The Protein Ontology (PRO) and its web resources


The Protein Ontology (PRO) provides the formal and logical representation of proteins (including isoforms, variants and modified forms) and protein complexes. PRO content is gathered either by manual curation from the scientific literature or by large-scale processing of resources that provide curated protein and pathway information. The information found in the ontology, the annotation and the mapping files is stored in a database that is used in the PRO website ( to facilitate data integration and easy data retrieval. The PRO homepage is the starting point to navigate through the Protein Ontology resources, providing access to quick browse, links to several documents and information pages, the ftp download page, the term request and annotation pages, the ontology browser, and the advanced search. In this seminar I will give a background on the Protein Ontology, its content and the current web resources along with some working examples.  PRO is part of the Open Biomedical Ontology Foundry and it is funded by NIH. 


Dr. Cecilia Arighi is a Research Assistant Professor at the Department of Computer and Information Sciences, University of Delaware. Dr. Arighi has a Ph.D in Biochemistry and has worked in the bioinformatics field for the last 5 years after joining the Protein Information Resource (PIR) at Georgetown University (currently co-hosted at University of Delaware). She is highly interested in the accurate representation of protein information (e.g sequence, evolution, function, post-translational modifications, and pathways) that can be reasoned both by humans and computers to provide the basis for hypothesis generation. Dr. Arighi has been trained as a biocurator and has been actively engaged on various biocurator-related activities including (i) curation and quality control (at PIR) for UniProtKB database; (ii) curation of the Protein Ontology (PRO) and development of its curation interface (RACE-PRO); (iii) the development (in collaboration with text mining group) and evaluation of natural language processing tools to assist the biologists in retrieving information about proteins; and the (iv) organization of the interactive task for BioCreative III.  Within the Protein Ontology project, she has been involved in the design of the protein ontology framework, in leading the curation efforts, in community outreach activities, and developing the PRO web resource.