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VIVO uses the common shorthand prefix when referring to an ontology in the ontology editor, such as bibo: (short for Bibontology), foaf: (short for Friend of a Friend), or core: (short for VIVO core). The prefix stands for the fully qualified namespace for the ontology – http://purl.org/ontology/bibo/ for the Bibontology, http://xmlns.com/foaf/0.1/ for FOAF, and http://vivoweb.org/ontology/core# for VIVO core.
When an ontology namespace has not been added to this list, no prefix appears before a class or property name in the ontology editor. If then a class or property name happens to be duplicated from one ontology to another (e.g., bibo:Image and foaf:Image), it's not evident on the VIVO ontology editor's pick lists which name is which.
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The added ontology should be visible in the ontologies listed under "Ontology List".
For example:
- To add the SWRC ontology to VIVO:
- Go to Site Admin > Ontology List > Add New Ontology
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- Ontology Name="SWRC"
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- Namespace URI=http://swrc.ontoware.org/ontology
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- Namespace Prefix="swrc"
- Create New Record button
Keep in mind
- Type namespace URIs carefully and include the final / or # depending on the namespace URI format of the ontology involved
- Adding an ontology namespace to VIVO's ontology list does not import the specified ontology's classes or properties (or data for individuals). To add an ontology with an RDFi file, please see Add/remove RDF
- If local requirements introduce the need to create additional ontology classes and properties for your installation of VIVO, do not create extensions in the VIVO core namespace or the namespace of any other existing ontology. First create a new ontology for your extensions as described above and give it a namespace with the following pattern: http://vivo.mydomain.edu/ontology/vivo-mydomain. For example, Cornell ontology extensions would be in the namespace (http://vivo.cornell.edu/ontology/vivo-cornell/) . Note the trailing right-slash character. Then, when creating classes or properties, be sure to select this new ontology in the "ontology" dropdown list.
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Site Admin > Data input - Add individual of this class*
- Choose a type of individual you want to create in the drop down menu
- Click on the
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- Add individual of this class button > Individual Editing Form
- Enter data into the following fields:
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- Individual Name, Specific Type [new moniker] and any others you wish.
For example: Add a Faculty Member
Site Admin > Data input - Add individual of this class
- Choose the class "Faculty Member" and click the button
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- Add Individual of this class > Individual Editing Form
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- Individual Name=Jane Faculty
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- Specific Type [new moniker]=Assistant Professor
NOTE: In Ontology terminology, an "individual" is equivalent to a node. A node is anything from a person to a conference.
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Class groups are what the name implies: informal groupings of classes to organize pick lists, search results, and the VIVO Index page. Most often they mirror the top levels of the class hierarchy, with notable exceptions: *
- Sometimes it is important to highlight one or two classes that may logically fall one place in the class hierarchy but warrant an independent category. At Cornell, for instance, courses are separated from other activities into their own class group to reflect their prominence in the academic life of the institution.
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- Some classes are not intended to serve as public, free-standing data elements such as people, organizations, grants, or publications. Examples include Educational Background, a class to hold information about one degree on a person's list of degrees in the educational background section of their VIVO profile. Information about a single degree earned would make little sense outside of the context of the person's profile and would not be added or modified out of that context.
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- A class that is not in a class group *will not appear on the pick list for adding new individuals*on the Site Admin page or on the list of classes (by class group) on the Index page. To add an individual in a class not in a class group, navigate to the class in the class hierarchy and click the Add New Individual in this Class button.
To review, add or edit class groups, see Class Groups.
