- The National Cancer Institute thesaurus (NCIt) is a large and complex ontology. NCIt is frequently updated; a new release is made available approximately every month. Tracking structural changes in NCIt is important for the editors of its content. In this paper we describe a methodology and tool using diff partial-area taxonomies to visually summarize structural changes between two NCIt releases. Diff partial-area taxonomies provide a comprehensible view of the overall impact of the changes. This methodology is illustrated using the Biological Process hierarchy. Specifically, we illustrate how diff partial-area taxonomies reflect change that occurred due to major restructuring of this hierarchy between September 2004 and December 2004. During this time the hierarchy nearly doubled in size and a large portion of the classes were extensively modified. Several kinds of change patterns are identified and discussed.
Large ontologies, such as the National Cancer Institute
thesaurus (NCIt) [
Our current research framework [
extensively studied. Various methodologies for computing
ontology diffs, which provide a detailed report of individual
changes, have been developed. For example, Noy et al. [
NCIt is a large ontology composed of over 114,000 classes
(i.e., concepts) and tens of thousands of restrictions (i.e., roles
or relationships). A new version of NCIt is released, in OWL
[
Fig 1. (a) An excerpt of 15 classes from NCIt’s Biological process hierarchy (Sept 2004). Classes are represented as labeled boxes and upward directed arrows indicate subclass relationships. Labeled, dashed bubbles indicate that a set of classes have restriction with the given set of object properties. For example, Cellular Process has a restriction Has associated location with a range of Cell. This restriction is inherited or refined by its descendants. Cell Cycle Stage introduces a restriction with the object property Is part of process. (b) The same excerpt after various changes occurred to the content (Dec 2004). (c) The diff partial-area taxonomy derived from these two releases. Diff areas are shown as boxes that are colored and organized into levels according to their number of object property types. For example, the six classes in the Has associated location bubble in (b) are replaced by the green box labeled Has associated location. Newly introduced areas are shown with a green outline, removed areas with a red outline, and modified areas with a yellow outline. Diff partial-areas are shown as boxes in their respective diff areas. Introduced partial-areas have a green background, removed a red background, modified a yellow background, and unmodified a white background (see Cell Cycle (1) in Fig 2). Each diff partial-area is labeled with the name of its root class, the number of classes in the diff partial-area in the to release (in parenthesis), and a numeric summary of the changes that occurred. For example, the modified partial-area Cellular Process (6) is shown in the {Has associated location} diff area, it contains 6 classes, and between the Sept 2004 and Dec 2004 releases one new class that was added to the ontology (Cell Death Process) is now summarized by this diff partial-area (“+1 New”) and another class (Cell Cycle Stage) has moved to modified diff partial-area from its removed partial-area in the {Has associated location, Is part of process} removed area (“+1 Moved” on the Cellular Process (6) modified partial-area). The class DNA Sequence Alteration, in the same removed area, lost both of its restrictions and moved to the Ø modified area. This is reflected as a removed partial-area DNA Sequence Alteration (0) and as part of the “+4 Moved” description in the Biological Process (7) modified partial-area.
of the Biological Process hierarchy’s content, finding a
significant number of inconsistencies in its modeling.
Gonçalves et al. [
We define an abstraction network as a compact summary
of an ontology’s content and structure. An abstraction network
is composed of nodes that summarize sets of “similar” classes.
Nodes are organized into a hierarchy based on the underlying
subsumption hierarchy. For a review of abstraction networks
see Halper et al. [
In Ochs et al. [
partial-area summarizes and visualizes changes in the introduction and inheritance of restrictions on a hierarchy’s classes. In OWL ontologies, such as NCIt, an owl:Restriction axiom consists of a property, a constraint (e.g., someValuesFrom), and range class(es). For example, the class Cellular Process has a restriction with the Has associated location object property and a range of Cell. Similarly, the class Mutation has a restriction with the object property has initiator chemical or drug and a range of Mutagen. For diff partial-area taxonomy derivation we consider the object property in each restriction (e.g., Has associated location).
