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
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).
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: name of term, 2. internal mx id, 2. xref (if applied), 3. term curator and year.
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)
- 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.
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.
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
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'.