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Site Admin > Class Hierarchy
- Click on class to be edited >
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- Class Control Panel
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- Edit Class button > Class Editing Form
- Change as desired:
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- Class name, Class group from pick list, Ontology from pick list (this would typically be your local ontology), and Internal Name (all lower case, no spaces between words)
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- Note that if the new class is not in a class group, it will not appear on the list of classes when adding individuals on the Site Admin or Individual Control Panel pages
- The
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- Display level and Update level choices should be left at the least restrictive level of public; these annotations on the class are not currently active
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- Add a short definition and example if possible
- Ignore (leave blank)
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- Display Limit and Display Rank, which are currently active on object and data properties only
- Leave any entries for
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- custom entry form, custom display view, custom short view, and custom search view as is (most frequently blank)
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- Submit changes - edited class should be visible under appropriate class group from Site Admin > Class Groups
To add a new class
Site Admin > Class Hierarchy
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To add a new subclass in the desired place in the hierarchy, navigate to the desired class via the hierarchy as described above or by selecting* Class Hierarchy > All classes* and searching for the name of the desired class in alphabetical order within the listing.
- Click on the name of the desired class for subdividing and select
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- Class Control Panel > Add New Subclass of This Class. (Or in rare cases when adding a top-level class, Class Hierarchy > Add new class > Class Editing Form)
- Add
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- Class name, choose appropriate Class group from pick list, choose your local Ontology from pick list, and add Internal Name (all lower case, no spaces between words)
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- Note that if the new class is not in a class group, it will not
appear on the list of classes when adding individuals on the Site Admin
or Individual Control Panel pages - The
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- Display level and Update level choices should be left at the least restrictive level of public; these annotations on the class are not currently active
- Add
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- short definition and example if possible
- Ignore (leave blank)
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- Display Limit and Display Rank, which are currently active on object and data properties only
- Leave any entries for
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- custom entry form, custom display view, custom short view, and custom search view as is (most frequently blank)
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- Submit changes - the Class Control Panel appears. To get back to the class hierarchy select Class Control Panel > Show Class Hierarchy or Class Control Panel > Show All Classes.
The added class should be visible in the Site Admin > Class Hierarchy, via Site Admin > Class Hierarchy > All classes, and under the appropriate class group from Site Admin > Class Groups
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Site Admin > Class Hierarchy
- Click on class to be edited >
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- Class Control Panel
- Click on
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- Add New Individual in This Class > Individual Editing Form
- Specify appropriate
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- Individual name, choose Specific type from pick list or add new Specific type by choosing [new moniker] and typing it in the field provided, add URL and Anchor Text for URL associated with the URL if desired, add Blurb to describe individual being added if appropriate.
- If appropriate (e.g., if item being added is time-associated) add
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- Sunrise (date item first becomes visible) and Sunset (date item stops being visible), add Timekey if item is to be sorted chronologically in a list of similar items.
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- Create New Record > Class Control Panel - added item should be visible upon clicking Show All Individuals in This Class.
To add a class autolink to a tab and associate all individuals/entities of a certain type with that class
For example: Add a Class Autolink to Librarian tab to bring items of type Librarian into Librarian tab)
- Go to tab
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- People at top of VIVO screen > click on tab/link Faculty > click on tab/link Librarians
- At the bottom of this page: "edit tab:
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- Librarians" > Tab Control Panel
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- Add Class Autolink > Tab=Librarians; Vclass=Librarian
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- Create New Record > Tab Control Panel > Vclass Librarian should be visible above Remove Checked Class Autolinks button
Class Groups
Class groups are a means to organize the classes in VIVO into groups. They represent the facets seen when VIVO is searched (people, activities, events, organizations, etc).
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Site Admin > Class Management - Class Groups *
- Class Groups screen - click on the class group you would like to edit > Classgroup Editing Form
- Change the
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- Class group name of the class group as desired
- Change the
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- Display rank of the class group to change where it displays in the Class Groups screen
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- Submit Changes > Class Groups screen - edited class group should show up according to the display rank number assigned
To add a new class group
Site Admin > Class Management - Class Groups *
- Class Groups screen - click on Add new class group button
- Add desired
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- Class group name
- Change the
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- Display rank of the class group from default (-1) to change where it displays in the Class Groups screen
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- Create New Record > Class Groups screen - new class group should show up according to the display rank number assigned
Property Management
Properties
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Site Admin > Ontology Editor - Property Management - Object Property Hierarchy
- Click
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- Add new object property button > Property Editing Form
For example: Let's create a new object property called knows by filling the following fields.
