Mobi User Manual

The Ontology Project Tab displays high-level information about the ontology. This includes the ontology annotations and properties, ontology imports, and a preview of the serialized ontology RDF.

The top of this tab contains the title of the ontology and its IRI. The IRI shown is the Version IRI, Ontology IRI, or a blank node identifier. The IRI can be copied quickly by clicking on it.

On the upper left side of this tab is a section containing a list of all the applied OWL Ontology Properties and Annotations. There are controls included to add, remove, and edit these properties.

On the lower left side of this tab is a section containing a list of all direct and indirect ontology imports. If an imported ontology could not be resolved, it will appear red. To add a new imported ontology, click on the plus button and either enter the IRI of an ontology available on the web or select an ontology within Mobi. To refresh the cached versions of the imported ontologies and attempt to resolve any unresolved imports, click on the refresh button.

On the right of this tab is a card used to generate a preview of the ontology as RDF. There is a drop down with several different RDF serializations to choose from. Clicking Refresh will generate a preview of the saved state of the ontology in the specified RDF format in the area below. The preview will be limited to the first 5000 results. Additionally, there is a button for downloading the ontology in the selected format.

The Overview Tab provides quick access to classes and their associated properties as compared to the Classes and Properties tabs. Properties are associated to classes through the use of rdfs:domain.

The left side of this tab contains the list of all classes and their associated properties, including imports. Any properties that have no rdfs:domain are grouped into a folder in the hierarchy called "Properties". You can expand a class to view its properties by clicking the "+" icon or double-clicking the class name. Properties are displayed with a symbol representing the data type of the range property. If an entity has been changed and those changes have not been committed, it will appear bold and an indicator will be shown on the right of the entity name. Imported classes and properties will appear grey and italicized. The list also includes a search bar that will filter the list to classes/properties with annotations or local names containing your search query and the ability to apply one or more filters. The Hide unused imports filter will remove all imported entities from the list that are not used by any of the entities defined in the ontology. The Hide deprecated entities filter will remove all entities annotated with the owl:deprecated property. Clicking on an item in the tree will load that entity’s information into the other sections in this tab.

The title of the selected class or property, its IRI, and its type(s) are displayed at the top of the tab along with buttons to delete the entity and view its change history (see Entity History). The IRI can be copied quickly by clicking on it. The middle sections in this tab allow you to add, remove, and edit Annotations and Axioms for the selected class or property. Imported classes and properties cannot be edited.

If you selected a property, a section with checkboxes for adding different characteristics to the selected property is shown in the top right of the Overview Tab.

The last section on the right displays all the locations where the selected entity is used within the saved state of the ontology. For classes, this is anywhere the selected class is used as the object of a statement. For properties, this is anywhere the selected property is used as the predicate or object of a statement. Usages are grouped by the predicate of the statement and can be collapsed by clicking on the predicate title. Links in the usages section, as with links in various other components of the editor, can be clicked to navigate to that entity. If the number of usages exceeds 100, a button to load the next 100 is shown at the bottom of the section.

The Classes Tab allows you to view, create, and delete classes in the opened ontology.

The left side of the tab contains a hierarchical view of the classes, including imports, nested according to their rdfs:subClassOf property. That is, a class’s children are classes which are defined as subclasses of the particular class. Since classes can be defined as a subclass of multiple classes, they may appear several times within the hierarchy. If a class has been changed and those changes have not been committed, it will appear bold and an indicator will be shown on the right of the class name. Imported classes will appear grey and italicized. The list also includes a search bar that will filter the list to classes with annotations or local names containing your search query and the ability to apply one or more filters. The Hide unused imports filter will remove all imported classes from the list that are not used by any of the entities defined in the ontology. The Hide deprecated entities filter will remove all classes annotated with the owl:deprecated property. Clicking on an item in the hierarchy will load that class’s information into the other sections in this tab. Double clicking on a class with children will toggle the display of the children.

The title of the selected class, its IRI, and its type(s) are displayed at the top of the tab along with buttons to delete the class and view its change history (see Entity History). The IRI can be copied quickly by clicking on it. The middle sections in this tab allow you to add, remove, and edit Annotations and Axioms for the selected class. Imported classes cannot be edited.

The section on the right of the Classes Tab displays all the locations where the selected class is used within the saved state of the ontology. That is, anywhere the selected class is used as the object of a statement. Usages are grouped by the predicate of the statement and can be collapsed by clicking on the predicate title. Links in the usages section, as with links in various other components of the editor, can be clicked to navigate to that entity. If the number of usages exceeds 100, a button to load the next 100 is shown at the bottom of the section.

