1. Literature Databases June 17, 2003 Learning objectives- What is the general arrangement of biological data in the public databases? How does one retrieve information on a particular subject in the literature? National Center for Biotechnology Information (NCBI) Databases outside of NCBI New topic-amino acid characteristics

2. Primary public domain bioinformatics servers Public Domain Bioinformatics Facilities European Bioinformatics Institute (EBI) United Kingdom National Center For Biotechnology Information (NCBI) United States Genome Net (KEGG & DDBJ) Japan Databases Analysis Tools Databases Analysis Tools Databases Analysis Tools

3. NCBI ENTREZ A platform that provides access to and links to databases with biological information ENTREZ PubMed GenBank Protein databases Genomes PopSet Taxonomy OMIM MedLine

4. NCBI ENTREZ GenBank Protein databases Genomes PopSet Taxonomy OMIM MedLine Literature Database Database of DNA sequences that have been collected to analyze the evolutionary relatedness of a population. Database of human genes and genetic disorders 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. Database of genomes from organisms and viruses Database of names of organisms with sequences in GenBank or Prot

5. Literature Databases Medline OMIM CSULA Library BIOSIS Agriculture Melvyl (Books at UC Libraries) Other molecular life science databases Science Direct Pub Med Central Free Medical Journals Wiley InterScience

6. Bibliography databases 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 label associated with it. This label tags the field.

7. Medline Database Producer:National Library of Med Database size:>12 million records 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

8. 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)gmgarb0I@pdt.bcc.louisville.edu 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.)

9. 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)

10. MedLine Indexing Subject experts at NLM read incoming articles for inclusion into the database. Identification of the topics Consult the MeSH to select appropriate terminology to match the topics. The MeSH terms are added to the entry into MedLine along with other information on the article. Using the MeSH terms allows one to be more comprehensive in searching.

11. MeSH (Medical Subject Headings) Selected from 19,000 Thesaurus terms Major headings are indicated as * in MedLine DB Subheadings-used as qualifiers-assist in narrowing a search.

12. MeSH (Medical Subject Headings continued) Advantages of MeSH Structured vocabulary Find relevant articles that may not contain keywords mentioned in title or abstract Eliminates irrelevant records Disadvantages of MeSH Scientific jargon not covered Human indexers at NLM may not be consistent Not every concept in article can get thesaurus term Lag time between indexing and initial placement in the MedLine database can be long.

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

14. How to keep a running tab on your favorite subject? Set up Cubby. An automatic retrieval system that searches PubMed and deposits the literature citations in your own account (there is no charge). Requires a login. Demonstration