1. LIPID MAPS

2. LIPID MAPS: Bioinformatics Organizational Structure Shankar Subramaniam (PI) Eoin Fahy (Coordinator) – Lipid Chemistry, MS data analysis M Madhusudan – LIMS Dawn Cotter – LIPID MAPS Website Babu Guda – Lipid Biology (Genes, proteins, pathways) Purnima Guda – Lipid Biology (Genes, proteins, pathways)

3. LIPID MAPS: Hardware/Software Infrastructure Utilization of existing server infrastructure at SDSC Primarily Sun Solaris-based Additional LIPID MAPS Solaris server for chemistry development work Extension of existing Oracle databases used by the AFCS project to cater for LIPID MAPS needs Data backup/recovery/security already in place for Oracle DB servers and other bioinformatics servers

4. LIPID MAPS: User Software Infrastructure Web –based front-end Familiar web browser interface Easy learning curve Online help Access control for public vs private areas of website CVS versioning control

6. LIPID MAPS: Data Collection Experimental conditions/protocols LIMS system Java based – client software runs on multiple platforms (e.g. Windows) Use of barcodes for reagents,solutions,protocols Interfaces with Oracle database at SDSC Multi-level access control

7. LIPID MAPS LIMS System Benefits: 1)Data validation 2)Maintain Data Integrity 3)Standardize Data Inputs/Outputs 4)Automate Data Transfer between Labs 5)Paper Free Electronic Notebook

8. LIPID MAPS Laboratory Information Management System (LIMS) Sample Preparation Sample Processing Sample Handling Data Input GUIs Oracle Database Barcode Test tube/ Sample vial IP Barcode printer Barcode Scanner Sample tracking Data Integrity/ Storage

9. LIPID MAPS LIMS: Solution GUI

10. LIPID MAPS: Data Collection/Organization Existing Lipid structural data: LIPIDAT Database: 12,528 structures LipidBank Database: 6,565 structures Currently merged and stored in Oracle database Oracle chemistry cartridge (Sun Server) –Import molfile and Chemdraw formats using Oracle procedures –Structures are stored within Oracle tables –Exact or substructure search over the web Add novel lipid structures as they become available Objective: Database of unique lipid structures

11. LIPID MAPS: Key Chemistry Table Fields Lipid_ID (number) Compound (Blob) Core Class Main Class Sub Class Lipidat_ID Lipidbank_ID Common Name Synonyms Systematic name Molecular weight Formula

12. LIPID MAPS: Data Integration from public sources Key issues: Author permissions (LipidBank) Importing structure file formats (molfile,Chemdraw,gifs) Ambiguities in structures (esp. stereochemistry) Consistency in drawing structures within a class Classification conventions Nomenclature conventions Adding updated records (Tracking LIPIDAT/LipidBank ID’s)

13. LIPID MAPS Structure Database-Approach High quality structures/names (Core labs,Avanti, others) (Empty) New structures identified in LIPID MAPS experiments LIPID MAPS DB LIPIDAT LIPIDBANK Editing

14. LIPID MAPS Classification:Strategy 6 LIPID MAPS core classes –I: Fatty Acids /Eicosanoids [FA] –II: Neutral Lipids [NL] –III: Glycerophospholipids [GP] –IV: Sphingolipids [SP] –V: Sterols [ST] –VI: Isoprenoids [IP] Glycolipids [GL] represent an additional class outside these cores Additional sub-categories (Main class, Sub class) within cores.

15. LIPID MAPS: Core class-I: Fatty Acids and Conjugates I: Fatty Acids /Eicosanoids [FA] –Fatty Acids and Conjugates [1] Saturated Fatty Acids (a) Unsaturated Fatty Acids (b) Hydroxy and Keto Fatty Acids (c) Fatty Acyl Amides (d) Fatty Acyl CoAs (e) –Eicosanoids [2] Prostaglandins (a) Leukotrienes (b) Thromboxanes (c) Lipoxins –Oxidized Fatty Acids [3 ] Isoprostanes (a) Neuroprostanes (b) –Other [0]

16. LIPID MAPS: Core class - II: Neutral Lipids II: Neutral Lipids [NL] –Monoacylglycerols [1] –Diacylglycerols [2] –Triacylglycerols [3] –Sterol esters [4] –Fatty Alcohols & Aldehydes [5] –Wax esters [6] –Other [0]

17. LIPID MAPS: Core class -III Glycerophospholipids III: Glycerophospholipids [GP] –Diacylglycerophospholipids [1] Diacylglycerophosphocholines (a) Diacylglycerophosphoethanolamines (b) Diacylglycerophosphoserines © Diacylglycerophosphoglycerols (d) Diacylglycerophosphoglycerophosphates (e) Diacylglycerophosphoinositols (f) Diacylglycerophosphoinositolphosphates (g) Diacylglycerophosphates (h) Diacylglycerophosphoglycerophosphodiacylglycerols (I) CDP-diacylglycerols –Monoacylglycerophospholipids [2] –Ether-linked glycerophospholipids [3] –Oxidized Glycerophospholipids [4] –Other [0]