The Properties Tab allows you to view, create, and delete properties in the opened ontology.

The left side of the tab contains a hierarchical view of the data, object, and annotation properties, including imports. The data, object, and annotation properties are grouped into three separate folders within the hierarchy that will open and close when clicked. Properties are nested according to their rdfs:subPropertyOf property. That is, a property’s children are properties which are defined as subproperties of the particular property. Properties are displayed with a symbol representing the data type of the range property. If a property has been changed and those changes have not been committed, it will appear bold and an indicator will be shown on the right of the property name. Imported properties will appear grey and italicized. The list also includes a search bar that will filter the list to properties with annotations or local names containing your search query and the ability to apply one or more filters. The Hide unused imports filter will remove all imported properties from the list that are not used by any of the entities defined in the ontology. The Hide deprecated entities filter will remove all properties annotated with the owl:deprecated property. Clicking on an item in the hierarchy will load that property’s information into the other sections in this tab. Double clicking on a property with children will toggle the display of the children.

The title of the selected property, its IRI, and its type(s) are displayed at the top of the tab along with buttons to delete the property and view its change history (see Entity History). The IRI can be copied quickly by clicking on it. The middle sections in this tab change depending on whether you have selected a data, object, or annotation property. If the selected property is a data or object property, the sections for adding, removing, and editing Annotations and Axioms are shown. If the selected property is an annotation property, only the Annotation sections is shown. Imported properties cannot be edited.

If the selected property is a data or object property, a block with checkboxes for adding different characteristics to the selected property is shown in the top right of the Properties Tab. Imported properties cannot be edited.

The last section on the right of the tab displays all the locations where the selected property is used within the saved state of the ontology. That is, anywhere the selected property is used as the predicate or object of a statement. Usages are grouped by the predicate of the statement and can be collapsed by clicking on the predicate title. Links in the usages section, as with links in various other components of the editor, can be clicked to navigate to that entity. If the number of usages exceeds 100, a button to load the next 100 is shown at the bottom of the section.

The Individuals Tab allows you to view, edit, create, and delete individuals in the opened ontology.

The left side of the tab contains a view of all individuals, including imports, nested under their classes based on the rdfs:subClassOf property. If an individual has been changed and those changes have not been committed, it will appear bold and an indicator will be shown on the right of the individual name. Imported individuals will appear grey and italicized. The list also includes a search bar that will filter the list to individuals with annotations or local names containing your search query and the ability to apply one or more filters. The Hide unused imports filter will remove all imported individuals from the list that are not used by any of the entities defined in the ontology. The Hide deprecated entities filter will remove all individual annotated with the owl:deprecated property. Clicking on an item in the list will load that individual’s information into the other sections in this tab.

The title of the selected individual, its IRI, and its type(s) are displayed at the top of the tab along with buttons to delete the individual and view its change history (see Entity History). The IRI can be copied quickly by clicking on it. The section to the center and right of the tab allow you to add, remove, and edit Data, Object, and Annotation Properties for the selected individual. The options for Data and Object Properties are populated from the ontology and its imports. The user entered values in both the annotation and datatype property overlays are validated against the type field of the overlay. Imported individuals cannot be edited.

The types of an individual are editable by clicking the pencil icon at the end of the types list. The overlay allows you to add and remove types from the ontology and its imports. The "Named Individual" type is required.

The Schemes Tab will appear if the editor detects the opened ontology is a SKOS vocabulary. It displays information about all the concept schemes and their directly related concepts defined in the opened vocabulary.

The left side of the tab contains a hierarchical view of the concept schemes, including imports. The top level items are the concept schemes, or subclasses of skos:ConceptScheme, and their children are all concepts, or subclasses of skos:Concept, within that scheme. This could be defined through the skos:hasTopConcept, skos:topConceptOf, or skos:inScheme properties. If a concept scheme or concept has been changed and those changes have not been committed, it will appear bold and an indicator will be shown on the right of its name. Imported concept schemes and concepts will appear grey and italicized. The list also includes a search bar that will filter the list to concepts/schemes with annotations or local names containing your search query and the ability to apply one or more filters. The Hide unused imports filter will remove all imported schemes from the list that are not used by any of the entities defined in the ontology. The Hide deprecated entities filter will remove all schemes annotated with the owl:deprecated property. Clicking on an item in the hierarchy will load that concept scheme’s or concept’s information in the other sections in this tab. Double clicking on a concept scheme with children will toggle the display of the children.

