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

Life Sciences Research- A Multi Step Process Hypothesis Generation Knowledge Mining Sequence Analysis Laboratory Bench Work Mol Biol Information Service

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

Too much information 83,130 31,596

Literature Retrieval Resources

What is CellSpace ? C ellSpace 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: 1.molecule: proteins, genes, drugs 2.function: biological processes and disease states 3.cell type 4.organism

__ ++__ Molecules Functions Cells & Systems Organisms Molecules Functions Cells & Systems Organisms Literature Association Molecules: Molecules Drugs Genes Proteins Functions: Biological Functions Disease States Cells & Systems: Cells, Sub-cellular Components,Tissues and Organs CellSpace Knowledge Miner What is 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 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. What you can do with CellSpace?

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

1 2 3 Drag and drop 5 4 Click to select

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

CellSpace Knowledge Miner

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 How CellSpace Works?

The Network Browser tool displays literature association networks for a gene. The Set Cover Article 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.PubGene

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 PubGene

BiblioSphere

BiblioSphere

BiblioSphere

BiblioSphere

BiblioSphere

BiblioSphere

Resources comparison AvailabilityCoverageUpdate frequency CellSpace Commercial 2 weeks free trial 655 Medline journals Every 2 weeks PubGene V2.1 free V2.3 - commercial All Medline Journals SP: H,M,R V2.1-once in a year V2.3- every 2 weeks BiblioSphere20 use/month free All Medline Journals Abstract only SP: H,M,R continuous

Resources comparison Search Terms CellSpace Mol: gene, protein, Drugs Func: Biological func, Disease state, Cell and tissue type, PubGeneGene name BibliosphereGene name

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

Information Hubs UCSC Genome Bioinformatics Resources Gene’s detail pageGenome 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

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

Information Hubs

Information Hubs

Information Hubs

Information Hubs

Information Hubs

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

Resources Comparison AvailabilityTypeSP CoverageNoteworthy Features UCSCFreeH,M,R, etcExpression, Proteome/Fam ily Browser SwissProt/ uniprot FreeCuratedALLProtein information LocusLinkFreeH,M,R,N,P etc Link to NCBI resources GeneCardsFreeHExpression GeneLynxFreeH,M,R Proteome BKLCommercialCuratedH,M,R,Y,N, Pathogenic Fungi Literature excerpts HPRDFreeCuratedHProtein interaction

Genome Browsers :

Nucleic Acids Research Database Issue Molecular Database Catalog

Growth of Molecular databases

Database Catalog

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

Nucleic Acids Research Database Issue Web Server Catalog

Sequence Analysis healthlinks.washington.edu/index.cfm?id=210BCCB7-511A-4C6B-8B40-DFC47AABEA7F

Sequence Analysis

Sequence Analysis

DNAStar LaserGene PC/Mac

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

Sequence Analysis VectorNTI Advanced software suit consists of five independent yet interconnected components: Vector NTI core: the cornerstone application for Vector NTI suite, provides tools for sequence analysis and molecule manipulation. AlignX: a multiple sequence alignment tool ContigExpress: a DNA sequence assembly and sequencing project management tool GenomBench: a tool for genomic DNA sequence analysis and annotation BioAnnotator: a tool for functional annotation of DNAs and proteins

Sequence Analysis Using vector NTI molecular biologists can: Perform routine sequence analysis tasks such as restriction mapping, identifying protein coding regions or finding sequence motifs and carrying out sequence similarity searches Generate recombinant cloning strategies and protocols Design and analyze PCR primers Catalog a growing number of plasmids and PCR primers, in order to track the origin and lineage of recombinant molecules Run in silico gel electrophoresis Perform and edit multiple sequence alignments on proteins and nucleic acids Create publication quality graphics and more

Laboratory Resources Hypothesis generation Knowledge Mining Sequence Analysis Laboratory Bench work Protocols: Useful Laboratory Resources:

Laboratory Resources Basic Protocol Alternate Protocol Commentary Critical Parameters Troubleshooting Time Considerations Key References Internet Resources

Laboratory Resources

HSLS Mol Biol Information Service

Website Usage Report

Workshop 1: Information Hubs 2: Sequence Similarity Searching 3: DNA Protein Analysis Tools 4: CellSpace Knowledge Miner 5: VectorNTI May 2003-April 2004 Workshops

Total: 70 One-on-one Consultation

“…..only half of biomedical researchers using genome databases are familiar with the tools that can be used to actually access the data.” “….. all scientists on the planet must be empowered to use these powerful databases to unravel longstanding scientific mysteries.” atabases to unravel longstanding scientifi c… Andreas D. Baxevanis & Francis S. Collins Nature Genetics, September 2002, Vol 32