PA About

Pubmed Api

What is PubMed?

Pubmed is a website clinicians and researchers visit to look for research articles. I recently visited the API website, only to be disappointed with its outdated design.

I've extracted and emphasized the key points from that information, while also acknowledging some potential gaps. A more detailed account can be found by following the link provided earlier.

The base URI for the API is https://eutils.ncbi.nlm.nih.gov/entrez/eutils/

See the demo here

Table of contents:

1. API Key

2. Basic Searching

3. Storing Search Results

4. Getting Summaries

5. Getting Full Data

6. Spelling Suggestions

7. Related Articles

8. Database Statistics annd Search Terms

1

API Key

API keys can be obtained from http://www.ncbi.nlm.nih.gov/account/ after you create an account
Once the key has been generated, users are required to incorporate it into every E-utility request by assigning it to the api_key parameter.
Example request including an API key:

esummary.fcgi?db=pubmed&id=123456&api_key=ABCDE12345

2

Basic Searching

Endpoint: esearch.fcgi?db=&term=

By utilizing this API endpoint, you can initiate a search for a specific term, and in response, you will receive a collection of UIDs, which serve as unique identifiers for articles.

Functions: Provides a list of UIDs matching a text query.
UID: Unique Identifier
Base Url: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed
Output: List of UIDs matching a query
Example: Get the PMIDs (PubMed Ids) for articles about breast cancer published in Science 2008
URI: URI
Try it here 

            

        

        
You can remove the &retmode=json to default it to xml.


        
{
    "header":  {
    "type":  "esearch",
    },
    "esearchresult":  {
        "querykey": "1",
        "idlist": [
            "19008416",
            "19208416",
            "18008416",
            "16208416",
        ],
    "translationset": "..."
}


        

            

                3
            

            
Storing Search Results

        

        
Can be used to save your results in the pubmed server.

        
Later on, when combining the results as I will explain, it will be necessary for you to utilize
            this information.

        
esearch.fcgi?db=&term=&usehistory=y

        

            Input: Any query; Entrez database (&db);
                &usehistory=y
        

        

            Output: Web environment (&WebEnv) and query key
                (&query_key).
        

        

            Example: Get the PubMed IDs (PMIDs) for articles about
                breast cancer published in Science in 2008.
        

        
Check this URI

        
Use &retmode=json to get the json output

        
This will return a WebEnvId in the response

        
Use WebEnvId in a subsequent request like this.

        
esearch.fcgi?db=&term=&usehistory=y&WebEnv=$web1

        
Use the "epost" endpoint to save the set of UIDs in the database

        
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi?db=gene&id=7173,22018,54314,403521,525013
        

        
This will also return a WebEnvId which you can use in a subsequent request.

        
{
    "header":  {
    "type":  "esearch",
    },
    "esearchresult":  {
        "querykey": "1",
        "webenv": "MCID_63a5a3e077047a",
        "idlist": [
            "19008416",
            "19208416",
            "18008416",
            "16208416",
        ],
    "translationset": "..."
}



        

            

                4
            

            
Getting Summary

        

        
It provides summaries of studies for a given list of pubmed IDs separate by commas.

        

            https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=16899775,33164953&version=2.0
        

        
Use &retmode=json to get the json output

        

            

                5
            

            
Getting Full Data

        


        

            Endpoint: efetch.fcgi?db=&id=
                        &rettype=&retmode=json
        

        

            Input: List of UIDs (&id); Entrez database (&db);
                Retrieval type (&rettype); Retrieval mode (&retmode)`
        

        

            Link

            

                6
            

            
Spelling Suggestions

        

        

            EndPoint:
            espell.fcgi?term=&db=/database/
        

        

            Input:
            
                Entrez text query (&term); Entrez database (&db)
            
        

        

            Output:
            
                XML or json containing the original query and spelling suggestions.
            
        

        

            Example:
            
                Find spelling suggestions for the PubMed Central query ‘fiberblast cell grwth’.
            
        

        

            https://eutils.ncbi.nlm.nih.gov/entrez/eutils/espell.fcgi?term=rhuinitis&db=pubmed
            
        

        

            

                7
            

            
Related Articles

        

        

            Responds to a list of UIDs in a given database with either a list of related UIDs (and relevancy scores) in the
            same database or a list of linked UIDs in another Entrez database
        

        

            Batch mode – finds only one set of linked UIDs
        

        

            elink.fcgi?dbfrom=&db=&id=uid_list/uid_list
        

        

            Input:
            
                List of UIDs (&id); Source Entrez database (&dbfrom); Destination Entrez database (&db)
            
        

        

            Output:
            
                XML containing linked UIDs from source and destination databases
            
        

        

            Example:
            
                Find one set of Gene IDs linked to nuccore GIs 34577062 and 24475906
            
        

        

            https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&db=pubmed&id=34525277 
        

        

            

                8
            

            
Optional Parameters

        

        

            retmode:
            
Set this to json to return in a json format 

        

        

            restart:
            
Index of first UID to be shown

        

        

            restart:
            
Total number of UIDs to be shown

        

        
    
            sort:
            
  • Sort by the following:
    • 
            
  • - relevance (default)
    • 
            
  • - pub_date (descending order by publication date)
    • 
            
  • - Author - (by first author)
    • 
            
  • - JournalName
    • 
        

        

            
                Link
            
        

        

            3. datetype:
        

        
    
            
  • - &datetype=mdat - modification date
    • 
            
  • - &datetype=pdat - publication date
    • 
            
  • - &datetype=edat - entrez date
    • 
        

        

            3. mindate, maxdate:
        

        
    
            
  • - self-explanatory
    • 
            
  • - format should be yyyy/mm/dd or yyyy or yyyy/mm
    • 
        

        

            

                8
            

            
Database Statistics and Search Fields

        

        

            Endpoint:
            einfo.fcgi?db=/database/
        

        

            Output:
            
                XML containing database statistics
            
        

        

            Note: If no database parameter is supplied, einfo will return a list of all valid Entrez databases
        

        

            Example:
            
                Find database statistics for Entrez Pubmed
            
        

        

            
                Link
            
        

        

            Use &retmode=json to get the json output