1. Knowledge Enabled Information and Services Science Glycomics project overview

2. Knowledge Enabled Information and Services Science Life Science Ontologies ProPreO An ontology for capturing process and lifecycle information related to proteomic experiments 398 classes, 32 relationships 3.1 million instances Published through the National Center for Biomedical Ontology (NCBO) and Open Biomedical Ontologies (OBO) Glyco An ontology for structure and function of Glycopeptides 573 classes, 113 relationships Published through the National Center for Biomedical Ontology (NCBO)

3. Knowledge Enabled Information and Services Science Two aspects of glycoproteomics: oWhat is it? → identification oHow much of it is there? → quantification Heterogeneity in data generation process, instrumental parameters, formats Need data and process provenance → ontology-mediated provenance Hence, ProPreO models both the glycoproteomics experimental process and attendant data ProPreO ontology

4. Knowledge Enabled Information and Services Science ProPreO population: transformation to rdf Scientific Data Computational Methods Ontology instances

5. Knowledge Enabled Information and Services Science “Protein RDF” chemical mass monoisotopic mass amino-acid sequence n-glycosylation concensus Protein Data amino-acid sequence Chemical Mass RDF Monoisotopic Mass RDF Amino-acid Sequence RDF “Peptide RDF” chemical mass monoisotopic mass amino-acid sequence n-glycosylation concensus parent protein Calculate Chemical Mass Calculate Monoisotopic Mass Determine N-glycosylation Concensus Key Protein Path Peptide Path amino-acid sequence Extract Peptide Amino-acid Sequence from Protein Amino-acid Sequence ProPreO population: transformation to rdf Scientific Data Computational Methods RDF

6. Knowledge Enabled Information and Services Science Semantic annotation of scientific/experimental data

7. Knowledge Enabled Information and Services Science 830.9570 194.9604 2 580.2985 0.3592 688.3214 0.2526 779.4759 38.4939 784.3607 21.7736 1543.7476 1.3822 1544.7595 2.9977 1562.8113 37.4790 1660.7776 476.5043 parent ion m/z fragment ion m/z ms/ms peaklist data fragment ion abundance parent ion abundance parent ion charge ProPreO: Ontology-mediated provenance Mass Spectrometry (MS) Data

8. Knowledge Enabled Information and Services Science <parameter instrument=“micromass_QTOF_2_quadropole_time_of_flight_mass_spectrometer” mode=“ms-ms”/> Ontological Concepts ProPreO: Ontology-mediated provenance Semantically Annotated MS Data

9. Knowledge Enabled Information and Services Science Semantic annotation of Scientific Data Annotated ms/ms peaklist data <parameter instrument=“micromass_QTOF_2_quadropole_time_of_flight_mass_spectrometer” mode = “ms/ms”/> 830.9570 194.9604 2

10. Knowledge Enabled Information and Services Science N-GlycosylationProcessNGP N-Glycosylation Process (NGP) Cell Culture Glycoprotein Fraction Glycopeptides Fraction extract Separation technique I Glycopeptides Fraction n*m n Signal integration Data correlation Peptide Fraction ms datams/ms data ms peaklist ms/ms peaklist Peptide listN-dimensional array Glycopeptide identification and quantification proteolysis Separation technique II PNGase Mass spectrometry Data reduction Peptide identification binning n 1

11. Knowledge Enabled Information and Services Science Storage Standard Format Data Raw Data Filtered Data Search Results Final Output Agent Biological Sample Analysis by MS/MS Raw Data to Standard Format Data Pre- process DB Search (Mascot/ Sequest) Results Post- process (ProValt) OIOIOIOIO Biological Information Semantic Annotation Applications Semantic Web Process to incorporate provenance

12. Knowledge Enabled Information and Services Science Raw2mzXMLmzXML2PklPkl2pSplitMASCOT SearchProVault Raw mzXMLPklpSplit MACOT result ProVault result Experimental Data Semantic Annotation Metadata File SPARQL query-based User Interface Semantic Metadata Registry PROTEOMECOMMONS PROTEOMICS WORKFLOW Integrated Semantic Information and knowledge System (Isis) ProPreO ontology EXPERIMENTAL DATA Have I performed an error? Give me all result files from a similar organism, cell, preparation, mass spectrometric conditions and compare results. Is the result erroneous? Give me all result files from a similar organism, cell, preparation, mass spectrometric conditions and compare results.

13. Knowledge Enabled Information and Services Science Semantic Biological Web Service Registry Semantic Web Service

14. Knowledge Enabled Information and Services Science Gly | Asn | Gly | Ser moiety_2 moiety_1 123 5 4 1 2 3 4 GLYDE-CT : GLYcan Data Exchange Based on a Connection Table Format

15. Knowledge Enabled Information and Services Science Data, ontologies, more publications at Biomedical Glycomics project web site: http://knoesis.wright.edu/research/bioinformatics/index.html Thank You