1. Bioinformatics Core (B) Progress and Future Goals www.functionalglycomics.org

2. Ensemble or group of glycan structures resulting from coordinated expression of several biosynthetic enzymes Non-template biosynthesis Challenges Chemical heterogeneity Challenges in isolation and analysis Challenges in representation/processing glycan Information Multivalent interactions involving multiple glycan motifs with multivalent CRDs on proteins Glycan-Protein Interaction Glycan Structure-Function Relationships Challenges Understanding biochemical basis for glycan-protein interactions How glycan specific genotype governs whole organism phenotype Constructing biological pathways and interaction networks Advancing Glycomics Key Issues & Challenges

3. Consortium for Functional Glycomics www.functionalglycomics.org Active collaborative effort to advance glycomics Goal: Understand role of glycan–protein interactions in cell-cell communication Develop technologies and resources to obtain data at various levels from molecule  mouse Integrated approach to glycan structure-function

4. Bioinformatics Core (B) Bioinformatics Core (B) Vision & Approach Vision: Present the dynamic “face” of the Consortium via Internet to best utilize the value of the resources and datasets generated by its participants and the broader scientific community. Object-based Relational Database implemented using Oracle Middleware implemented using Entity-Class Operations, Servlets in Java Static Pages (SHTML) for Web Site Dynamic pages (JSPs) for database driven Entry, Dissemination and Queries Part of CFG database overall ontology map

5. Core B Organization Core Operations & Management Bioinformatics Scientific liaisons, User specifications, Bioinformatics applications Information Technology Database, web, software applications, user interface development Administration Ram Sasisekharan (Core Coordinator), Rahul Raman (Core Director) Ada Ziolkowski (Admin Staff) Core B Team Maha Venkataraman, Subu Ramakrishnan, Savitri Subramanian, Thomas Lutteke Ganesh Venkataraman, Wei Lang, Eric Berry, Nishla Keiser, Ishan Capila, Chipong Kwan and Consultants MIT Information Systems Server Maintenance MIT Information Systems Database Administration

6. Consortium DB Data Objects, Relationships, Raw and Parsable Data Public Databases GBP, Glycans, Glycoenzymes User Interface Data Acquisition Web-based Forms Annotation Tools User Interface for Information Dissemination GBP Molecule Pages GlycoEnzyme Molecule Pages Glycan Structures Database Consortium Data Dissemination Implementation Strategy Implementation Strategy Databases and Interfaces

7. Implementation Strategy Implementation Strategy Schema of CFG Data Objects and Integration Glycobiology, 16(5), 82R-90R

8. Highlights of Progress Highlights of Progress Years 1-4 Infrastructure set-up Database implementation Software development Interactions with Cores for data acquisition and dissemination Years 1 - 2 Acquisition of Core data Public release of databases CFG data dissemination GBP molecule pages Glycan structures DB Years 3-4

9. Highlights of Progress Highlights of Progress Quarters 1-3 of Year 5 CFG data acquisition and dissemination Streamlining the process to upload printed array data from Cores D and H Enhancing interfaces for disseminating scientific Core data Implementation of data dissemination and research tracking interfaces for PIs Specialized databases and molecule pages Data organization and implementation of glycosyltransferase database Updating expert contribution fields for C-type lectins in GBP database Other key highlights Bioinformatics satellite session at the Society for Glycobiology 2005 meeting – discussion of glycan analysis methods and data exchange formats Renewal application and preparation for Council review Publications “Glycomics: An integrated systems approach to structure-function relationships of glycans.” Nature Methods, 2(11): 817-24 “ Advancing glycomics: implementation strategies at the consortium for functional glycomics. ” Glycobiology, 16(5): 82R-90R

10. CFG Scientific Core Data CFG Scientific Core Data Data Organization Experiment Information Brief description of scope of experiment or analysis Experiment Information Brief description of scope of experiment or analysis Protocols Standardized Protocols used in an experiment or analysis Protocols Standardized Protocols used in an experiment or analysis Sample/Resources Detailed information on sample / resource utilized [mouse, tissue, cell, GBP] Sample/Resources Detailed information on sample / resource utilized [mouse, tissue, cell, GBP] Data Summary Summary of interpretation of data by Scientific Core Data Summary Summary of interpretation of data by Scientific Core Raw Data Raw data files generated by the analysis – Images, Excel, binary formats Raw Data Raw data files generated by the analysis – Images, Excel, binary formats Annotated Data Processed information on entities such as gene, mouse, GBP, etc. stored in DB tables Annotated Data Processed information on entities such as gene, mouse, GBP, etc. stored in DB tables

11. CFG Scientific Core Data CFG Scientific Core Data Statistics (as of June 2006) Gene Microarray (E) 47 Experiments (33) 617 Samples (387) 3546 data files (1826) Mouse Phenotyping (G) 16 KO Strains (11) 266 Experiments (149) 3116 data files (1100) Glycotechnology (C) Mouse: 11 tissues, 8 KO strains, 92 MALDI-MS spectra Human: 11 Tissues 108 MALDI- MS spectra Cell Lines: 12 Cell Lines 27 Spectra GBP-Glycan (H) 247 Samples (143)

12. CFG Scientific Core Data CFG Scientific Core Data Enhanced dissemination interfaces Navigation and downloading of CFG Data – Gene Expression, MALDI-MS Glycan Profiling, Mouse Phenotyping and Glycan Array - DEMO

13. Gene Microarray Data

16. Mouse Phenotyping Data

19. Mouse Phenotyping Protocols

20. Glycan Array Data

24. CFG Data Integration Expression of glycan related genes in wildtype mouse spleen

25. CFG Data Integration Glycan profile of spleen of FucT-VII KO mice with differences in histology staining

26. Tracking PI Research Progress Tracking PI Research Progress Data dissemination and resource tracking interface PI Core A Database Request ID Data IDs Core Submit Online Request Form Copy of submitted request emailed with Request ID in database SC Post Status Prioritizing/ Approved Request Approval Process Upload Data with Request ID

27. Tracking PI Research Progress Tracking PI Research Progress Data dissemination and resource tracking interface Navigating PI information page to find associated resource requests and data - DEMO

33. Automated Acquisition Data from public databases, links to public resources Data from Cores Interface to CFG resources and data Expert Contribution Filling out fields as experts on the molecule Molecule Information Portal GBP Molecule Page Interfaces Three main components Glycan array data Mouse phenotyping data Transgenic mouse line Contribution from experts obtained for C-type lectins

34. GBP Molecule Pages Updating expert contributions for C-type lectins GBP Molecule Page example for C-type lectins with filled expert contribution fields - DEMO

35. GBP Molecule Pages

36. DC-SIGN Molecule Page Expert Contributions

37. DC-SIGN Molecule Page

40. PDB IDs of DC-SIGN complexed with glycan ligands identified using PDB2LINUCS tool Expert Contributions

42. DC-SIGN Molecule Page

43. GT Database Development Expert annotation of glycosylation pathways Type II Extension/ Termination Composite Structure FucTs expert annotation 343 Genes 40 Sialyl-T 24 Fucosyl-T 69 GlcNAc-T 47 Gal-T 54 GalNAc-T 78 Sulfo-T 31 Man-T

44. Automated Acquisition Data from public databases, links to public resources Data from Cores Interface to CFG resources and data Molecule Information Portal GT Database Development Glycosylation interface & GT molecule pages Glycan profiling of GT KO mice Mouse phenotyping data Transgenic mouse line Gene expression (Year 6 goals)

45. Glycan Structures Database

46. Glycan Structure Search Interface

50. Glycan DB Search Results