Welcome to the PGModel Home page.

PGModel was developed jointly by Carol Friedman and Yves Lussier.

PGModel is an information model representing genotypic and phenotypic entities, modifiers, and relations, such as those expressed in text. PGModel bridges the modeling gap between textual information and ontology-anchored databases because it allows for translation of information in textual narratives to a formal data structure comprising knowledge of genotypic and phenotypic concepts from established ontologies along with modifiers and relationships. This model provides links to formal knowledge and allows for reasoning within traditional ontologies, while it also provides for fine-grained representation of information in natural language. This feature is necessary for enabling expressiveness, such as that found in natural language, and also for enabling subsequent fine-grained retrieval of structured information that was extracted from text.

PGModel was developed using the Protégé knowledge management tools, with the OWL data file format. In addition, the Ontoviz Protégé plug-in can be used to graphically visualize components of the model. Two OWL data files associated with PGModel are available for download and browsing. One file pgmodelabbrev is an abbreviated version that contains an example of instances generated from information extracted from text. The file pgmodel is the complete version of PGModel but has no instances. The files can be viewed using Protégé Version 3 (build 141) by using the ‘Build’ function in the ‘File’ menu to build a new project. Choose the OWL data file format and the particular owl data file you wish to view. When you save the owl files on your computer, be sure to use the .owl extension. Both pgmodel and pgmodelabbrev also include comments and examples chosen from actual text.