The title of the selected concept scheme or concept, its IRI, and its type(s) are displayed at the top of the tab along with buttons to delete the entity and view its change history (see Entity History). The IRI can be copied quickly by clicking on it. The middle sections in this tab allow you to add, remove, and edit Annotations, Data Properties, and Object Properties for the selected concept scheme or concept. Imported concept schemes and concepts cannot be edited.

The third section on the right of the Schemes Tab displays all the locations where the selected concept scheme or concept is used within the saved state of the vocabulary. This is anywhere the selected concept scheme or concept is used as the object of a statement. Usages are grouped by the predicate of the statement and can be collapsed by clicking on the predicate title. Links in the usages section, as with links in various other components of the editor, can be clicked to navigate to that entity. If the number of usages exceeds 100, a button to load the next 100 is shown at the bottom of the section.

The Concepts Tab will appear if the editor detects the opened ontology is a SKOS vocabulary. The Concepts Tab displays information about all the concepts defined in the opened vocabulary.

The left side of the tab contains a hierarchical view of the concepts, including imports. The concept hierarchy is determined using all of the SKOS broader and narrower properties. If a concept scheme or concept has been changed and those changes have not been committed, it will appear bold and an indicator will be shown on the right of its name. Imported concepts will appear grey and italicized. The list also includes a search bar that will filter the list to concepts with annotations or local names containing your search query and the ability to apply one or more filters. The Hide unused imports filter will remove all imported concepts from the list that are not used by any of the entities defined in the ontology. The Hide deprecated entities filter will remove all concepts annotated with the owl:deprecated property. Clicking on an item in the hierarchy will load that concept’s information in the other sections in this tab. Double clicking on a concept with children will toggle the display of the children.

The title of the selected concept, its IRI, and its type(s) are displayed at the top of the tab along with buttons to delete the concept and view its change history (see Entity History). The IRI can be copied quickly by clicking on it. The middle blocks in this tab allow you to add, remove, and edit Annotations, Data Properties, and Object Properties for the selected concept. Imported concepts cannot be edited.

The third section on the right of the Concepts Tab displays all the locations where the selected concept is used within the saved state of the vocabulary. This is anywhere the selected concept is used as the object of a statement. Usages are grouped by the predicate of the statement and can be collapsed by clicking on the predicate title. Links in the usages section, as with links in various other components of the editor, can be clicked to navigate to that entity. If the number of usages exceeds 100, a button to load the next 100 is shown at the bottom of the section.

The Search Tab allows you to perform a keyword search through all the entities within the saved state of the opened ontology and its imports.

The left side of the tab contains a simple search bar and a list of search results. To perform a search, type a string into the search bar and press the ENTER key. The results are separated by type headers which are collapsible. Each result is displayed with its display name. Properties are displayed with a symbol representing the data type of the range property. Clicking on a result will load that entity’s information into the right section of this tab. The right section displays the entity’s display name, IRI, types, and properties. The parts of the property values that match the search text will be highlighted. The right section also includes a Go To button that will open the entity in the appropriate tab. Double clicking on an entity in the list will also open that entity in the appropriate tab.

The Visualization Tab depicts the ontology in a force-directed graph layout. Each node represents a class, with dotted lines symbolizing the relationship between parent class and subclass, and solid lines representing the object properties.

The ontology visualization feature enables users to easily understand data within an Ontology by allowing them to navigate across the classes and their relationships. The feature allows users to zoom, pan, select, drag, hover, and click nodes and links.

The number of classes displayed is limited to 500. Any in progress changes you have will not be rendered until they are committed. After initial graph calculation, the state of the graph will persist while users keep the Ontology open. The graph will only be re-rendered when there is a new commit.

The side panel of the Visualization tab displays a searchable list of all the classes in the import closure (i.e. direct and imported) grouped by parent ontology. The checkboxes next to each class indicate whether a class is currently shown in the visualization and can be toggled to customize the displayed graph. Selecting the checkbox next to a class will update the graph by adding a new node with the class name, subclass relationships with other displayed classes, and object properties with other displayed classes. Deselecting the checkbox next to a class will remove these three things. Selecting a class in the side panel will highlight the node in the graph if displayed. Selecting a node in the graph will also highlight in the side panel. The side panel also includes a "Filter" dropdown with three options to help find the classes of interest in the list.

