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Ansuman Chattopadhyay, PhD Information Specialist in Molecular Biology and Genetics

Selection of Resources for the Development of an Information Service Program in Molecular Biology and Genetics. Ansuman Chattopadhyay, PhD Information Specialist in Molecular Biology and Genetics Health Sciences Library System University of Pittsburgh. Topics.

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Ansuman Chattopadhyay, PhD Information Specialist in Molecular Biology and Genetics

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  1. Selection of Resources for the Development of an Information Service Program in Molecular Biology and Genetics Ansuman Chattopadhyay, PhD Information Specialist in Molecular Biology and Genetics Health Sciences Library System University of Pittsburgh

  2. Topics • Multi Step Life Sciences Research • Literature Retrieval • Sequence Analysis • Laboratory Resources • University of Pittsburgh HSLS Molecular Biology Information Service Program

  3. Life Sciences Research- A Multi Step Process Hypothesis Generation Knowledge Mining Sequence Analysis Laboratory Bench Work Mol Biol InformationService

  4. Literature Retrieval Resources Hypothesis Generation Knowledge Mining Laboratory Bench Work Sequence Analysis PubMed --CellSpace Knowledge Miner --PubGene --Genomatix BiblioSphere

  5. Too much information 83,130 31,596

  6. Literature Retrieval Resources www.cellomics.cellspace.com http://www.pubgene.org http://www.genomatix.de/

  7. What is CellSpace ? www.cellomics.cellspace.com • CellSpace is a bioinformatics tool-- a knowledge mining system that automatically detects, analyzes, and reports the logical relationships between four types of terms found in the research literature: • molecule: proteins, genes, drugs • function: biological processes and disease states • cell type • organism

  8. What is CellSpace ? CellSpace Knowledge Miner Literature Association Cells & Systems Molecules Organisms Functions • Molecules: • Molecules • Drugs • Genes • Proteins Molecules Functions Cells & Systems • Functions: • Biological • Functions • Disease • States Organisms Cells & Systems: Cells, Sub-cellular Components,Tissues and Organs

  9. What you can do with CellSpace? • Start with a single protein (or other molecule) and • find its functions, the diseases in which it is implicated, • and related molecules. • Start with a disease or biological function and find • related molecules, or related functions. • Start with two or more functions, and find the related • molecules that they have in common

  10. What you can do with CellSpace? • Start with results from a high-throughput experiment • (such as a cluster of co-regulated genes from • microarray analysis), and easily find the functions • that they share. • Start with the results of proteomics experiments, and • quickly screen the data to distinguish published • interactions from novel ones. • .View the literature that supports the connections • found in CellSpace.

  11. Start with a disease or biological function and find related molecules, or related functions CellSpace Knowledge Miner • Find molecules related to apoptosis

  12. 5 1 2 Drag and drop 3 4 Click to select

  13. Find molecules associated with “apoptosis” Get references Results are presented with statistical likelihood value

  14. CellSpace Knowledge Miner

  15. How CellSpace Works? CellSpace computers analyze the National Library of Medicine's MEDLINE database, performing proprietary statistical correlation analyses regarding the organisms, cell types, biological processes, and molecules reported in 655 selected life science research journals. The molecular relationships extracted from the literature are then stored in the CellSpace database, which can be queried via the CellSpace user interface. The information is updated every two weeks

  16. PubGene The Network Browser tool displays literature association networks for a gene. The Set CoverArticle Search tool will let you search the literature using a set covering algorithm. The set covering algorithm is particularly useful to search for literature references for large sets of terms.

  17. PubGene

  18. PubGene The query gene is shown with bright red font in the graph, its direct neighbors are shown with darker red font, and neighbours of neighbours are shown with black font

  19. BiblioSphere

  20. BiblioSphere

  21. BiblioSphere

  22. BiblioSphere

  23. BiblioSphere

  24. BiblioSphere

  25. Resources comparison

  26. Resources comparison

  27. Information Hubs Hypothesis Generation Knowledge Mining Sequence Analysis Laboratory Bench Work The molecular biology and genetics resources that can serve as information hubs, an access point to retrieve a broad range of information through a small number of selected web-based public databases

  28. Information Hubs • UCSC Genome Bioinformatics Resources • Gene’s detail page Genome Browser • Family Browser Proteome Browser • SwissProt • LocusLink / Entrez Gene • Gene Cards • Gene Lynx • Incyte Proteome Bioknowledge Library • Human Protein Reference Database • Organism Genome Consortium sites

  29. Gene Expression Data Sequence Genomic,mRNA Protein Information Hubs LocusLink UCSC Family browser RNA Structure SwissProt Protein Structure OMIM GeneCards CGAP Other Species UCSC Gene’s Detail Page GO Annotations Molecular function Bio pathways Cellular component GeneLynx PubMed Mouse Genome Informatics AceView UCSC genome browser UCSC Proteome browser

  30. Information Hubs http://genome.ucsc.edu/cgi-bin/hgGene?hgsid=31408663&db=hg16&hgg_gene=U14680&hgg_chrom=chr17&hgg_start=41570859&hgg_end=41650551

  31. Information Hubs http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=672

  32. Information Hubs

  33. Information Hubs http://bioinfo.weizmann.ac.il/cards-bin/carddisp?BRCA1&search=BRCA1&suff=txt

  34. Information Hubs http://www.hprd.org/protein/00218

  35. Information Hubs

  36. Information Hubs Sequence Disease Expression in Organ/Tissue Cell Type Tumor Type Gene Ontology terms Proteome BioKnowledge Library Protein Interactions Gene Regulation Protein Modifications Literature Excerpts

  37. Resources Comparison

  38. Genome Browsers :

  39. Molecular Database Catalog http://nar.oupjournals.org/ • Nucleic Acids Research Database Issue

  40. Growth of Molecular databases

  41. Database Catalog http://www.infobiogen.fr/services/dbcat/

  42. Sequence Analysis Hypothesis Generation Knowledge Mining Sequence Analysis Laboratory Bench Work MolBiol Tools: Restriction mapping, PCR primer design Sequence Search Sequence Alignment Sequence Manipulation

  43. Web Server Catalog http://nar.oupjournals.org/ • Nucleic Acids Research Database Issue

  44. http://www.bioinformatics.vg/ Sequence Analysis http://healthlinks.washington.edu/index.cfm?id=210BCCB7-511A-4C6B-8B40-DFC47AABEA7F http://www.hsls.pitt.edu/guides/genetics

  45. Sequence Analysis http://www.bioinformatics.vg/

  46. Sequence Analysis

  47. Sequence Analysis

  48. Sequence Analysis

  49. Sequence Analysis DNAStar LaserGene PC/Mac PC/Mac

  50. Sequence Analysis Vector NTI Software Database DNA/RNA Protein Oligo Enzyme Gel Marker Blast Result Analysis Result Vector NTI core AlignX ContigExpress GenomBench BioAnnotator

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