Difference between revisions of "App/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 [http://hymglossary.tamu.edu Hymenoptera Glossary]. Information on how to use it is included below.
+
== Overview ==
  
----
+
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. From this page you can:
 +
* click 'new' to add a new term
 +
* click 'list' to view a list of existing terms
 +
* search for a term
 +
* choose one of many options from the options list
  
<table>
+
== Welcome Screen ==
<tr>
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[[Image:Ontology.png|700px]]
<td width="400">
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<br />
[[App/ontology/index]] - Welcome Screen<br />
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<p>
The first screen you see when you log in and select the Hymenoptera Ontology project link.
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When you see this screen you are ready to begin! There are five '''tabs''' across the top:
</td>
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<ul>
<td>
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<li>Ontology - this is the default screen (the one you see here)</li>
[[ Image:welcomeSmall.png]]
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<li>OTUs - the taxa to which morphological concepts apply</li>
</td>
+
<li>Refs - where are references, keywords, tags, and serials are added and edited</li>
</tr>
+
<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>
</table>
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<li>Tags - the master list of tags for your perusal.</li>
 +
</ul>
 +
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 />
 +
<br />
 +
<br />
 +
== Search for a Term ==
 +
<br />
 +
<br />
 +
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: label (purple), class (green) or tag (orange).
 +
<br />
 +
<br />
  
----
 
  
<table>
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== Options ==
<tr>
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<td width="400">
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[[App/ontology/index]] - 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>
+
<td>
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[[Image:searchSmall.png]]
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</td>
+
</tr>
+
</table>
+
  
----
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[[Image:Ontology_options.png|700px]]
 +
<br />
 +
There are many other options including:
 +
* List by first letter of term (by first letter).
 +
* List of terms without any relationships (without relationships).
 +
* List of terms without a definition (without definitions).
 +
* List of terms without xrefs (without xrefs).
 +
* List of the latest edits (latest edits).
 +
* List of terms that will be excluded and included if an OBO file is exported (exclusion/inclusion list)
 +
* 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.
 +
* [[App/ontology/tree]] - (tree)
 +
* [[App/ontology/filter]] - (tag filter)
 +
* [[App/ontology/list_personal]]
 +
* Search definitions using a text string (search definitions).  Returns all the terms that contain that string in its definition.
 +
* [[App/ontology/batch_load]] - (batch upload or sync)
 +
* Dump an OBO formatted file (dump OBO).
 +
* [[App/ontology/proofer]] - (proof)
 +
* A few non-traditional methods to visualize the ontology (visualize).
 +
* [[App/ontology/admin]] - (Manage)
 +
* 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.
 +
<br />
  
<table>
+
== General information ==
<tr>
+
<td width="400">
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[[App/ref#Searching]] - Search for Reference]]<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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</td>
+
<td>
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[[Image:litSearchSmall.png]]
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</td>
+
</tr>
+
</table>
+
  
----
 
  
<table>
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=== Use ===
<tr>
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<td width="400">
+
[[App/ref#Adding_References]] - Add a Reference<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).
+
</td>
+
<td>
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[[Image:AddLitSmall.png]]
+
</td>
+
</tr>
+
</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]. 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.
  
<table>
+
=== Configuration ===
<tr>
+
<td width="400">
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[[App/ontology/new_term]] - Add a Term<br />
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If your term isn't in the database you can add it using this form.
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</td>
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<td>
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[[Image:addTermSmall.png]]
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</td>
+
</tr>
+
</table>
+
  
----
+
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'. Check the project settings to set a default namespace, public ontology, root term, inclusion/exclusion keywords, remark. More information regarding project level ontology setting are found in [[App/proj/edit]]
  
<table>
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=== In App usage ===
<tr>
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<td width="400">
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[[ App/ontology/batch_load]] - 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]]
+
</td>
+
</tr>
+
</table>
+
  
----
+
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'. 
  
<table>
+
=== API ===
<tr>
+
<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>
+
</tr>
+
</table>
+
  
----
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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.
 