18. LIPID MAPS: Core class -IV Sphingolipids IV: Sphingolipids [SP] –Sphingoid bases [1] –Ceramides [2] –Phosphosphingolipids [3] –Neutral glycosphingolipids [4] –Acidic glycosphingolipids [5] –Other [0]

19. LIPID MAPS: Core class -V Sterols V: Sterols [ST] –Sterols [1] –Steroids [2] –Secosteroids [3] –Steroid conjugates [4] –Bile Acids and derivatives [5] –Other [0]

20. LIPID MAPS: Core class -VI Isoprenoids VI: Isoprenoids [IP] –C5-C25 compounds [1] –C30 compounds [2] –Vitamins and Quinones [3] –Dolichols [4] –Other [0]

21. LIPID MAPS: VII Glycolipids Glycolipids [GL] –Diacylglycerol glycans [1] –Diacylglycerophosphoinositol glycans [2] –Other [0]

22. LIPIDAT Phosphocholine structure Stereochemical ambiguities, non-standard nomenclature 3,5,9-Trioxa-4-phosphatetracosan-1-aminium, 4-hydroxy-N,N,N-trimethyl-10-oxo-7- [(1-oxotridecyl)oxy]-, inner salt, 4-oxide, (R)-

23. LIPID MAPS Phosphocholine structure 1,2-Didodecanoyl-sn-glycero-3-phosphocholine (1,2-Dilauroyl-sn-glycero-3-phosphocholine)

24. LIPIDAT phosphoinositol structure Stereochemical ambiguities, non-standard nomenclature D-myo-Inositol, 1-[2,3-bis[(1-oxotetradecyl)oxy]propyl hydrogen phosphate], (R)-

25. LIPID MAPS phosphoinositol structure 1,2-Ditetradecanoyl-sn-glycero-3-phospho -1D-myo-inositol (1,2-Dimyristoyl-sn-glycero-3-phospho -1D-myo-inositol)

26. LIPID MAPS: Data Collection Experimental data: Mass spectrometry ABI/SCIEX QTRAP 4000: file formats Experimental acquisition parameters Quantitation parameters Quantitation results CID spectra (fragmentation patterns)- JCAMP format LC elution profiles (image) Parsing programs have been written to interpret QTRAP 4000 data and export it to Oracle DB

27. LIPID MAPS :MS Data Query

30. Lipid MS database schema (Vanderbilt data)

31. LIPID MAPS: Data Collection Experimental data: Other MS instruments Need to have examples of data formats Microarray Data Other experimental data

32. LIPID MAPS: Data Collection -Networks Collection of genes, proteins and other elements involved in lipid metabolism, signaling and structural frameworks Adapting in-house gene and protein annotation pipelines for use in LIPID MAPS Compilation of current information on known pathways and networks –GO (http://www.geneontology.org)http://www.geneontology.org –KEGG (http://www.genome.ad.jp/kegg/)http://www.genome.ad.jp/kegg/ Experimental data emerging from LIPID MAPS consortium

34. LIPID MAPS: Data Presentation Web –based interface –LIPID MAPS website: http://www.lipidmaps.orghttp://www.lipidmaps.org Use of web –browser plugin to view/query chemical structures (also a Java-based option) Browser forms-based query builder: –Query chemistry, gene, protein, pathway data –Query and analyze MS, microarray experimental data –Link to other informatics tools/websites, e.g. SDSC Biology Workbench

35. LIPID MAPS: www.lipidmaps.org websitewww.lipidmaps.org

36. LIPID MAPS: Chemistry Tools (under development)

37. LIPID MAPS: Structure Search

38. LIPID MAPS: Retrieve Results

39. LIPID MAPS: View Structures (Chemdraw Plugin)

40. LIPID MAPS: Text Search

41. LIPID MAPS: Text Search-contextual menus

42. LIPID MAPS: Text Search results

43. LIPID MAPS: Structure Editing interface

44. LIPID MAPS: Pathways/Networks Presentation Parts lists Function Sub-cellular location Functional domains Pathways Interactions

45. AFCS Example: Pathways/Networks Display

46. LIPID MAPS: Bioinformatics Challenges Establishment of consistent classification, nomenclature and structure-display for lipids Automation of experimental data transfer and assimilation from core sites –Dealing with non-standard/legacy experimental data Mining of highly heterogeneous public sources for data regarding lipid pathways, networks and interactions Maintaining, updating, synchronizing lipidomics knowledge base