Cecilia Arighi, a research assistant professor in the Department of Computer and Information Sciences at the University of Delaware, presented this poster at the Pistoia Alliance Conference in Boston on April 12, 2011. on the Protein Ontology, part of the Open Biomedical Ontology Foundry.

1. The Protein Ontology: a structured representation of protein
forms and complexes
Cecilia Arighi1 and PRO consortium
1Center for Bioinformatics and Computational Biology, University of Delaware
INTRODUCTION PRO entry report
The Protein Ontology (PRO) provides a formal, logically-based For Protein
classification of specific protein classes, including structured 1-Ontology
representations of protein isoforms, variants and modified forms.
Initially focused on proteins found in human, mouse and Escherichia
coli, PRO now includes representations of protein complexes (Fig1).
The PRO Consortium works in concert with the developers of other 2-Features
biomedical ontologies and protein knowledge bases to provide the
ability to formally organize and integrate representations of precise
protein forms so as to enhance accessibility to results of protein
research. PRO (http://pir.georgetown.edu/pro) is part of the Open 3-Annotation
Biomedical Ontology Foundry (PMID:20935045).
PRO meta-structure: sub-ontologies, relations and
categories
For complex
4-Relationship to
complex components
Fig3. Sample PRO report for a c-myc protein form and a c-myc complex. (1)
Ontology section, with ID, name and synonyms, definition, comments and
Fig1. The left panel shows the ProEvo and ProForm subontologies, the right panel
hierarchy links. (2) Sequence and features for representative entities. (3) The
shows the ProComp subontology and the central panel shows the typical
resources used to define or annotate PRO terms. annotation for the particular protein form (or complex) described in the
entry expressed via relationships to other ontologies and/or databases. (4)
Complex entry report shows the relationship of the complex to its
Illustration of PRO with c-myc protein components.
c-myc is a transcription factor that is important in the regulation of cell
proliferation. c- myc undergoes various post-translational
PRO integrated view in Cytoscape
modifications leading to different functional outcomes:
1) c-myc acetylation (Ac) stabilizes the protein and promotes to
complex with max; this active form positively regulates transcription
of genes involved in cell proliferation.
2) c-myc phosphorylation (p) on T58 targets c-myc for proteosomal
degradation, down-regulating transcription.
3) c-myc phosphorylation on S62 and S71 via Ras (PI3K) pathway leads
to transcriptional repression of tsp1 and promotes angiogenesis.
Fig4. The ontology and annotation can be imported in Cytoscape to connect
PRO framework allows the representation of c-myc forms and protein forms and complexes along with annotation. Illustrated with protein
complexes (Fig2) and the annotation of their corresponding attributes c-myc. Partial annotation for the highlighted (pink) terms is shown in the data
(Fig3) . table.
PRO hierarchy connects myc objects in PRO and GO PRO distribution files
2-Annotation file
3-Mapping files
1-Ontology in OBO format
Fig5. PRO files can be downloaded from FTP site. These include (1) the
ontology in OBO format, (2) the accompanying annotation file in a tab
delimited format, and (3) mappings to external databases.
PRO is also available in other formats in the OBO Foundry website.
Fig2. The terms related to c-myc can be viewed via the PRO browser (Partial view). PRO term requests
There are c-myc terms for protein and complex. Column 1: protein terms; Column
New terms can be requested via the PRO tracker at
2: ontology level; Column 3: sequence feature (Ac, acetylation; g, glycosylation; p,
http://sourceforge.net/tracker/?func=add&group_id=266825&atid=1135711.
phosphorylation).
PRO Consortium: Funded by National Institutes of Health (R01GM080646)