The side panel can be hidden or shown with a button.

The check out select box located underneath the selected ontology in the left display, provides a list of all the available branches and tags on the ontology. To checkout a branch or tag, simply select the branch in the drop-down menu. Checking out a tag will open the ontology at the tagged commit in read-only mode. If you have checked out a commit from the Commits Tab, the commit will be in the dropdown list and show as selected. Note that the select box will be disabled if you have any uncommitted changes on the current branch. To edit a branch name or description, click on the edit icon next to the branch in the drop-down menu. You cannot edit the master branch of an ontology.

To delete a branch or tag, click on the delete icon next to the branch/tag in the drop-down menu. If a branch is deleted, all commits on that branch that are not part of another branch will be removed, as well as the branch itself. If a tag is deleted, the commit is not removed. Note that these actions cannot be undone.

Every edit made to an entity within an ontology is automatically saved and an indicator is shown in the top right if the most recent changes have been saved successfully. The Changes Tab displays all saved and uncommitted changes in the opened ontology. Saving changes without committing allows a user to edit an ontology through a number of browser sessions before making any commits to the commit history. These changes are unique to the user, and are available to other users once a commit is performed. They are grouped by individual entity and display the triples on the entity grouped by property. When a “Show Full” toggle is active, the changes display is updated to include all the other triples on that changed entity.

Within each collapsible block in the list are the added and deleted triples for a particular entity IRI. If there are no changes to the ontology, this page will be empty. To commit these changes, select the Commit Changes button in the Button Stack. To remove these changes, click Remove All Changes.

If new commits have been made to the branch by other users while you are editing or viewing an ontology, a warning symbol will be displayed in the section title and a message will be displayed in the section notifying you that there are new commits on the branch. If you have no saved changes, there will be a link to update the current ontology by pulling in the latest changes. If you have saved changes, there will be a message notifying you to either commit your changes or remove them. If you choose to commit your changes, you can still continue working and there will be a link to pull in the latest changes and re-sync with the branch.

The Ontology Editor also supports merging the head commit of the branch you are currently viewing into the head commit of another branch. Two branches can only be merged if there are no conflicts between the head commits of each branch. To perform a merge, select the green Merge Branches button in the button stack.

The merge view displays the name of the current (source) branch, a select box for the branch (target) you want to merge into, and a checkbox for whether or not you want the source branch to be deleted after it is merged. The view also shows an aggregated view of all changes made in the source branch that will be merged into the target branch along with a list of all the commits that will be added to the target branch from the source branch.

Clicking Submit will attempt to perform the merge. If there are no conflicts between the changes on both branches, a new commit will be created merging the two branches, and a success message will appear in the top right corner of the screen.

Conflicts arise when the application cannot determine how to automatically merge specific changes to entities between two branches. If conflicts exist between the two branches, the merge process will be halted and the screen will update to notify you of those conflicts and provide you a way to resolve them. Each conflict is listed by entity within the ontology and with a marker indicating whether or not it has been resolved. Click on a conflict in the list to start resolving them.

When resolving a conflict, the tool displays the changes to the entity from both branches. To resolve the conflict, select the version of the entity you wish to keep. You can either click the Back to List button to go back to the list of all the conflicts or the Previous or Next buttons to iterate through the list of conflicts.

Once all conflicts have been resolved, the Submit with Resolutions button will become active and you can complete the merge operation. Completing the merge will create a new commit that incorporates your conflict resolutions into the target branch, and displays a success message in the upper right corner of the screen.

The Commits Tab provides a table and graph of all the commits made in the history of the branch you are currently viewing. The username of the creator, ID, message, and date for each commit are displayed within the table. The graph displays each commit connected to its parent commits continuing backwards until the initial commit. To view more information about a particular commit in the history, such as the added and deleted statements, click on its id or associated circle in the graph. The table also includes buttons for "checking out" a commit in the history. Clicking a View button will open the ontology at that commit in read-only mode. This is useful for creating tags to indicate versions on the ontology (see Button Stack and Checking Out Branches/Tags/Commits).

Clicking on a See History button next to a selected entity in one of the tabs will open a view containing the change history of that specific entity in the ontology. The view is split into two columns. The left side contains a dropdown containing all the commits where that entity was changed and defaults to the latest commit. Any added triples will be green and any deleted triples will be red. The right side contains a table of all the commits where that entity was changed. The table behaves the same as the table in the Commits Tab, just without the graph. To return to the main editor, click the back button in the top left.

