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The Protein Ontology: a structured representation of protein                                forms and complexes           ...
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The Protein Ontology: A structured representation of protein forms and complexes


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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.

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The Protein Ontology: A structured representation of protein forms and complexes

  1. 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 DelawareINTRODUCTION PRO entry reportThe Protein Ontology (PRO) provides a formal, logically-based For Proteinclassification of specific protein classes, including structured 1-Ontologyrepresentations 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 other 2-Featuresbiomedical 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 ( is part of the Open 3-AnnotationBiomedical Ontology Foundry (PMID:20935045).PRO meta-structure: sub-ontologies, relations andcategories 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 andFig1. The left panel shows the ProEvo and ProForm subontologies, the right panel hierarchy links. (2) Sequence and features for representative entities. (3) Theshows the ProComp subontology and the central panel shows the typicalresources 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 itsIllustration of PRO with c-myc protein components.c-myc is a transcription factor that is important in the regulation of cellproliferation. c- myc undergoes various post-translational PRO integrated view in Cytoscapemodifications leading to different functional outcomes:1) c-myc acetylation (Ac) stabilizes the protein and promotes tocomplex with max; this active form positively regulates transcriptionof genes involved in cell proliferation.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 leadsto transcriptional repression of tsp1 and promotes angiogenesis. Fig4. The ontology and annotation can be imported in Cytoscape to connectPRO framework allows the representation of c-myc forms and protein forms and complexes along with annotation. Illustrated with proteincomplexes (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 requestsThere are c-myc terms for protein and complex. Column 1: protein terms; Column New terms can be requested via the PRO tracker at2: ontology level; Column 3: sequence feature (Ac, acetylation; g, glycosylation; p, Consortium: Funded by National Institutes of Health (R01GM080646)