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Databases – especially for literature June 17, 2008

Databases – especially for literature June 17, 2008. Learning objectives: Become aware of the general arrangement of biological data in the public databases. Be able to retrieve information on a particular subject in the literature. Databases

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Databases – especially for literature June 17, 2008

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  1. Databases – especially for literatureJune 17, 2008 • Learning objectives: • Become aware of the general arrangement of biological data in the public databases. • Be able to retrieve information on a particular subject in the literature. • Databases • National Center for Biotechnology Information (NCBI) • Databases outside of NCBI • Writing assignment

  2. Today • Announcements • Due dates • Wed, 9 AM, email inclass and homework from Molecular Life Science Review • Friday PM – know whether you prefer the patent or primary article writing assignment

  3. Today • Schedule • “Finish” last part of Molecular Life Science review • Heme binding domain in sickle and wt • Homologies in evolutionary and structural/functional sense • * vs. : in ClustalW • Lecture on Lit Databases • Workshop for Lit Databases

  4. Who . . . • Has used PubMed? • Has done a search using PubMed • Has NCBI report to them weekly on new articles regarding a specific topic? • Has published an article in a journal listed on PubMed?

  5. Some public domain bioinformatics servers Public Domain Bioinformatics Facilities Genome Net (KEGG & DDBJ) Japan European Bioinformatics Institute (EBI) United Kingdom National Center For Biotechnology Information (NCBI) United States Databases Databases Analysis Tools Analysis Tools Databases Analysis Tools Kyoto Encyclopedia of Genes and Genomes DNA Data Bank of Japan

  6. OMIM Taxonomy NCBI ENTREZ • A platform that provides access to and links to databases with biological information ENTREZ PubMed Others! PopSet Genomes Protein databases GenBank MedLine • NCBI Handbook Yellow = Databases

  7. NCBI ENTREZ MedLine Literature Database OMIM Database of human genes and genetic disorders GenBank Database of all publicly available DNA sequences Database of amino acid sequences from SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq. Protein databases Database of genomes from organisms and viruses Genomes Database of DNA sequences that have been collected to analyze the evolutionary relatedness of a population. PopSet Taxonomy Database of names of organisms with sequences in GenBank or PIR

  8. Literature Databases • At NCBI • http://www.ncbi.nlm.nih.gov/Literature/ • CSULA Library • Melvyl (Books at UC Libraries) • Other molecular life science databases • Science Direct • Pub Med Central* • Free Medical Journals* • LinkOut Journals • Wiley InterScience

  9. Medline Database • Producer: National Library of Med • Database size: >14 million references • Publications Indexed: More than 4500 journals • Years Covered: 1966-present • Update Frequency: Daily • Index Medicus, Index to Dental Literature, and International Nursing Index • Papers in press are available

  10. Medline databases (the part the “user” doesn’t see) • Handbook on PubMed/Medline • Medline Developer Tools • Record-describes a publication • Journal article • Book • Book chapter • Meeting abstract • Records are subdivided into fields • Author • Title • Publication Name • Language • Each field has a two-letter (or more) label associated with it. This label tags the field.

  11. MEDLINE Sample Record Garbo GM, et al. In vivo and in vitro photodyna...[PMID:9796439] UI - 99012531 (Unique Identifier) PMID- 9796439 (PubMedIdentifier) DA - 19981130 DCOM- 19981130 (Date completed) LR - 20010323 IS - 0031-8655 (International Standard Serial Number) VI - 68 IP - 4 DP - 1998 Oct (Date of Publication) TI - In vivo and in vitro photodynamic studies with benzochlorin iminium salts . . . (Title) PG - 561-8 AB - Benzochlorin iminium salts (BIs) are hydrophobic photosensitizers based on an octaethylbenzochlorin nucleus that absorb in the near-IR region of the . . . AD - Division of Surgical Oncology, University of Louisville, KY 40202, USA. gmgarb0I@pdt.bcc.louisville.edu(Authors’ address) LA - eng (Language) ID - CA 65561/CA/NCI PT - Journal Article (Publication type) CY - UNITED STATES (Country of Publication) TA - Photochem Photobiol JC - P69 JID - 0376425 RN - 0 (Deuteroporphyrins) (CAS Registry No. or EC No.)

  12. MEDLINE Sample Record SB - IM (Subset) MH - Adenocarcinoma/*drug therapy (Medical Subject Heading) MH - Animal MH - Cell Survival/*drug effects/radiation effects MH - Deuteroporphyrins/*therapeutic use/toxicity MH - Drug Carriers MH - Emulsions MH - Female MH - Fibrosarcoma MH - Imines/*therapeutic use/toxicity MH - Leukemia L1210 MH - Light MH - Mammary Neoplasms, Experimental/*drug therapy MH - Mice MH - Mice, Inbred C3H MH - Neoplasms, Radiation-Induced MH - *Photochemotherapy MH - Photosensitizing Agents/*therapeutic use/toxicity MH - Support, U.S. Gov't, P.H.S. MH - Tumor Cells, Cultured EDAT- 1998/10/31 03:03 MHDA- 1998/10/31 03:03 PST – ppublish (print publication) SO - Photochem Photobiol 1998 Oct;68(4):561-8. (Source)

  13. Medical Subject Headings (MeSH) • MeSH is NLM's controlled vocabulary used for indexing articles for MEDLINE. MeSH terminology provides a consistent way to retrieve information that may use different terminology for the same concepts. • Who has published?

  14. OMIM-Online Mendelian Inheritance in Man • A catalog of human genes linked to diseases • Started by Victor A. McKusick at Johns Hopkins University • A good place to start when you want to research a certain disease or biological molecule associated with a disease. • This database is cross-referenced to PubMed and other NCBI-based databases

  15. In-Class Assignment • Before beginning this assignment, decide on a molecular topic in which you are interested and keep it in mind as you work through the tutorials. • Complete the PubMed tutorial, starting at • http://www.nlm.nih.gov/bsd/pubmed_tutorial/m1001.html • Be sure to use the menu at left, and complete at least: • Using PubMed • My NCBI • For each menu item, use “next” arrow to progress through the tutorial. • You will automatically be moved from tab to tab. • We will confirm that the next two items have been completed in class on Thursday. • Set up a My NCBI account to keep a running tab on your favorite subject • Make at least one of your NCBI weekly searches relevant to your internship. • http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.My_NCBI • Bring up you r My NCBI page, print scrreen to a word document, print it out, and hand in.. • Subscribe to NCBI newsletter • http://www.ncbi.nih.gov/About/newsletter.html • Copy me on your email request.

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