Link Filters

Link filters are used to pick certain links between terms from a collection of links between terms. Note that links are different kinds of objects than terms. Links represent relationships between terms.

In this guide, links are usually written in the form

child_term -relation-> parent_term

So if there is an is_a relationship between "heart development" and "development", that link would be written as

"heart development" -is_a-> "development"

The Link Filter Interface

To add or change link filters in a user configurable filter designer (such as the Global Filters component), click the "Link filters" tab

The link filter interface looks like this:

Notice the field that says "Self". This is called the "link facet". Other than this new field, the link filter interface looks exactly like the term filter interface.

The link facet determines what characteristics of the link will be considered when filtering. There are 4 possible link facets:

Child - This link facet indicates that the link should be filtered based on the attributes of the link's child term. If this facet is selected, the rest of the filter simply specifies the search criteria to apply to the child term.
Type - This link facet indicates that the link should be filtered based on the attributes of the link's type (aka relation). If this facet is selected, the rest of the filter specifies search criteria to apply to the link type.
Parent - This link facet indicates that the link should be filtered based on the attributes of the link's parent term (aka relation). If this facet is selected, the rest of the filter specifies search criteria to apply to the link parent.
Self - This facet indicates that the link should be filtered based on attributes of the link itself. If this facet is selected, the rest of the filter specifies special, link-specific search attributes.

If any of the first three facets (child, type, or parent) are selected, the filter behaves just like a term filter (see Building Filters and Term Filters for more information). The have/don't have, Aspect, Attribute, Comparison, and Value fields are specified to select the desired terms, and the links whose appropriate facets match the filter will be matched.

If the Self facet is selected, however, a special set of link-specific attributes becomes available.

Link-Specific Attributes

The following attributes are available when the Self facet has been selected:

Namespace (single text value) - Searches the namespace of the link itself (NOT the namespace of the child, type or parent term). See The Parent_Editor and Changing Link Attributes for information on setting the namespace of a link.
Is intersection (boolean value) - Whether this link has been marked an intersection link. See Cross Products for information on intersection links.
Is necessary (boolean value) - Whether this link has been marked necessarily true. See The Parent_Editor and Changing Link Attributes for more information.
Is implied (boolean value) - Whether this is an implied link. Links may be marked implied when they are loaded (if they were loaded by a reasoner-generated file), but most of the time implied links have been created by the OBO-Edit reasoner. This kind of implied link will only exist if the reasoner is enabled. When searching, this attribute will only find implied links that have not been trimmed. See The OBO-Edit Reasoner for more information.
Is redundant (boolean value) - Whether this is a redundant link. The OBO-Edit reasoner may mark a user-created link redundant if it reiterates information implied by other links in the ontology. Links will only be marked redundant if the reasoner is enabled. See The OBO-Edit Reasoner for more information.

Special Behavior of the Search Aspect

If the Self facet is selected, search aspects work a little differently. In a term filter, the search aspect specifies an alternate collection of related terms to find a match. In a link filter, the search aspect specifies an alternate collection of related links.

For example, when the Self aspect is selected, the ancestor aspect searches all the ancestor links (NOT ancestor terms) to find a match.

A global link filter that seems like a good idea but slows everything down

If your ontology has a lot of "disjoint_from" links, the graph display can become rather tangled, so it might occur to you to add a global link filter to hide those links: "Find links where Type that don't have a ID that equals the value disjoint_from" or, in the syntax at the bottom of the link search panel, link.type(ID NOT equals "disjoint_from").

The problem with this link filter is that any time you perform an ontology edit (for example, using the Text Editor to change the wording of a definition or add a dbxref), OBO-Edit runs all the link filters, and this "disjoint_from" filter is very expensive to perform. You will thus see very slow editing performance--for example, with this filter in place, a text edit of the GO ontology takes 13 seconds to commit.

Fortunately, there's a better solution: you can add this link filter to the Graph Editor instead of as a global link filter. To do this, click the little wrench/spanner icon in the Graph Editor titlebar to get to the Graph Editor configuration interface, then select the Link Filters tab, and click the "Filter links" checkbox to enable you to add the anti-disjoint_from link filter.

When you've set up the filter, click the little checkmark in the Graph Editor titlebar to save the filter and return to the Graph Editor display.