Literature Databases June 14, 2005 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 Writing assignment

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

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 NCBI Handbook

NCBI ENTREZENTREZ 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 PIR

Literature Databases Medline/Pubmed OMIM CSULA Library BIOSIS Bookshelf (from NCBI) Melvyl (Books at UC Libraries) Other molecular life science databases Science Direct Pub Med Central Free Medical Journals LinkOut Journals Wiley InterScience

Medline 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 two-letter (or more) label associated with it. This label tags the field.

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

MEDLINE Sample Record Garbo GM, et al. In vivo and in vitro photodyna...[PMID: ] UI (Unique Identifier) PMID (PubMedIdentifier) DA DCOM (Date completed) LR IS (International Standard Serial Number) VI - 68 IP - 4 DP Oct (Date of Publication) TI - In vivo and in vitro photodynamic studies with benzochlorin iminium salts... (Title) PG 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. (Authors’ 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 RN - 0 (Deuteroporphyrins) (CAS Registry No. or EC No.)

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): (Source)

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.MeSH Tutorial using MeSH terms to search Medline using PubMed

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

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

In-Class Assignment