The Edit IRI overlay provides the user with a simple way to edit and create valid IRIs. The Begins with field (required) is the beginning of the IRI. This is more commonly known as the namespace. When editing the IRI of entities within an ontology, this value is typically the ontology IRI. The Then field (required) is the next character in the IRI. This value can be thought of the separator between the namespace and local name (described below). The provided values for the Then field are "#", "/", and ":". The Ends with field (required) is the last part of the IRI. This value is commonly known as the local name. It is used in the drop down lists in this application as the easiest way to identify what the IRI references. Clicking the refresh button on the left will reset the three fields to their original values. You cannot create/save an edited IRI that already exists within the ontology. Clicking Cancel will close the overlay. Clicking Submit will save the IRI with the entered values for the selected entity and update the ontology.

The Axiom Overlay is how you add new axioms to entities in your ontology. The Axiom dropdown provides a list of common axioms for the type of entity you have selected. Once selected, there are two ways to add a value. The first is choosing from a list of entities within the ontology and its imports. The second is writing out a class expression or restriction in Manchester Syntax in the Editor. Entities are referenced by their local name and must be present in the ontology or its imports.

Property Value Displays are a common way Mobi displays multiple values for a property on an entity. These properties could be data properties, object properties, annotations, axioms, etc. The display consists of the title section and the values section. The title section includes a bold title and the property IRI. The values section lists all the values set for the displayed property along with the type, if the value is a literal, and edit and delete buttons when you hover over the value. The functionality of the edit and delete buttons for values differ depending on where the Property Value Display is being used. If a value of a property is a class restriction or expression, it will be represented in a simplified format or Manchester Syntax if it is supported. These values can be deleted, but not edited.

The Button Stack is visible in any Ontology tab in the bottom right hand corner of the screen and holds a variety of buttons that are shown when the stack is hovered over.

To add a new entity to the ontology, click on the main Create Entity button in the stack. This will open an overlay with options for what kind of entity to create and once you have selected an option, an appropriate overlay will be shown for creating that type of entity. After creating the entity, a snackbar will appear at the bottom allowing you to navigate directly to your new entity.

If you have made changes to an ontology, the Commit Changes button will become active. Clicking on this button will bring up the Add Commit overlay.

The Add Commit overlay provides a textarea for you to enter in a Comment that will be associated with that commit. This commit usually specifies what changes where made in the commit so that others can read the message and understand what happened at that point in time. You can still commit your changes if you are not currently viewing the head commit of the current branch. Clicking Cancel will close the overlay. Clicking Submit will add all your saved changes to a new commit object whose parent is the commit you were viewing and close the overlay.

See the Merging Branches section for details on how the merging branches works.

The Create Branch button allows you to create a new branch from the commit and branch you are viewing, including past commits. This action can be performed even if you have unsaved or saved changes. Clicking on the button will bring up the Create New Branch overlay.

The Create New Branch overlay provides fields for entering information about the branch as a whole. The Title field (required) will set the dcterms:title of the branch. The Description field will set the dcterms:description of the branch. Clicking Cancel will close the overlay. Clicking Submit will create a new branch with the entered information whose head commit was the commit you were viewing and close the overlay.

The Create Tag button allows you to create a human readable and persistent pointer to the commit you are currently viewing. Clicking this button will bring up an overlay where you can type in the title for the Tag and customize it’s IRI. Once the Tag is created, the ontology will open the ontology in read-only mode at the tagged commit.

The Upload Changes button allows you to upload a new version of your ontology from a file and apply the changes. Clicking this button will bring up an overlay where you can select the file with the changed ontology. Uploaded changes will not be automatically committed, but will allow you to review changes before making a new Commit.

The table below describes which file extensions are mapped to which RDF Formats when an ontology file is uploaded to Mobi. In the event more than one RDF Format is possible for a single extension, all RDF Formats are attempted.

In order to create a branch or tag, click the corresponding button in the action bar.

The branches dropdown provides a searchable list of branches and tags which can be checked out. To checkout a branch or tag, simply select the branch in the drop-down menu. Checking out a tag will open the ontology at the tagged commit in read-only mode. If you have checked out a commit from the commit history table, the commit will be in the dropdown list and show as selected. Note that the ability to check out a branch or tag will be disabled if you have any uncommitted changes on the current branch.