+
<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>
+
</table>
+
 
+
----
+
 
+
<table>
+
<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]]
+
</td>
+
</tr>
+
</table>
+
 
+
----
+
 
+
 
+
<table>
+
<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.
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A list and explanation of [[ontology specific keywords]].
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</td>
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<td>
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[[Image:Keywords small.png]]
+
</td>
+
</tr>
+
</table>
+
 
+
----
+
 
+
<table>
+
<tr>
+
<td width="400">
+
[[App/ontology/show_term]] - 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>
+
<td>
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[[Image:markSmall.png]]
+
</td>
+
</tr>
+
</table>
+
 
+
----
+
 
+
<table>
+
<tr>
+
<td width="400">
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[[App/ontology/admin]] - Manage the ontology (Admin)<br />
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Click the 'more-options' link then "manage".
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</td>
+
<td>
+
[[Image:Manage small.png]]
+
</td>
+
</tr>
+
</table>
+
 
+
 
+
----
+
 
+
<table>
+
<tr>
+
<td width="400">
+
[[App/ontology/tree]] - Navigate and create relationships within a tree view <br />
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Click the 'more-options' link then "tree".
+
</td>
+
<td>
+
[[Image:Tree small.png]]
+
</td>
+
</tr>
+
</table>
+
 
+
----
+
 
+
<table>
+
<tr>
+
<td width="400">
+
[[App/ontology/filter]] - Filter by tags <br />
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Click the 'more-options' link then "tag filter".
+
</td>
+
<td>
+
[[Image:Filter by tags small.png]]
+
</td>
+
</tr>
+
</table>
+
 
+
----
+
 
+
<table>
+
<tr>
+
<td width="400">
+
[[App/ontology/list_personal]] - Filter by personally edited <br />
+
Click the 'more-options' link then "personally edited".
+
</td>
+
<td>
+
[[Image:Filter personally edited small.png]]
+
</td>
+
</tr>
+
</table>
+
 
+
 
+
----
+
 
+
<table>
+
<tr>
+
<td width="400">
+
[[App/ontology/proofer]] - Extract terms from a block of text<br />
+
Click the 'more-options' link then "proof".
+
</td>
+
<td>
+
[[Image:Extract terms small.png]]
+
</td>
+
</tr>
+
</table>
+

Latest revision as of 12:04, 20 May 2010

Contents

[edit] Overview

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. From this page you can:

  • click 'new' to add a new term
  • click 'list' to view a list of existing terms
  • search for a term
  • choose one of many options from the options list

[edit] Welcome Screen

Ontology.png

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).


[edit] Search for a 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: label (purple), class (green) or tag (orange).


[edit] Options

Ontology options.png
There are many other options including:

  • List by first letter of term (by first letter).
  • List of terms without any relationships (without relationships).
  • List of terms without a definition (without definitions).
  • List of terms without xrefs (without xrefs).
  • List of the latest edits (latest edits).
  • List of terms that will be excluded and included if an OBO file is exported (exclusion/inclusion list)
  • 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.
  • App/ontology/tree - (tree)
  • App/ontology/filter - (tag filter)
  • App/ontology/list_personal
  • Search definitions using a text string (search definitions). Returns all the terms that contain that string in its definition.
  • App/ontology/batch_load - (batch upload or sync)
  • Dump an OBO formatted file (dump OBO).
  • App/ontology/proofer - (proof)
  • A few non-traditional methods to visualize the ontology (visualize).
  • App/ontology/admin - (Manage)
  • 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.


[edit] General information

[edit] Use

There is some information on how the ontology is being used here at the Hymenoptera Anatomical Ontology wiki. A public example of the ontology in use can be found here. 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.

[edit] 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'. Check the project settings to set a default namespace, public ontology, root term, inclusion/exclusion keywords, remark. More information regarding project level ontology setting are found in App/proj/edit

[edit] 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'.

[edit] 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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