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

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3. 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 Xanthomonas oryzae pv. oryzae were 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 decarboxylase function – Tryptophan metabolism – Have known alleles and homologs with disease resistance phenotype 4

5. Annotation: Ontology Requirements ObjectObject type Feature or ontologyFeature type Attribute and score context XX Plant/gene/ gene-product / allele/population Molecular FunctionGO PATO Any of the ontologies including the environment ontology for adding context to the annotation. E.g. PEP carboxylase activity (GO-MF) in maize is required for C4 carbon assimilation (GO-PB). The process occurs in the plastid (GO-CC) of the leaf mesophyll cell (PO). Biological ProcessGO Cellular componentGO Plant structurePO Plant growth stagePO (bio)chemicalChEBI DiseaseDO Protein DomainsPRO InterPro PathwayPathway?? TraitTO 5

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

7. 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. 8 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] 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

9. 9 [PMID: 23637705] 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).

10. 10 PRO in iPTMnet Framework 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 ) http://proteininformationresource.org/iPTMnet PTM network of enzyme-substrate relationships and protein-protein interactions => iPTMnet with rich relations

11. 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 PTM Enzyme-Substrate Database 11

12. iPTM Network Coupled with functional annotation and biological context (homology, disease, tissue/cell..) => Hypothesis generation and discovery 12 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?

13. Human BUB1B Phosphorylation Network 73 nodes 24 phosphorylated forms 9 protein kinases 10 phospho-specific PPIs 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). 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 unphosphorylated CDC27 Phosphorylation on CDC27/Phos:1 sites does not regulate CDC27 interaction with BUB1B

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 auxin pathways, and crosstalks with 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 14

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

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