To delete a branch or tag, click on the delete icon next to the branch/tag in the drop-down menu. If a branch is deleted, all commits on that branch that are not part of another branch will be removed, as well as the branch itself. If a tag is deleted, the commit is not removed. Note that these actions cannot be undone.

Changes that have been uploaded to a shapes graph record are automatically saved and an indicator is shown in the action-bar. Users are able to reach the changes page by clicking the Show Changes button found in the right-hand side of the action bar.

The changes page displays all saved and uncommitted changes in the opened shape graph. Saving changes without committing allows a user to edit an shape graph through a number of browser sessions before making any commits to the commit history. These changes are unique to the user, and are available to other users once a commit is performed. They are grouped by individual entity and display the triples on the entity grouped by property. When a “Show Full” toggle is active, the changes display is updated to include all the other triples on that changed entity.

The Changes Page displays all the uncommitted changes and the commit history table for the opened shapes graph record. This provides users the ability to upload changes without committing and allows a user the opportunity to review proposed changes to a shapes graph in a more digestible manner before adding any commits to the commit history. Clicking the Remove All Changes button will clear all the changes uploaded into the shape graph, resetting to the state of the current commit.

Users can also view a shapes graph record at a specific commit in time by clicking the View button next to the corresponding commit in the commit history table.

Merging branches works much the same as the Ontology Editor. By clicking the Merge Branch button found in the action-bar, users are brought to the merge view of the Shapes Editor.

The merge view displays the name of the current (source) branch, a select box for the branch (target) you want to merge into, and a checkbox for whether or not you want the source branch to be deleted after it is merged. The view also shows an aggregated view of all changes made in the source branch that will be merged into the target branch along with a list of all the commits that will be added to the target branch from the source branch.

Clicking Submit will attempt to perform the merge. If there are no conflicts between the changes on both branches, a new commit will be created merging the two branches, and a success message will appear in the top right corner of the screen.

The Upload Changes button in the action-bar allows you to upload a new version of your shapes graph from a file and apply the changes. Clicking this button will bring up an overlay where you can select the file with the changed shapes graph. Uploaded changes will not be automatically committed, but will allow you to review changes before making a new Commit.

The Source Ontology Overlay allows you to select the source ontology for the mapping from all uploaded ontologies in the local Mobi repository.

The left side of the overlay contains a searchable list of all the ontologies in the local Mobi repository and a select for the version of the ontology to use. For most ontologies, this will only contain the "Latest" value. However, if an ontology was previously selected for a mapping and that ontology has changed since then, there will be an option for the "Saved" version of the ontology. The right side of the overlay displays information about the ontology from its record in the Catalog and a sample of the classes in that ontology. Setting the source ontology will remove any class and property mappings in the mapping that are incompatible. Class mappings and property mappings are incompatible if the class or property that is referenced no longer exists in the imports closure of the source ontology. Property mappings are also incompatible if they are a different type or have a different range.

The IRI Template overlay provides you a way to edit each portion of the IRI template of a class mapping. The template will be used to generate the IRIs for each instance created by a class mapping.

The Begins with field (required) is the beginning of the IRI. This is more commonly known as the namespace. The Then field (required) is the next character in the IRI. This value can be thought of the separator between the namespace and local name (described below). The provided values for the Then field are "#", "/", and ":". The Ends with dropdown field (required) is the last part of the IRI. This value is commonly known as the local name. The values in this dropdown are "UUID", which represents generating a unique identifier as the local name for each generated instance of each row, and the title of each column, which represents using the value of that column as the local name for each generated instance of each row. Clicking Cancel will close the overlay. Clicking Submit will save the IRI template.

The overlay for mapping into an ontology contains several configurations on how the mapping result data will be committed. First, you must select the Ontology and Branch that will receive the new commit. After that, there are radio buttons that will determine how the mapping result data will be treated when the commit is made. The first option will treat all the mapping result data as new data, meaning no existing data in the ontology branch will be removed. The second option will treat all the mapping result data as changes to the existing data on the ontology branch. This means that if there are entities or properties on entities in the ontology that are not present in the mapping result data, they will be removed.

A sample workflow using this tool would be to create an ontology in the Ontology Editor and create a branch that will received all mapped data commits. Then run your mapping from the Mapping Tool, committing to the new branch as additions. Finally in the Ontology Editor, merge that branch with the mapped data commit into the MASTER branch. Then any subsequent runs of the mapping with updated data would be committed as changes to the mapped data branch and merged into the MASTER branch.