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- Parent property = none (a root property)
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- Property Group = affiliation
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- Display Level = public
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- Update Level = public
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- Ontology = select the local ontology (see Site Configuration > Ontology Editor > Ontology List)
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- Local name for property = knows
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- Label for public display = knows
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- Inverse property ontology = select the local ontology again
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- Local name for inverse property = knownBy
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- Inverse property label for public display = known by
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- Domain class = Person
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- Range class = Person
Fields below this on the form control specialized functionality and may be left blank or in their initial state.*
- Public Description = Enter any explanatory message for users when adding or editing this property
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- display tier for this property = leave blank for now. Once you have some examples populated, compare how the order of this property's display vis a vis other properties in the affiliations group and adjust this value as necessary to control property display order. You may also wish to move this property to another property group such as contact if you wish to have it appear lower down on a person's VIVO page.
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- display tier for this property's inverse = leave blank for now. Note that an object property and its inverse may be in different groups as well as have different display rank values.
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- related object individuals to display without collapsing = 5. You may have noticed that VIVO collapses long lists of related individuals to save vertical space on a page. This number controls how many are displayed before the rest of the list are collapsed. This setting is on a per-property basis, meaning that one person can't elect to show 3 friends and another 25.
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- sort related individuals by = blank. Normally related individuals are sorted in alphabetical order, which works well for names of people and departments but also means that people's names are optimally entered last name first and departments should not all start with "Department of". Seminars may, however, be optimally sorted by the date and time they are to be offered, and news releases by their release dates.
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- sort direction = blank. Enter "desc" to reverse the normal ascending sort order.
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- data property by which to sort related individuals = select data property The original VIVO options for sorting related entities were driven by a special, pre-defined set of data properties including the individual name, "timekey" (date and time for an event), "sunrise" (a creation date for the individual), and "sunset" (an end date for the individual). This set of options can now be expanded to any data property, and the select list includes a full list of data properties from any ontology in the VIVO system. Note that not all data properties will appear on editing forms due to domain restrictions on data properties and the operative range restrictions on the object property currently being edited. For our example we are dealing with the type Person, so picking a data property from the country names ontology as a sort property would make no sense.
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- transitive = blank. Under OWL 2.0, properties may be declared transitive, meaning in our example that if person A knows B, and B knows C, A also knows C. This is not necessarily true, so do not check this box. At this point VIVO does nothing with this setting if checked except enable the setting to be passed to reasoners.
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- symmetric = blank. This setting indicates that if the property is asserted in 1 direction, it should automatically be asserted in the other direction. For our example, if A knows B, B may or may not believe he or she knows A, so leave it unchecked.
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- functional = blank. This setting would indicate that there can only be one statement of this object property for any one subject individual. VIVO does not yet enforce this setting, either through how it provides editing controls or by any kind of data validation.
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- inverse functional = blank. This setting provides a further limitation on values by requiring that only one statement for this property be present for each subject individual, but also that the related individual be unique – no other individual could have a property statement with the same range object. VIVO does not yet enforce this setting either.
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- custom entry form = blank. This is used to provide the name of a JSP file substituted by VIVO for the normal default object property editing form. It should only be populated by your VIVO system administrator, and any entry here not corresponding to a working JSP file in the correct directory on the local VIVO server will cause a system error.
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- delete object when statement deleted? = blank. As noted on the form itself, this should be checked only if the implcations are fully understood, and refers to the deletion of dependent resources such as Educational Background entries that could only apply to one individual. Warning: checking this box may cause unintended and unwanted data deletion!
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- select from existing choices when adding statements? = checked (this is the default behavior). For most object properties it is natural to offer a list of choices for the object individual based on the range class specified for the property above (or on a property restriction added only for members of a certain class). Occasionally this behavior is not desired, as with the educational background example just above, when one person should not pick any individual belonging to any other person. When this box is unchecked, the only option presented when adding a new value of this property is to create a new individual of the appropriate type specified as the range class of the property.
