cROP Plant Ontologies & Protein Ontology (PRO)

1. cROP Plant Ontologies & Protein Ontology (PRO) PRO-PO-GO Meeting Amherst, NY May 16, 2013 Cathy H. Wu, Ph.D.

3. PRO Communities • Ontology Developers • GO ontology: Interfaces of GO/PRO complexes; GO definition (e.g., GO:0005109) • GO annotation: precise annotation of protein forms in PomBase • Cell Ontology: Define cell types based on protein types • Annotation Ontology for annotating scientific documents on the web • Brucellosis Ontology (IDOBRU), extension of the Infectious Disease Ontology (IDO) • Semantic Resources • Semantic Web Applications in Neuromedicine (SWAN); Neuroscience Information Framework (NIF) • Pathway/Process-Modeling Resources • Reactome, MouseCyc, EcoCyc, MaizeCyc • Chemical/Proteomic Resources: PubChem, IUPhar, P3DB, Top-Down Proteomics, PDB • Pharma/Clinical Communities: Drug Discovery & Disease Biomarker • Alzforum • Salivaomics KB/SALO (Saliva Ontology): Saliva Biomarkers • Clinical flow cytometry, immunology (ImmuPort) community

4. Biological Questions • List all the genes expressed differentially in the leaves of Rice plant varieties IRBB5 and IR24 at the 5-leaf visible growth stage, when the plants were infected with Xanthomonasoryzaepv. oryzaewere grown in a growth camber. IRBB5 is resistant and IR24 is susceptible to rice bacterial blight disease. • Filter the differentially expressed gene set for those with • LRR-domains • Transmembrane domains (e.g. in excess of 1) • Receptor like kinase function • Plasmamembrane cellular location • OR those having Tryptophan decarboxylasefunction • Tryptophan metabolism • Have known alleles and homologs with disease resistance phenotype

5. Annotation: Ontology Requirements

6. GO: response to pathogen Disease Ontology Example Building genotype-phenotype associations Allele-B GO: Receptor like Kinase Gene:XA21 maps_to Allele-A has_function inheres_in belongs_to Oryza genotype

7. PRO Workflow • Data Sources • Manual annotation (curator, collaborator, user): sourceforge tracker; RACE-PRO • Semi-automated processing of external databases (e.g., UniProtKB, Reactome, MouseCyc, EcoCyc); coverage of 12 reference genomes in progress • Integration with text mining: RLIMS-P/eFIP(Phosphorylation and Functional Impact) RACE-PRO Annotation Interface: Capture knowledge of protein forms/ complexes of interest to support integrated analysis

8. PRO representation of the spindle checkpoint PRO search query to retrieve PRO terms that contain the phrases “spindle checkpoint” or “spindle assembly checkpoint” or “mitotic checkpoint” and combined Cytoscape web view of the search results nodes retrieved by the search are blue; related nodes (parents and children) are gray Use of the protein ontology for multi-faceted analysis of biological processes: a case study of the spindle checkpoint. Ross et al. (2013) Front Genet. 4:62. [PMID: 23637705]

9. Phosphorylated forms of BUB1B in PRO Four species-independent BUB1B phosphorylated forms (blue nodes). Display options set to show parents and all children, including organism level terms. Sequence alignment of human, frog, and mouse BUB1B highlighted to indicate experimentally determined phosphorylation sites (blue) and predicted phosphorylation sites (red). [PMID: 23637705]

10. PRO in iPTMnet Framework PTM network of enzyme-substrate relationships and protein-protein interactions =>iPTMnet with rich relations • Data Mining: iProClass database for molecular and omics data integration • Text Mining: RLIMS-P/eFIP system for knowledge extraction from literature • Ontology: PRO for knowledge representation of PTM forms • Web portal linking data and analysis/visualization tools for scientific queries (http://proteininformationresource.org/iPTMnet)

11. PTM Enzyme-Substrate Database • Literature-curated kinase-substrate data • PhosphoSitePlus, Phospho.ELM, HPRD • PhosphoGRID • P3DB, PhosPhAt • UniProtKB, PRO • Database content • Substrates: 28,000; P-Sites: 126,000; Kinases: 700 • Substrate/site-kinase pairs: 13,000 • Covering: human, mouse, rat, other vertebrates, Drosophila, C. elegans, yeast and plants • Curated phosphorylation papers: 10,000 • Full-scale processing of PubMed abstracts: 22 million • Phosphorylation papers identified by RLIMS-P: 143,000 • Phosphorylation-PPI related papers identified by eFIP: 10,000

12. iPTM Network • Exploring Relations • Substrate-centric: • What PTM forms of a protein and their modifying enzymes are known? • Enzyme-centric: • What substrates are known for a given PTM enzyme? • Interaction: • What interacting partners are known for each PTM form of a given protein? • Pathway: • What modifications and enzymes are known in a given signaling pathway? • Coupled with functional annotation and biological context (homology, disease, tissue/cell..) • => Hypothesis generation and discovery

13. Human BUB1B Phosphorylation Network • 73 nodes • 24 phosphorylated forms • 9 protein kinases • 10 phospho-specific PPIs • BUB1B/Phos:2 interacts specifically with PPP2R5A • UB1B/Phos:2 phosphorylated by two important mitotic kinases: CDK1 and PLK1 • BUB1B interacts with both phosphorylated and unphosphorylatedCDC27 • Phosphorylation on CDC27/Phos:1 sites does not regulate CDC27 interaction with BUB1B Construction of protein phosphorylation networks by data mining, text mining, and ontology integration: analysis of the spindle checkpoint. Ross et al. (2013) Database (Oxford) (in press).

14. BR Signaling • Brassinosteroids (BRs): a class of growth-promoting hormones, which plays role in plant growth and development. • BR signaling is highly integrated with the light, gibberellin, and auxinpathways, and crosstalkswith other receptor kinase pathways to modulate stomata development and innate immunity. BR signaling curation Step 1: Search RLIMS-P with core genes (bri1, bak1, bin2, bsu1, bzr1, bes1) and “brassinosteroid mediated signaling pathway” to identify phosphorylation papers with phosphorylation information (kinase, substrate, site) Step 2: Use RACE-PRO to curate phosphorylated protein forms, their kinases, PPIs, and associated GO functions, process, subcellular component

15. BR Signaling Pathway Core proteins and other associated proteins annotated with GO related to BR signaling pathway (blue)

16. SCF complexes & Auxin/Jasmonate Signaling Cullin-1 Rubylated • SCF Complexes formed in response to auxin and jasmonate signaling • Link to ChEBI for small molecule-containing complexes