Entrez Gene, Databases, MedLine, PubMed, UMLS

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The UMLS integrates and distributes key terminology, classification and coding standards, and associated resources to promote creation of more effective and interoperable biomedical information systems and services, including electronic health records.

What is the UMLS?
The UMLS, or Unified Medical Language System, is a set of files and software that brings together many health and biomedical vocabularies and standards to enable interoperability between computer systems.


MEDLINE is the U.S. National Library of Medicine's® (NLM) premier bibliographic database that contains over 19 million references to journal articles in life sciences with a concentration on biomedicine. A distinctive feature of MEDLINE is that the records are indexed with NLM Medical Subject Headings (MeSH®).

Entrez Gene Database

Entrez Gene is NCBI's repository for gene-specific information. Access to this information either through the Entrez Gene website or by flat files via NCBI's ftp site can be time consuming and limiting in regards to the number of and what questions you can ask about the data. A better solution for intense data mining is to create a relational database.

Biomedical term mapping databases

Wren, J. D., J. T. Chang, J. Pustejovsky, E. Adar, H. R. Garner, and R. B. Altman, "Biomedical term mapping databases", Nucleic acids research, vol. 33, no. suppl 1: Oxford Univ Press, pp. D289–D293, 2005.

Scaling up Biomedical Event Extraction to the Entire PubMed

Björne, J., F. Ginter, S. Pyysalo, J. 'ichi Tsujii, and T. Salakoski, "Scaling up Biomedical Event Extraction to the Entire PubMed", Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, Uppsala, Sweden, Association for Computational Linguistics, pp. 28–36, July, 2010.


PubMed comprises more than 21 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

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