hierarchy from Sept 2004. In Fig 2b we show the excerpt after some modifications were made in Dec 2004. The most significant changes were in the removal of restrictions from several of the classes (e.g., Mutation).
to sets of classes that explicitly, or through inheritance, have class restrictions that use the same types of object properties. For example, in Fig 1a, the classes Cell Cycle Stage and DNA Sequence Alteration have restrictions that use the Has associated location and Is part of process object properties. In a later release, shown in Fig1b, Cell Cycle Stage no longer has an Is part of process restriction and DNA Sequence Alteration now has no restrictions. A diff area is named after the set of object properties used in the class restrictions (e.g., {Has associated location, Is part of process}). Based on the state of such sets of classes we define four kinds of diff areas.
An introduced area is a diff area with a set of classes that have restrictions with a specific set of object properties in to but no such class exists in from (e.g., {Has initiator chemical or drug} in Fig 1c). A removed area indicates that there existed a set of classes that had restrictions with a specific set of object properties in from but no such class exists in to (e.g., {Is part of process} in Fig 1c). A modified area indicates that there exists a set of classes that have restrictions with a specific set of object properties in both from and to but the set of classes is not the same (e.g., {Has associated location} in Fig 1c). An unmodified area indicates that there exists the same set of classes that have restrictions with a specific set of object properties in both from and to.
same diff partial-area taxonomy (e.g., Mutation in Fig 1c). This occurs when the set of object properties used in restrictions on the class changes (e.g., Has associated location and Is part of process were removed from Mutation, as captured by the removed area and the introduced area).
its superclass(es). The set of root classes may differ in from and to. Each root class represents an introduction point for a set of object properties used in restrictions. Thus, root classes are associated with their diff area. For example, in Fig 1a Cell Cycle Stage introduced a restriction with the Is part of process object property, which its superclass, Cell Division Process, does not have. Thus, Cell Cycle Stage is a root class in the {Has associated location, Is part of process} diff area. There may be multiple root classes in a diff area (e.g., Cell Cycle Stage and DNA Sequence Alteration in {Has associated location, Is part of process}. Descendants of a root class in the same diff area have restrictions with the same object properties. For example, Cell Viability Process and Cell Division Process, children of Cellular Process, inherit the Has associated location restriction from their parent.
all of the classes that are the root’s descendants in its diff area. To summarize changes to these subhierarchies in each diff area we introduce diff partial-areas, which summarize changes to the subhierarchies of classes in each diff area.
class in to but not a root class in from, and all of its descendant classes that are in the same diff area in to (e.g., Mutation in Fig 1). A removed partial-area consists of a class that is a root class in from but not in to and all of its descendant classes in the same diff area in from (e.g., Subcellular Process in Fig 1). A modified partial-area consists of a class that is a root class in both from and to and all of its descendants in to. However, the set of descendants in the diff area in to is not the same as the set of descendants in the diff area in from (e.g., Cellular Process in Fig 1). An unmodified partial-area consists of a root class in both from and to and all of its descendants in the diff area. The set of descendants in the diff area are the same in from and to. # Diff Partial -areas 65
areas in a diff partial-area taxonomy. For example, in Fig 1c, there is a Mutation (3) introduced partial-area and a Mutation (0) removed partial-area. This occurs when the set of object properties used in restrictions on a root class changes between from and to and the class is a root in both versions.
how the structure of the Biological Process hierarchy changes between two releases. Instead of displaying hundreds of individual, axiom-level changes (e.g., a restriction was removed from Mutation, a subclass was added to Cellular Process, etc.), diff partial-area taxonomies visually capture changes to sets of similar classes (i.e., diff partial-areas), reducing the amount of knowledge a user has to view and providing the “big picture” of the changes.
