| Ontology
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The Rat Genome Database is a rich and growing repository of biomedical
research data using rattus as the model organism. To extend the
usability of RGD, new approaches as to how the information in the database
is regrouped, cataloged and presented are being developed. One of the
newest approaches to creating another method of knowledge representation
is the implementation of ontologies that classify related concepts within
hierarchies. We decided to use the ontologies as a means to present and
view data in the RGD website. |
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| What is an ontology | |||||||||||||
Ontologies, as used in biomedical context, are controlled vocabularies in which a set of related concepts and ideas that are relevant to a field are organized in a hierarchical fashion, similar to an outline. The more general concepts are placed in the higher levels and more specific concepts are assigned to lower levels. In a simple ontology of concepts relating to proteins, we might find the following terms: protein, enzyme, structural proteins, kinase, polymerase, binding protein, polymerase, isomerase, collagen, transferase, keratin, DNA-binding protein, RNA-binding protein, protease. In the ontology, they might be organized as follows: Protein would be at the top of the hierarchy being the most general concept. Directly under that would be enzyme, structural protein, and binding protein. Under enzyme then would be the concepts kinase, polymerase, isomerase, transferase, protease. Similarly, collagen and keratin would fall under structural protein, etc.
The above organization illustrates an important feature of ontologies: concepts have relationships between them. In the above case enzyme is a parent concept and kinase is one of its children. Kinase is a more specific type of enzyme and the type of relationship they have is called an is_a relationship. Other relationship types can be defined for ontologies, but the other more common type is called the part_of relationship. One illustration of the latter would be the stomach is part_of the digestive system in an ontology of anatomical terms. Because of the complexity of biomedical data, the simple outline-like hierarchy used in the example is usually insufficient to capture biological knowledge, so the rules in ontology creation allow for concepts to have multiple parents along with multiple children (see below figure). To expand the original illustration, protein, can have a parent biomolecule. Biomolecule in turn can have a child catalytic biomolecule. Catalytic biomolecule in turn can be a parent of enzyme along with protein. This is allowable as long as the concepts increase in specificity as they go lower in the hierarchy and that no concept is the parent of its own ancestor. That constraint confines these ontologies to what is called a directed acyclic graph (DAG) structure.
As a hierarchy of related concepts, ontologies provide an ideal framework onto which data and information can be organized. Typically, specific examples, or instances, are linked, or annotated, to the concepts. An ontology with annotations is called a knowledge base. RGD uses ontologies to provide new avenues by which the user can find, and focus on, its objects’ information. Currently the gene ontology is implemented to give another contextual framework for its gene objects as well as keywords for RGD’s general search. [ back to top ] |
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| How do I use the ontology browser | |||||||||||||
The ontology browser is a representation of ontologies in html format. Each page provides the context in which a term is located vis-à-vis its ancestors, or paths, its siblings (other children for a given parent) and its children (Figure 3). The table has four columns. From left to right, the columns contain: the term, the terms accession number, the number annotations to the term and the number of annotations to the terms plus annotation to its descendants. The term listing is also a link to its ontology report while the accession number is a link to the terms browser page. To navigate to the ontology browser, click on the accession number to the corresponding term’s browser page. To obtain details on the term, click on term itself to get to its report. In the ontology browser page, the specific term is bolded. The terms indented to the same extent its siblings while the terms indented one step further to the right below it are its children. The terms with less indentation above it are its ancestors in that path, each level of indentation represents a generation.
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| The ontology browser can be accessed via several routes. From the home page, clicking on the ontology link gets the user the ontology search page (Figure 4).
Typing in a term, a portion of a term or an accession number and selecting the appropriate ontology and clicking the GO button returns a table listing terms containing the entered string or a term associated with the submitted accession number. The columns in the table are organized in the same manner as those in the ontology browser pages (Figure 5). Clicking the accession number (second column) sends the user to its term’s browser page while clicking on the term accesses the term’s ontology term report.
The general search also provides a route to the browser through the user typing in the exact term on accession number into the general search box. If the term has annotations, the objects annotated to the term will be listed and will provide links (accession number) on the search report to the term’s browser page, or to the term’s ontology report Lastly, in the object reports, links to the appropriate browser pages and ontology reports are available in the ontology portion. Currently, links from the gene report allow the user to access the gene ontology data in the ontology browser. [ back to top ] |
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| What data is available in the ontology report | |||||||||||||
| The ontology report contains information about the term and links to objects annotated to the term. The topmost section summarizes information about the term itself. This is followed by a table that lists objects annotated to the term. A link accesses a version of the page that lists objects annotated to the term as well as its descendants. Lastly, the paths to the terms are listed at the bottom of the page. Watch ontology report page via Genome Viewer tool:
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