Difference between revisions of "App/ontology"

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== Overview ==
 
== 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.  
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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. From this page you can:
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* click 'new' to add a new term
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* click 'list' to view a list of existing terms
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* search for a term
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* choose one of many options from the options list
  
 
== Welcome Screen ==
 
== Welcome Screen ==
[[Image:welcome.png]]
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[[Image:Ontology.png|700px]]
 
<br />
 
<br />
 
<p>
 
<p>
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<br />
 
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<br />
 
<br />
== Search for Term ==
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== Search for a Term ==
 
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[[Image:search.png]]
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<br />
 
<br />
 
<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: name of term, 2. internal mx id, 2. xref (if applied), 3. term curator and year.
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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: label (purple), class (green) or tag (orange).
 
<br />
 
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<br />
 
<br />
  
== Add a Term ==
 
[[Image:AddTermv2.png]]
 
  
Adding terms is also fairly easy:
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== Options ==
# 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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== Add a Relationship ==
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[[Image:Ontology_options.png|700px]]
[[Image:RelateTerms.png]]
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<br />
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.
 
<br />
 
<br />
 
 
== Add Tags ==
 
[[Image:tag.png]]
 
<br>
 
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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A list and explanation of [[ontology specific keywords]].
 
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== Mark Up Your Definitions ==
 
[[Image:mark.png]]
 
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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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== Other Options ==
 
 
=== Batch Upload ===
 
[[Image:batch.png]]
 
<br />
 
You can also batch load a list of terms you have in simple text.<br />
 
<br />
 
<br />
 
 
=== Manage the Ontology ===
 
[[Image:Manage ontology.png]]
 
<br />
 
<br />
 
 
=== Navigate and Create within a Tree ===
 
[[Image:Tree ontology.png]]
 
<br />
 
<br />
 
 
=== Filter by Tags ===
 
[[Image:Tag filter.png]]
 
<br />
 
A list and explanation of [[ontology specific keywords]].
 
<br />
 
<br />
 
 
=== Filter by Personally Edited ===
 
[[Image:Filter personally edited.png]]
 
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<br />
 
 
=== Extract Terms from a Block of Text ===
 
[[Image:Proffer not public.png]]
 
<br />
 
<br />
 
 
=== Other Options ===
 
 
There are many other options including:  
 
There are many other options including:  
 
* List by first letter of term (by first letter).
 
* List by first letter of term (by first letter).
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* List of terms without xrefs (without xrefs).
 
* List of terms without xrefs (without xrefs).
 
* List of the latest edits (latest edits).
 
* 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)
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* 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.
 
* 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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* [[App/ontology/tree]] - (tree)
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* [[App/ontology/filter]] - (tag filter)
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* [[App/ontology/list_personal]]
 
* Search definitions using a text string (search definitions).  Returns all the terms that contain that string in its definition.
 
* Search definitions using a text string (search definitions).  Returns all the terms that contain that string in its definition.
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* [[App/ontology/batch_load]] - (batch upload or sync)
 
* Dump an OBO formatted file (dump OBO).
 
* Dump an OBO formatted file (dump OBO).
* A few non-traditional methods to visualize the ontology (visualize).  
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* [[App/ontology/proofer]] - (proof)
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* A few non-traditional methods to visualize the ontology (visualize).
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* [[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.
 
* 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 ==
 
== General information ==
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=== Use ===
 
=== Use ===
  
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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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.
  
 
=== Configuration ===
 
=== 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'. 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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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]]
  
 
=== In App usage ===
 
=== In App usage ===

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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