Biological Process hierarchy was conducted in two phases. In the first phase we found that the hierarchy only underwent significant changes in the Nov 2004 and Dec 2004 releases (see Results). In the second phase we reviewed a diff partialarea taxonomy created using Sept 2004 as from and Dec 2004 as to. To browse diff partial-area taxonomies we have developed a software tool (described below). When an interesting change is identified via the diff partial-area taxonomy tool, a user can browse the explicit and implicit causes of each change. Fig 2. (a) An excerpt from the Sept 2004 – Dec 2004 Biological Process diff partial-area taxonomy. Each diff area is labeled with its total number/kind of diff partial-area (many of which have been hidden). (b) An example of how changes to the set of classes summarized by a diff partial-area are displayed. (c) An example of how a user can obtain information on why diff partial-areas were introduced or removed.
located in the modified area Ø, captures two major changes. First, it shows that 367 new classes were added to the hierarchy and these classes were modeled without restrictions. Additionally, 131 classes moved to Biological Process (538) from other diff partial-areas, indicating that their restrictions have been (explicitly or implicitly) removed in Dec 2004.
for deriving abstraction networks and diff abstraction
networks. In Ochs et al. [
With this software tool a user can select two versions of an ontology, and a subhierarchy within the ontology, and the tool will create a diff partial-area taxonomy. The tool enables a user to search and navigate diff partial-area taxonomies quickly. The visual display in the tool is based on the visual scheme used in Fig 1c and Fig 2. Each element is selectable and upon selection the tool provides information about what changed in a selected diff partial-area taxonomy element.
For each diff partial-area the modifications to its set of classes are identified when the user selects the diff partial-area in the tool’s display (an excerpt of information is shown in Fig 2b). If a diff partial-area is introduced or removed, the structural changes that affected the root class (and all of the descendants) are explicitly identified (e.g., addition/removal of restrictions at the root or at an ancestor of the root). Fig 2c provides an example of this information for the Mutation (12) introduced partial-area in {Has initiator chemical or drug}. Has initiator process and Has initiator chemical or drug restrictions removed by an NCIt editor. Has result biological process restriction removed from Pathogenesis, an ancestor, and no longer inherited. Same changes for Leukemogenesis, which was in the removed partial-area Leukemogenesis (0) [-1] and is now in Oncogenesis (7). Has associated location restriction removed by an NCIt editor. Five classes retained this restriction and are in an introduced partial-area Telomere Maintenance (5). Is part of process restriction removed from Mutation by an NCIt editor. Is part of process restriction removed from Subcellular Process and Has associated location restriction removed from DNA Sequence Alteration, ancestors of Mutation. Only two classes (Mutation, Silent Mutation) are in both. Most classes from the removed partial-area are now in introduced partial-area Gene Mutation (11), in {Has associated location, Has initiator chemical or drug}. The Mutation (12) introduced partial-area summarizes 10 classes from subtypes of Mutation that lost the same (and additional) restrictions (e.g., Germline mutation).
New class was modeled using a Is part of process restriction and its superclass has no restrictions.
Subhierarchy of Mutation classes that retained the Has associated location restriction.
Subhierarchy of classes from the Subcellular Process (0) [-87] removed partial-area that retained the Is part of process restriction. Three new classes were also added to the ontology within this subhierarchy (e.g., Farnysylation).
No classes were removed from the Biological Process hierarchy in this time period. Has initiator chemical or drug restriction removed by an NCIt editor. All classes are now in Biological Process (538) in Ø.
Is part of process restriction removed from Subcellular Process by an NCIt editor. A subhierarchy of 56 classes moved to Biological Process (538) in Ø. The other classes are in introduced partial-areas (e.g., a subhierarchy of 15 classes is in PostTranslational Modification (18) in {Is part of process}).
Biological Process hierarchy, several hundred changes were applied to its content. The hierarchy has not undergone any significant remodeling since that time period. For example, between 2013 and 2016 the only change that occurred was the addition of 32 new classes and the removal of two classes. The significant changes that were applied between Sept 2004 and Dec 2004 shaped the hierarchy as it still exists today. For example, the addition of 419 (70%) new classes greatly increased the hierarchy’s size (596 in Sept 2004).
restrictions were removed from 115 classes and 22 restrictions were added to 21 classes. These explicit changes, made by an NCIt editor, implicitly affected restrictions at 54 other classes. Table 3 shows the number of classes which had a certain number of restrictions in the Sept 2004 and Dec 2004 releases.