The basic Mobi services can be configured using the following files:

By default, all resources besides provenance data are stored in the system repository which is an RDF triplestore located in the data/repos/system directory of the Mobi distribution. The provenance data is stored within the prov repository. Each repository in Mobi is uniquely identified by its id. To change the data location, id, or title of either repository, edit the dataDir, id, and title properties respectively in the appropriate file. Apache Karaf will dynamically reload any changes made to this existing file.

You can create new repositories to be used for storage in Mobi. First, choose either a "native" repository or a "memory" repository. These two types of repositories are defined in the NativeRepositoryConfig and MemoryRepositoryConfig classes in the com.mobi.repository.impl.sesame module. Once you have chosen the type of repository, make a new .cfg file in the {MOBI_HOME}/etc directory with a file name that starts with either "com.mobi.service.repository.native" or "com.mobi.service.repository.memory". In the file, set the id, title, and dataDir properties you wish for the repository. The file should look like this:

Apache Karaf will automatically recognize the new configuration file and create the new repository.

The repository that all Catalog resources are stored with is controlled within the com.mobi.catalog.config.CatalogConfigProvider.cfg file. The storage repository for all other types of data are controlled individually in other configuration files. To change each of these repository configurations, open the associated .cfg file and change the id of the repository.target property to be the id of the new repository. For example to change the repository for storing Catalog resources to the repository in the example above, you would open the com.mobi.catalog.config.CatalogConfigProvider.cfg file and edit the repository target line to be:

Apache Karaf will automatically detect the changes and reload the new configuration.

The configuration for user authentication, authorization, and management are stored in the following files in the {MOBI_HOME}/etc directory:

Mobi utilizes JAAS for user authentication and basic authorization. By default, user credentials and information are managed by the RdfEngine service which is configured with the com.mobi.jaas.engines.RdfEngine.cfg file. The file contains an id of the repository to be used for storage, the encryption settings for JAAS which are enabled to start, and the two default roles: "user" and "admin". Apache Karaf will automatically detect any changes and reload the updated configurations.

The default user for Mobi is "admin" with password "admin". To change the credentials of the "admin" user or perform any other user management activities, utilize the Administration page, the My Account page, or the appropriate REST endpoints.

For more advanced authorization functionality, Mobi uses the an Attribute Based Access Control (ABAC) system called XACML. Policies describing the attributes for allowing or denying individual access requests are managed by the XACMLPolicyManager service which is configured with the com.mobi.security.policy.api.xacml.XACMLPolicyManager.cfg file. The file contains an id of the repository to be used for storage, the location the XACML policy files should be stored in, and whether the policy file location should be created if it does not already exist. Apache Karaf will automatically detect any changes and reload the updated configurations.

In addition to the aforementioned files, Enterprise Mobi also supports LDAP and SSO integrations which are explained in Post-Installation Configuration.

The configuration for the Mobi Email Service is stored in the following file in the {MOBI_HOME}/etc directory:

The Mobi Email Service is built on the Apache Commons Email API. The Email Service provides the ability to connect to a provided SMTP server and send an email using a configured email account. By default, the service is configured to connect to a Gmail SMTP server in the com.mobi.email.api.EmailService.cfg file. The service has configurations for smtpServer, port, emailAddress, emailPassword, security, and emailTemplate. Please see below for different configurations of popular email services.

The Mobi Email Email Service supplies a default email template that works across most email clients. The default file is located in the {MOBI_HOME}/etc directory. If you want to provide your own email template, modify the emailTemplate configuration to the new email template with either a relative or absolute path to the file. The email service will resolve relative file paths for an email template using the {MOBI_HOME}/etc directory as the base directory.

The email service provides a method for doing a simple string replace on the !|$MESSAGE!|$ binding within the template. For more complex HTML inserts, the service provides a method to replace all HTML between the two !|$BODY!|$ bindings. Custom templates must have the aforementioned bindings (!|$MESSAGE!|$ & !|$BODY!|$). The !|$MESSAGE!|$ binding must be between two !|$BODY!|$ bindings. For example:

Before installing Mobi, create a service account on the host server. The account will be used to run Mobi. The service account should meet the following requirements:

On a standard RHEL/CentOS system, this can be created using the following command:

Mobi requires the latest version of Java 1.17 to operate. On a standard RHEL/CentOS system, there is no package available via yum to install. So we suggest Downloading the Oracle installer from here and running it manually using the following commands:

The JAVA_HOME environment variable must be set for the user running Mobi. On a standard RHEL/CentOS system (after running the rpm above) this can be set using the following commands:

Set the max heap size in $MOBI_DIST/bin/setenv (e.g. JAVA_MAX_MEM=4G). In version 1.21, to include the JAVA_MAX_MEM and JAVA_MIN_MEM variables in the Mobi startup, add the following line beneath them in the setenv file.

