the protein ontology: a structured representation of protein forms and complexes
DESCRIPTION
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.TRANSCRIPT
The Protein Ontology: a structured representation of protein forms and complexes
Cecilia Arighi1 and PRO consortium1Center for Bioinformatics and Computational Biology, University of Delaware
INTRODUCTIONThe Protein Ontology (PRO) provides a formal, logically-basedclassification of specific protein classes, including structuredrepresentations of protein isoforms, variants and modified forms.Initially focused on proteins found in human, mouse and Escherichiacoli, PRO now includes representations of protein complexes (Fig1).The PRO Consortium works in concert with the developers of otherbiomedical ontologies and protein knowledge bases to provide theability to formally organize and integrate representations of preciseprotein forms so as to enhance accessibility to results of proteinresearch. PRO (http://pir.georgetown.edu/pro) is part of the OpenBiomedical Ontology Foundry (PMID:20935045).
PRO meta-structure: sub-ontologies, relations and categories
Fig1. The left panel shows the ProEvo and ProForm subontologies, the right panel shows the ProComp subontology and the central panel shows the typical resources used to define or annotate PRO terms.
PRO hierarchy connects myc objects in PRO and GO
Fig4. The ontology and annotation can be imported in Cytoscape to connect protein forms and complexes along with annotation. Illustrated with protein c-myc. Partial annotation for the highlighted (pink) terms is shown in the data table.
Fig2. The terms related to c-myc can be viewed via the PRO browser (Partial view). There are c-myc terms for protein and complex. Column 1: protein terms; Column 2: ontology level; Column 3: sequence feature (Ac, acetylation; g, glycosylation; p, phosphorylation).
Illustration of PRO with c-myc protein c-myc is a transcription factor that is important in the regulation of cell proliferation. c- myc undergoes various post-translational modifications leading to different functional outcomes:
2) c-myc phosphorylation (p) on T58 targets c-myc for proteosomaldegradation, down-regulating transcription.
3) c-myc phosphorylation on S62 and S71 via Ras (PI3K) pathway leads to transcriptional repression of tsp1 and promotes angiogenesis.
PRO entry report For Protein
For complex
PRO integrated view in Cytoscape
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.
1-Ontology
2-Features
3-Annotation
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 hierarchy links. (2) Sequence and features for representative entities. (3) The 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 components.
PRO framework allows the representation of c-myc forms and complexes (Fig2) and the annotation of their corresponding attributes (Fig3) .
4-Relationship to complex components
PRO distribution files
2-Annotation file
3-Mapping files
1-Ontology in OBO format
Funded by National Institutes of Health (R01GM080646)PRO Consortium:
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 term requestsNew terms can be requested via the PRO tracker at http://sourceforge.net/tracker/?func=add&group_id=266825&atid=1135711.
PRO is also available in other formats in the OBO Foundry website.