This extent of change is reflected by the large number of added and removed partial-areas in the diff partial-area taxonomy. In total, there are 118 introduced partial-areas, 105 removed partial-areas, 24 modified partial-areas, and 71 unmodified partial-areas. Table 4 lists the levels where these diff partial-areas are located, showing that there are a large number of removed partial-areas at higher indexed levels.
Process hierarchy included a 70% increase in size and a parallel decrease in restriction density. The remodeling coincided with the addition of two new kinds of object properties, Has mechanism of action and Has physiological effect, both of which have the Chemical or Drug hierarchy as a domain and Biological Process as a range. According to NCIt’s editors (SdC, NT) this addition influenced the remodeling of the Biological Process hierarchy.
of all possible restrictions for a class. Rather, restrictions are typically introduced only when there is a relevant use case for an NCIt user. This policy may explain why 367 (87.6%) of the new classes have no restrictions, and thus, are in Biological Process (538). The percentage of classes with no restrictions in Dec 2004 is very high (Table 3). In an on-going study we are reviewing the classes in Ø for missing restrictions (i.e., restrictions that should be added to classes to make them modeled consistently with other classes in the Biological process subhierarchy). A high percentage of missing restrictions were found.
The “big picture” of change reflected in the diff partialarea taxonomy is specifically illustrated by larger introduced or removed partial-areas. For example the Subcellular Process (0) removed partial-area, which contained 87 classes, and the emergence of Post-Translation Modification (18), a subhierarchy under Subcellular Process that retained the Is part of process restriction with a range of Post-Translational Regulation. Some significant changes are detected via modified partial-areas (e.g., the 367 new and 131 moved classes in Biological Process (538), which illustrates only 53 classes had no restrictions in Sept 2004). Another example is Cellular Process (53), with 26 new and seven moved classes.
removing two restrictions from 17 DNA Damage classes (as summarized by the DNA Damage (0) removed partial-area), leaving only the Has associated location and Has result biomedical process restrictions. Similarly, the class DNA Maintenance lost the Has associated location restriction and moved from {Has associated location, Is part of process} to {Is part of process} (as captured by the pair of DNA Maintenance diff partial-areas). This example illustrates an important benefit of the diff partial-area taxonomy in exposing the impact of remodeling. For consistency, DNA Maintenance should have kept the Has associated location restriction. Whatever was the cause for the removal in 2004, this restriction seems to be missing and it should be reintroduced. It is typical that a remodeling project causes undesired consequences. The diff partial-area taxonomy can help expose them so they can be corrected.
years ago. However, those changes shaped the Biological Process into its current form. We utilized a diff partial-area taxonomy created using the Sept 2004 release as from and the Dec 2004 release as to. This captured the end result of all the changes. However, there were two releases in Nov 2004 that contained intermediate changes. For example, in Nov 2004, there were 278 classes that were descendants of Subcellular Process and were modeled with an Is part of process restriction. This is captured by a Subcellular Process (279) [+ 192 New] modified partial-area in the diff partial-area taxonomy created using Nov 2004. In the Dec 2004 release the Is part of process restriction was eventually removed from Subcellular Process and many of its descendants.
We note that the diff partial-area taxonomy methodology is not limited to NCIt’s Biological Process hierarchy; it is applicable to any ontology. In future work we will apply the approach on an NCIt subhierarchy that underwent recent changes. With recent changes editors are aware of the intended effects of each change (for Biological Process this information was no longer available). This study will allow us to determine how accurately the elements of a diff partial-area taxonomy capture the intended effects of remodeling and if diff partial-area taxonomies can be used during the ontology design and development process, rather than as just a mechanism for reflecting on change.
A future component of integrating diff partial-area
taxonomies into the modeling process is a plugin for Protégé
[
review the structural changes resulting from a major remodeling of NCIt’s Biological Process hierarchy. Using a tool for deriving diff partial-area taxonomies we were able to identify significant amounts of change in the structure of this hierarchy. Issues related to the changes were discussed.
National Cancer Institute of the National Institutes of Health under Award Number R01CA190779. The content is solely the responsibility of the authors and does not necessarily represent the views of the National Institutes of Health.