Change the default SSL port in $MOBI_DIST/etc/org.ops4j.pax.web.cfg

Mobi comes bundled with default self-signed SSL certificates stored in a Java Keystore file in etc/keystore. To provide your own SSL certificates, simply replace the default keystore file with your own:

If there is a keystore password, it can be configured in the $MOBI_DIST/etc/org.ops4j.pax.web.cfg file using the following configuration properties:

We recommend that you configure Mobi as a Linux service for starting Mobi automatically as the service user. Follow the instructions below to implement the service on a standard RHEL/CentOS environment.

Once the service is enabled, Mobi should be running. The Mobi process will start and stop automatically with the server. Any time you start and stop Mobi manually, run the following systemctl commands: sudo systemctl stop mobi and sudo systemctl start mobi.

To configure the web authentication token duration, you must create a file called com.mobi.jaas.SimpleTokenManager.cfg with the property detailed below and put it in the etc/ directory of your Mobi installation before starting the application, otherwise the token duration will use the default of 24 hours.

An example file would look like this.

In Enterprise deployments only, Mobi can be configured so that users can log into the application with the Users/Groups defined in your organization’s directory, you must create a file called com.mobi.enterprise.ldap.impl.engine.LDAPEngine.cfg with the following properties and put it in the $MOBI_DIST/etc/ directory before starting the application. If a property is not required, you can delete the line from the config file. The list of possible fields for the config file are shown in the table below.

An example file would look like this.

In Enterprise deployments only, Mobi can be configured to integrate with an SSO provider for authentication. LDAP can be configured alongside the SSO provider to retrieve additional user details, but it is not required. If configured, it is recommended to disable direct authentication against the LDAP directory by adding ldap.disable-auth = false to the com.mobi.enterprise.ldap.impl.engine.LDAPEngine.cfg file. Mobi supports SAML, OAuth 2.0, and OpenID SSO providers.

Mobi provides a way to automatically encrypt plaintext passwords stored within service configurations on startup and subsequent updates. The setup for this is very short. All you have to do is ensure that a file called com.mobi.security.api.EncryptionService.cfg exists in the $MOBI_DIST/etc directory and contains the following fields:

This encryption config is present and enabled by default, meaning your passwords will be automatically encrypted. An alternate way of providing an encryption master password is via environment variable. To configure the use of an environment variable, use the following fields:

If you use an environment variable, make sure before you start Mobi that you have stored a unique password as the value for that environment variable.

Once the encryption config is added, start Mobi and if a Mobi service configuration includes a plaintext password, it will encrypt the value and update the configuration file. To change an encrypted value, simply replace it with the new plaintext value in the configuration file and after a few seconds it will be automatically re-encrypted and the file will be updated.

The XML translator uses the hierarchical structure of the XML input file in order to construct classes and object properties.

When generating the ontology, each element is simultaneously treated as a class and object property if it has child elements and is regarded as a datatype property if it does not. The output will resemble a file similar to the one below.

The generated data file is composed of elements that have been deemed a class and that have literal values attached to it. Each instance is given a unique IRI based on the namespace of the ontology with a trailing UUID attached at the end.

Given a JSON file like below, the JSON translator will use the nested structure of JSON objects in order to construct classes and object properties.

An output ontology is then generated using the passed in IRI or a UUID as the namespace. Classes and object properties relating these classes are created based on the keys present in the input file.

The generated data file is created by utilizing the literal values of each key object. For each instance of a JSON object there is in the input file an RDF entity is created with the same namespace as the ontology.

The CSV translation tool is the only translator that does not create multiple classes or any object properties. A singular class is generated per file, with the name of the file being used as the name of the class.

Each column header is treated as a different datatype property, with the translator parsing a certain number of rows to determine the range of the property.

When creating the instance data, each row within the file is treated as an instance of the class with the cell values being the object of the triples generated by the datatype properties.

The following diagram illustrates the relationship between the various preference related classes and properties: