:Filter personally edited.png]]
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<tr>
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<br />
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<td width="400">
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<br />
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[[App/ontology#Mark_Up_Your_Definitions]] - Mark-up your definitions<br />
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Click the 'markup definitions' link to highlight and link to terms in your definition that are already in the ontology.
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</td>
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<td>
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[[Image:markSmall.png]]
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</td>
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</tr>
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</table>
  
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=== Extract Terms from a Block of Text ===
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[[Image:Proffer not public.png]]
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<br />
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<br />
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=== Other Options ===
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<table>
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There are many other options including:
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<tr>
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* List by first letter of term (by first letter).
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<td width="400">
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* List of terms without any relationships (without relationships).
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[[App/ontology#Manage_the_Ontology]] - Manage the ontology (Admin)<br />
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* List of terms without a definition (without definitions).
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Click the 'more-options' link then "manage".
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* List of terms without xrefs (without xrefs).
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</td>
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* List of the latest edits (latest edits).
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<td>
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* List of terms that will be excluded and included if an obo file is exported (exclusion/inclusion list)
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[[Image:Manage small.png]]
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* List of references tied to the ontology, including if they are tagged to parts, tagged to parts with xrefs, used directly with parts or parts with xrefs (tied references). References can be tied to terms in two ways: either directly entered in the form when adding a new term or tagged to a term.
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</td>
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* Search definitions using a text string (search definitions).  Returns all the terms that contain that string in its definition.
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</tr>
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* Dump an OBO formatted file (dump OBO).
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</table>
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* A few non-traditional methods to visualize the ontology (visualize).
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* See up to date statistics on the ontology (stats). Including: total terms, terms changed, without relationships or definitions, figures on terms, number of tags on terms and number of relationships.
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== General information ==
 
  
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=== Use ===
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<table>
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<tr>
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<td width="400">
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[[App/ontology#Navigate_and_Create_within_a_Tree]] - Navigate and create relationships within a tree view <br />
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Click the 'more-options' link then "tree".
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</td>
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<td>
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[[Image:Tree small.png]]
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</td>
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</tr>
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</table>
  
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There is some information on how the ontology is being used [http://ontology.insectmuseum.org/ here at the Hymenoptera Anatomical Ontology] wiki.  A public example of the ontology in use [http://hymglossary.tamu.edu can be found here]. Since
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=== Configuration ===
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<table>
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<tr>
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<td width="400">
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[[App/ontology#Filter_by_Tags]] - Filter by tags <br />
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Click the 'more-options' link then "tag filter".
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</td>
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<td>
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[[Image:Filter by tags small.png]]
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</td>
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</tr>
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</table>
  
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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'. This portion of the mx software is rapidly developing since Summer 2009 due to support in part, by the National Science Foundation under grant DBI 0850223.
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=== In App usage ===
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<table>
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<tr>
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<td width="400">
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[[App/ontology#Filter_by_Personally_Edited]] - Filter by personally edited <br />
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Click the 'more-options' link then "personally edited".
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</td>
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<td>
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[[Image:Filter personally edited small.png]]
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</td>
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</tr>
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</table>
  
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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'. 
 
  
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=== API ===
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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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<table>
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<tr>
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<td width="400">
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[[App/ontology#Extract_Terms_from_a_Block_of_Text]] - Extract terms from a block of text<br />
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Click the 'more-options' link then "proof".
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</td>
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<td>
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[[Image:Extract terms small.png]]
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</td>
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</tr>
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</table>

Revision as of 14:44, 13 October 2009

The mx database infrastructure includes an ontology building module that is easy to use and quite powerful. We're using mx as the backend of our Hymenoptera Glossary. Information on how to use it is included below.

App/ontology - Welcome Screen
The first screen you see when you log in and select the Hymenoptera Ontology project link.

Error creating thumbnail: Unable to save thumbnail to destination

App/ontology#Search for Term - Search for Term
Search for the term you want to enter to see if it is already there.

Error creating thumbnail: Unable to save thumbnail to destination

App/ref#Searching - Search for Reference]]
If you have a list of terms from a reference you'll want to make sure your reference is already in the database.

Error creating thumbnail: Unable to save thumbnail to destination

App/ref#Adding_References - Add a Reference
If your reference is not in the database already you'll want to add it before adding your term(s).

Error creating thumbnail: Unable to save thumbnail to destination

App/ontology#Add_a_Term - Add a Term
If your term isn't in the database you can add it using this form.

Error creating thumbnail: Unable to save thumbnail to destination

App/ontology#Batch_Upload - Add Multiple Terms (Batch Mode)
If your terms aren't in the database you can add them using this form.

Error creating thumbnail: Unable to save thumbnail to destination

App/ontology#show_term - Add a Relationship
After your term is added you'll want to enter its relationships (e.g., your term is "part of" or a "type of" something).

Error creating thumbnail: Unable to save thumbnail to destination

App/ontology#Add_Tags - Add Tags
You can "tag" your term with alternative spellings, alternative definitions (different wording for the same concept - NOT entirely different definitions, which should have their own entries), your own comments etc. using the tag function.

Error creating thumbnail: Unable to save thumbnail to destination

App/tag - View/Edit Tags
If you made an error in your tag (e.g., wrong reference, page numbers, etc.) you can edit it.

Error creating thumbnail: Unable to save thumbnail to destination


App/keyword - View/Edit Keywords
Keywords are used in tags. A list and explanation of ontology specific keywords.

Error creating thumbnail: Unable to save thumbnail to destination

App/ontology#Mark_Up_Your_Definitions - Mark-up your definitions
Click the 'markup definitions' link to highlight and link to terms in your definition that are already in the ontology.

Error creating thumbnail: Unable to save thumbnail to destination

App/ontology#Manage_the_Ontology - Manage the ontology (Admin)
Click the 'more-options' link then "manage".

Error creating thumbnail: Unable to save thumbnail to destination


App/ontology#Navigate_and_Create_within_a_Tree - Navigate and create relationships within a tree view
Click the 'more-options' link then "tree".

Error creating thumbnail: Unable to save thumbnail to destination

App/ontology#Filter_by_Tags - Filter by tags
Click the 'more-options' link then "tag filter".

Error creating thumbnail: Unable to save thumbnail to destination

App/ontology#Filter_by_Personally_Edited - Filter by personally edited
Click the 'more-options' link then "personally edited".

Error creating thumbnail: Unable to save thumbnail to destination


App/ontology#Extract_Terms_from_a_Block_of_Text - Extract terms from a block of text
Click the 'more-options' link then "proof".

Error creating thumbnail: Unable to save thumbnail to destination
Retrieved from "http://mx.phenomix.org/index.php?title=App/ontology&oldid=2448"
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