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- offer create option = blank. This controls whether new individuals may be added when the users thinks no appropriate object individual yet exists, and triggers a picklist of the appropriate classes for object individuals. An example of when this would not be appropriate would be when selecting a country involved in an International Activity – since a standard ontology of country names has been added to VIVO, users should not be free to add additional countries.
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- sort related object individuals of inverse property by = blank. See similar setting above. This is likely to go away in favor of simpler controls, since object properties and their inverses are now separately editable.
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- inverse sort direction = blank. Also likely to go away for the same reason.
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- related object individuals of non-inverse property to display without collapsing = 5. Also likely to go away for the same reason.
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- Example = Enter a value if you wish to clarify the meaning of a property
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- Description for ontology editors = Enter information here that will not be displayed to users but is visible to ontology editors and would be exported with any RDFi version of the ontology from this VIVO installation.
Save your work by clicking Create New Record and return to the Object Property Control Panel screen for the new object property created.
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Site Admin > Ontology Editor - Property Management - Data Property Hierarchy
- Click the
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- Add new data property button > Datatype Property Editing Form
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- Property Name: create a new property that designates a local institution ID (i.e., UFID, WashID, UFDeptID, etc.
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- Property Group=identity
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- Display Level: this may vary depending on property. For person ID numbers, choose self-authenticated (available for viewing once the person has logged in) for department IDs choose Curators and Admin, since other users would typically have no need to see them.
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- Update Level: this may vary depending on the property. For ID numbers we will choose "nobody" (ID numbers should be entered by data ingest from the controlled Human Resource system of record)
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- Ontology: choose the local ontology (Florida, Cornell, WashU, Scripps, etc.) Adding a local ontology is described in the Site Administration > Ontology List section of this user guide.
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- Local Name: "washId" or "ufId" or "ufDeptId" Should be in camel case – start with lowercase, capitalize new words within it, and not include spaces
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- Domain Class=Person (Department IDs should use the Organization domain to be applicable across divisions, schools, centers, programs, and other units within universities)
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- Range Datatype=string (unless your institution's ids are guaranteed to always be an integer value, in which case use "integer between -2147483648 and 2147483647")
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- Functional property (has at most one value for each individual)= checked. This setting alerts the VIVO reasoner that only one value should be present for this property for any subject individual. Use the separate Display Limit control below to control whether users are presented the option of adding more than one value.
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- Example=provide several examples of valid local ids for your institution
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- Description for ontology editors=Provide any information as to why the datatype and range class are specified as they are
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- Public Description=This text will be inserted at the top of the form users see when they edit an id value – make it clear what you expect the editor or curator to enter, such as "Enter this person's University of Florida ID number"
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- Display Tier=This number controls the ordering of properties within one property group on a VIVO page. The property group's own display rank value controls ordering of groups. Lower numbers are drawn first.
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- Display Limit=1. This is a VIVO-specific control that affect the user edit controls but not the logic in the reasoner. Set this to 1 for any property you wish to limit to a single value per subject individual, even if the property itself is not set to be functional as part of its definition for reasoning processes.
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- custom entry form=blank. VIVO currently has no custom forms for data properties.
When all desired information has been entered, save the new data property using the Create New Record button. The Datatype Property Control Panel screen is shown with the new property as the active property.
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Site Admin > Property Management - Property Groups
- Click on property group to be edited >
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- Property Group Editing Form
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- Property group name=groupname example
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- Public description: fill in as desired to provide a brief explanation of what the property group is intended for--to show up on the list.
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- Display rank: if desired to change rank of property group display on the list
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- Create New Record button > Property Groups (edited property group should be visible at appropriate display rank)
To add new property group
Site Admin > Property Management - Property Groups
- Click on
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- Add new property group button > Property Group Editing Form
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- Property group name=groupname example
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- Public description: fill in as desired to provide a brief explanation of what the property group is intended for--to show up on the list.
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- Display rank: if desired to change rank of property group display on the list
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- Create New Record button > Property Groups (new property group should be visible at appropriate display rank)
Verbose Property Listing
Turning verbose property listing on will provide property information as an aid to specifying the desired order of appearance of what can become a large number of object and data properties appearing on a VIVO page.
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