Abstract
AbstractOne of the premises of the OBO Foundry is that development of an orthogonal set of ontologies will increase domain expert contributions and logical interoperability, and decrease maintenance workload. For these reasons, the Cell Ontology (CL) is being re-engineered. This process requires the extraction of sub-modules from existing OBO ontologies, which presents a number of practical engineering challenges. These extracted modules may be intended to cover a narrow or a broad set of species. In addition, applications and resources that make use of the Cell Ontology have particular modularization requirements, such as the ability to extract custom subsets or unions of the Cell Ontology with other OBO ontologies. These extracted modules may be intended to cover a narrow or a broad set of species, which presents unique complications.We discuss some of these requirements, and present our progress towards a customizable simple-to-use modularization tool that leverages existing OWL-based tools and opens up their use for the CL and other ontologies.
Highlights
Many bio-ontologies were initially conceived of as stand-alone monolithic entities, developed independently of other ontologies
More complex ontology classes are constructed combinatorially using simpler ontology classes as building blocks. These building-block classes may come from separate ontologies, or from orthogonal hierarchies within a single ontology
The strategy far has been for Cell Ontology (CL) to represent generalized cell types as far as possible, with taxonomic specificity indicated by constraints in the ontology, and for taxon-centric ontologies such as ZFA and FBbt to represent these cell types as they are instantiated in particular species, with OBO format “xrefs” linking the two
Summary
Many bio-ontologies were initially conceived of as stand-alone monolithic entities, developed independently of other ontologies. When working with the CL, it can be useful to extract the minimal subset of GO that is required to perform automated reasoning over the CL and obtain results that are valid and complete This subset can either be imported or merged into the source ontology. The GO states that lactation occurs only in Mammalia, allowing a module extraction tool to automatically generate a Drosophila subset that excludes this term Other requirements, such as generating labels specific to certain taxa remain unmet. The strategy far has been for CL to represent generalized cell types as far as possible, with taxonomic specificity indicated by constraints in the ontology, and for taxon-centric ontologies such as ZFA and FBbt to represent these cell types as they are instantiated in particular species, with OBO format “xrefs” (semantics-free cross-references) linking the two. In an effort to redress this, we have specified a list of capabilities such a tool should have for working with the CL, and present initial progress towards the implementation of such a tool
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