Difference between revisions of "Guides/ontology"

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[[Welcome Screen]]<br />
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[[App/ontology]] - Welcome Screen<br />
 
The first screen you see when you log in and select the Hymenoptera Ontology project link.
 
The first screen you see when you log in and select the Hymenoptera Ontology project link.
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<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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<ul>
 
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<li>Ontology - this is the default screen (the one you see here)</li>
 
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<li>OTUs - the taxa to which morphological concepts apply</li>
 
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<li>Refs - where are references, keywords, tags, and serials are added and edited</li>
 
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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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<li>Tags - the master list of tags for your perusal.</li>
 
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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).
 
 
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[[Image:welcomeSmall.png]]
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[[ Image:welcomeSmall.png]]
 
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[[Search for Term]]<br />
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[[App/ontology]] - Search for Term<br />
 
Search for the term you want to enter to see if it is already there.
 
Search for the term you want to enter to see if it is already there.
 
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[[Search for Reference]]<br />
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[[App/ref]] - Search for Reference]]<br />
 
If you have a list of terms from a reference you'll want to make sure your reference is already in the database.
 
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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[[Add a Reference]]<br />
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[[App/ref]] - Add a Reference<br />
 
If your reference is not in the database already you'll want to add it before adding your term(s).
 
If your reference is not in the database already you'll want to add it before adding your term(s).
 
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[[Add a Term]]<br />
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[[App/ontology/new_term]] - Add a Term<br />
 
If your term isn't in the database you can add it using this form.
 
If your term isn't in the database you can add it using this form.
 
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[[Add Multiple Terms (Batch Mode)]]<br />
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[[ App/ontology/batch_load]] - Add Multiple Terms (Batch Mode)<br />
 
If your terms aren't in the database you can add them using this form.
 
If your terms aren't in the database you can add them using this form.
 
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[[Add a Relationship]]<br />
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[[App/ontology/show_term]] - Add a Relationship<br />
 
After your term is added you'll want to enter its relationships (e.g., your term is "part of" or a "type of" something).
 
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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[[Add Tags]]<br />
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[[App/ontology/show_term]] - Add Tags<br />
 
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.
 
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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[[View/Edit Tags]]<br />
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[[App/tag]] - View/Edit Tags <br />
 
If you made an error in your tag (e.g., wrong reference, page numbers, etc.) you can edit it.
 
If you made an error in your tag (e.g., wrong reference, page numbers, etc.) you can edit it.
 
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[[View/Edit Keywords]]<br />
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[[App/keyword]] - View/Edit Keywords<br />
 
Keywords are used in tags.
 
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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[[Mark-up your definitions]]<br />
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[[App/ontology/show_term]] - Mark-up your definitions<br />
 
Click the 'markup definitions' link to highlight and link to terms in your definition that are already in the ontology.
 
Click the 'markup definitions' link to highlight and link to terms in your definition that are already in the ontology.
 
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[[Manage the ontology (Admin)]]<br />
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[[App/ontology/admin]] - Manage the ontology (Admin)<br />
 
Click the 'more-options' link then "manage".
 
Click the 'more-options' link then "manage".
 
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[[Navigate and create relationships within a tree view]]<br />
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[[App/ontology/tree]] - Navigate and create relationships within a tree view <br />
 
Click the 'more-options' link then "tree".
 
Click the 'more-options' link then "tree".
 
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[[Filter by tags]]<br />
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[[App/ontology/filter]] - Filter by tags <br />
 
Click the 'more-options' link then "tag filter".
 
Click the 'more-options' link then "tag filter".
 
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[[Filter by personally edited]]<br />
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[[App/ontology/list_personal]] - Filter by personally edited <br />
 
Click the 'more-options' link then "personally edited".
 
Click the 'more-options' link then "personally edited".
 
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[[Extract terms from a block of text]]<br />
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[[App/ontology/proofer]] - Extract terms from a block of text<br />
 
Click the 'more-options' link then "proof".
 
Click the 'more-options' link then "proof".
 
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Latest revision as of 15:51, 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 the term you want to enter to see if it is already there.

Error creating thumbnail: Unable to save thumbnail to destination

App/ref - 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 - 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/new_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_load - 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/show_term - 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/show_term - 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/admin - Manage the ontology (Admin)
Click the 'more-options' link then "manage".

Error creating thumbnail: Unable to save thumbnail to destination


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

Error creating thumbnail: Unable to save thumbnail to destination

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

Error creating thumbnail: Unable to save thumbnail to destination


App/ontology/proofer - 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=Guides/ontology&oldid=2460"
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