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Retrieving articles using PubMed
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Objective

 

  • To introduce PubMed database and its features.
  • To learn how to retrieve articles from PubMed of NCBI .

 

Theory

 

PubMed is a centralized NCBI repository containing millions of articles which can be accessed through a web based interface provided within NCBI. It can be accessed from the site www.ncbi.nlm.nih.gov/pubmed. PubMed is developed and maintained by the National Centre for Biotechnology Information (NCBI) at the U.S National Library of Medicines (NLM), located at the National Institute of Health. 

 

The NCBI (National Center for Biotechnology Information) acting as a resource database for molecular biology, computational biology, biochemistry, genetics information which aids in  developing new technologies for  managing the biological process that control health and  diseases.  NCBI established on November 4, 1988 as a part of National Library of Medicine (NLM) at the National Institute of Health (NIH). It can be accessed from the site www.ncbi.nlm.nih.gov/ . It maintains collaborations with several NIH institutes, industries and other governmental agencies. NCBI supports various databases which can be accessed online through Entrez search engine. A database is a collection of data which is collected from different literatures, experiments and other analysis and can be easily accessed, updated, and retrieved. NCBI is a repository of various databases like Nucleotide, Protein, Pubmed, GEO etc..

 

Entrez is a powerful search engine which allows users to search and retrieve different data from the National Center for Biotechnology Information (NCBI). Entrez integrates different scientific literatures, nucleotide and protein databases, protein domain data, population study datasets, expression data, pathways and systems of interacting molecules, complete genome details and taxonomic information into a tightly inter linked system. User can search and retrieve the queries from different databases with in the same interface all together. It can be accessed from the site www.ncbi.nlm.nih.gov/Entrez/

 

The major functions of NCBI are:

 

Creates public databases for storing, retrieving, and analyzing knowledge about molecular biology, biochemistry, and genetics.

Conducts research in computational biology, for analyzing the structure and function of biological molecules.

Develops software tools for analyzing genomic data

Disseminates biomedical information

 

Pubmed is one of the databases in NCBI and it contains about 22 million records of articles published from MEDLINE and various other biomedical, life science journals. Online books containing links to full text from PubMed Central and links to other NCBI molecular biology resources are also present in Pubmed database.

 

Medical Literature Analysis and Retrieval System Online (MEDLINE) is an online library of biomedical information. MEDLINE, is the National Library of Medicine’s database of journal articles from 1966; which is updated in a weekly manner. It contains articles from different fields which is relevant in the field of life sciences. PubMed provides free access to MEDLINE database which contains about 21.6 million records. MEDLINE uses MeSH (Medical Subject Headings) for retrieving information. It can be accessed from the site  www.nlm.nih.gov/bsd/pmresources.html . 

 

Medical Subject Headings(MeSH) acts as a controlled vocabulary (set of words used for searching in an organized manner) and also as a thesaurus for searching articles. It is created and updated by United States National Library of Medicine (NLM) which is world’s largest medical library. It can be accessed from the site www.ncbi.nlm.nih.gov/mesh . 

 

PubMed offers different search options according to the user’s convenience, which is very easy to use even for a beginner.  One can search articles by different searching methods. Search can be done by any query word, by the name of the author, by the Journal name or by their PMID.  PMID (PubMed identifier or PubMed unique identifier) is a unique number assigned to each PubMed record. PubMed offers to sort the records according to the date of publishment of papers.  Results are displayed year wise which can be accessed from a graphical view displayed on the right side of the PubMed result page.  PubMed offers additional filter options to make our search more specific. User can sort their search by choosing options from Species (Humans/Animals), Sex, Article types, Languages, Subjects, Ages, and Journal Categories. After selecting filters, user can activate his search by clicking the “Search” button,  in which result will be displaying  as a message on the top of the  page .The activated filters will be remain until it get deactivated by selecting the “clear” button. PubMed also offers to save our search records. PubMed Central (PMC) images can also be viewed from PubMed result page. It also allows downloading of documents in many standard formats that are usable through citation managers such as BibTeX, or some XML based citation extractors. 

 

PubMed Central is an archive of free journal publication in life sciences field.  It allows searching number of journals thereby providing the list of publications and their full text content without copyright violation. 

 

 

 

 

 

 

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