3. Project Research (Entrez API) - ramazankilimci/swe573-project GitHub Wiki

What is Entrez API?

Entrez API provides nine sets of utility to get the data programmatically. It uses a fixed URL syntax which then converted into a set of parameters. With the help of converted parameters, we can query 38 databases at the National Center for Biotechnology Information (NCBI). Query responses are returned in an XML format by Entrez API. Thus we can interpret these using programming languages such as Python, Java, Go, etc. First, we will give information regarding the PubMed database.

For more information : Entrez API Usage Guidelines and Requirements

What is PubMed?

PubMed provides information regarding Biomedical and Life Sciences since 1996. You can search and get the citations and abstracts from its database which has more than 32 million records. It does not keep the full text of articles. You can get links to a full-text article within NCBI or third parties. There are subset databases within PubMed which are PubMed Central(PMC) and MEDLINE. PMC provides full-text journal articles since 2000. MEDLINE is being used since the 1960s. Articles in the MEDLINE database are selected by the special committee according to their uniqueness, importance, and of course scientific content. We will now dive into the usage of Entrez API.

For more information about PubMed, PubMed Central and MEDLINE : Differences between PubMed, PMC, and MEDLINE

Sample Queries

1) Searching PubMed Database

Base URL: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi

In the first screenshot, we directly made our search using PubMed Website. I tried to find the most recent documents regarding Post Traumatic Stress Disorder. Here we that the most recent PMID is 33892743.

URL: https://pubmed.ncbi.nlm.nih.gov/?term=post+traumatic+stress+disorder&sort=date

Then I used Postman to search Entrez API. To get the same results, parameters have been shown in yellow: db, term, and pubdate. I like json format so I used retmode parameter to get it. Not it can be seen that we got the same PMID in green.

URL : https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=post+traumatic+stress+disorder+AND&retmode=json&sort=pubdate