Guides/ontology

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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 Hymenoptera Glossary. Information on how to use it is included below.


Welcome Screen
The first screen you see when you log in and select the Hymenoptera Ontology project link.
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).

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Search for Term
Search for the term you want to enter to see if it is already there.

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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.

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Add a Reference
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
If your term isn't in the database you can add it using this form.

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

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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).

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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.

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

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Mark-up your definitions
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)
Click the 'more-options' link then "manage".

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Navigate and create relationships within a tree view
Click the 'more-options' link then "tree".

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

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Filter by personally edited
Click the 'more-options' link then "personally edited".

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Extract terms from a block of text
Click the 'more-options' link then "proof".

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