WWW (Glibs workshop)
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This document summarizes various web resources available for carbohydrate chemistry, including encyclopedias, databases, and applications. It discusses searching strategies and challenges in locating relevant carbohydrate information online. The resources covered provide static content, structured data, or allow complex searches. Future directions proposed include better cross-linking of resources and interfaces.
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WWW (Glibs workshop)
- 1. Web resources for the Carbohydrate Chemist Roland Stenutz Stockholm University [email_address]
- 2. Content Technical considerations Resources by topic
- 3. Resources with static content GlycoWord – Encyclopedia www.glycoforum.gr.jp/science/word/wordE.html I UPAC-IUBMB Nomenclature http://www.chem.qmw.ac.uk/iupac/ Structural analysis – Laboratory manual www.casper.organ.su.se/sop/
- 4. Resources with static content Content is indexed by search engines, e.g. Google (www.google.com) and Altavista (www.altavista.com). Full text searches are best. Searches for compounds can be very difficult! Some tricks have to be used to get useful results. Compare nr of hits searching for “glucose” (3 10 6 ), “glucopyranose” (8 10 3 ) or “50-99-7” (2 10 3 ).
- 5. Databases glycoSCIENCES.DE www.glycosciences.de CAZy – Enzymes afmb.cnrs-mrs.fr/CAZY/acc.html PDB – Crystal structures www.rcsb.org/pdb/
- 6. Databases Large collection (100-100000) of related data. Searches can be complex, e.g. for (sub)structures. There are implied by the context; i.e. 5.15 might be a NMR chemical shift but not a price. There is very little garbage and redundancy in the databases. Can be difficult to find using search engines since they have little text that can be indexed.
- 7. Applications Most applications can be thought of as databases with an unlimited number of records. They require relatively complex interfaces since a request for data must contain all the information necessary to generate the data. They create content “on–the–fly”.
- 9. Interfaces
- 11. Structured answers – easy to transfer ***** Hit 2 ***** CC: CCSD:3436 AU: Adeyeye A; Jansson PE; Lindberg B; Abaas S; Svenson SB TI: Structural studies of the Escherichia coli O-149 O-antigen polysaccharide CT: Carbohydr Res (1988) 176: 231-236 FC: 014fe513 AM: 1H-NMR BS: (GS) Escherichia coli, (GT) O149 SB: Jansson PE DA: 01-08-1990 MT: LPS AN: O-antigen SI: CBank:6914 ---------------- structure: Repeat-4)-b-D-GlcpNAc-(1-3)-b-D-GlcpNAc4,6Py-(1-3)-b-L-Rhap-(1- ================end of record
- 12. Content Technical considerations Resources by topic
- 13. Structure Complex Carbohydrate Structure Database (CarbBank) www.boc.chem.uu.nl/sugabase/databases.html also glycosciences.de ECDB – E. coli O-antigen structures and NMR www.casper.organ.su.se/ECDB/ GlycoBase of USTL – oligosaccharides from amphibians ustl.univ-lille1.fr/glycobase/
- 14. Conformation PDB – Protein Data Bank, “Brookhaven DB” Protein structures, incl. glycoproteins www.rcsb.org/pdb GlycoMaps Database, SWEET-II etc… Conformational databases and applications for oligosaccharides www.glycosciences.de Disaccharide Database Conformational maps for some disaccharides www.cermav.cnrs.fr/databank/disaccharides
- 15. Spectroscopy SugaBase – NMR database, mainly 1 H, often incomplete. www.boc.chem.uu.nl/sugabase/databases.html CASPER – NMR from structure & structure from NMR. www.casper.organ.su.se/casper GlycoFragments – MS fragmentation from structure. www.glycosciences.de
- 16. Enzymes, Lectins and Glycoproteins CAZy – Carbohydrate Active Enzymes afmb.cnrs-mrs.fr/CAZY/ 3D Lectin Database www.cermav.cnrs.fr/lectines/ BPGD - Bacterial Polysaccharide Gene Database www.microbio.usyd.edu.au/BPGD/default.htm
- 17. Using Internet resources The question must be chosen with care! Ask the same question in different ways. Ask different search engines/data bases the same question and compare the results. Always – verify the results!
- 18. Searching Even if you know exactly what information you want it can be very difficult to find it. Information is spread-out in different locations and the question may need paraphrasing. It is very difficult to get a complete answer – but often you get a hint about how to proceed. e.g. you might not find the data sought but a reference to a paper that contains the data…
- 19. Portals One interface – several DB:s glycoSCIENCES.DE Searchable by structure/substructure bibliographic information NMR MS Contains CarbBank, Sugabase, + applications (3D-structure)
- 20. Future directions Consortium for Functional Glycomics Carbohydrate-protein interactions. Glycosylation disorders in knock-out mice. web.mit.edu/glycomics/consortium/ Japanese Consortium for Glycobiology & Glycotechnology Everything – and then some… www.jcgg.jp EuroCarbDB Structure (primary & 3D) & spectroscopy (NMR, MS) Russian initiative CarbBank/NMR (structure & NMR)
- 21. Future directions Cross-linking between resources – makes it easy to find related information. Portals – one interface to different resources. Better interfaces – current interfaces are often too complex. XML – allows data to be transferred directly to local applications.
- 22. Conclusion There is a wide range of carbohydrate related resources available on the WWW. Many provide useful information but all are rather limited in scope. There are problems transfering data between databases. The interfaces are difficult to use. Manuals or instructions are often missing.