pubmed-id

Simple interface to query or scrape IDs from PubMed (The US National Library of Medicine).

This tool was originally developed to obtain temporal data for the well-known PubMed graph dataset.

Usage

Command line interface

A CLI is included that allows querying the PubMed via their API or by web scraping.

usage: pubmed-id [-h] [-o OUTPUT_FILE] [-m {api,citedin,refs,scrape}]
                 [-w WORKERS] [-c SIZE] [--email ADDRESS] [--tool NAME]
                 [--quiet] [--log-level {critical,error,warning,info,debug}]
                 ID [ID ...]

positional arguments:
  ID                    IDs to query (separated by whitespaces).

optional arguments:
  -h, --help            show this help message and exit
  -o OUTPUT_FILE, --output-file OUTPUT_FILE
                        File to write results to (default: 'PubMedAPI.json').
  -m {api,citedin,refs,scrape}, --method {api,citedin,refs,scrape}
                        Method to obtain data with (default: 'api').
  -w WORKERS, --max-workers WORKERS
                        Number of processes to use (optional).
  -c SIZE, --chunksize SIZE
                        Number of objects sent to each worker (optional).
  --email ADDRESS       Your e-mail address (required to query API only).
  --tool NAME           Tool name (optional, used to query API only).
  --quiet               Does not print results (limited to a single item only
                        by default).
  --log-level {critical,error,warning,info,debug}
                        Logging level (optional).

Importing as a class

Quick example on how to obtain data from the API:

>>> from pubmed_id import PubMedAPI
>>> api = PubMedAPI(email="myemail@domain.com", tool="MyToolName")

For more information on the API, please check the official documentation.

Scrape data from website

Scraping the PMID or PMICD instead returns more data (strings shortened for brevity):

>>> api(6798965, method="scrape")

{
  "6798965": {
    "date": "1981 Aug 1",
    "title": "Characterization of N-glycosylated...",
    "abstract": "The N epsilon-glycosylation of...",
    "author_names": "A Le Pape;J P Muh;A J Bailey",
    "author_ids": "6798965;6798965;6798965",
    "doi": "PMC1163140",
    "pmid": "6798965"
  }
}

Note: some papers are unavailable from the API, but still return data when scraped, e.g., PMID 15356126. Please consider the Usage Guidelines from NCBI (see note below).

Obtain data from API

By default, the returned data is a dictionary with the PMCID, the PMID, and the DOI of a paper:

>>> api(6798965, method="api")

{
  "pmcid": "PMC1163140",
  "pmid": "6798965",
  "doi": "10.1042/bj1970405"
}

Either an integer (PMID), a string (PMID or PMCID), or a list is accepted as input when calling the class directly.

Note: NCBI recommends that users post no more than three URL requests per second and limit large jobs to either weekends or between 9:00 PM and 5:00 AM Eastern time during weekdays. See more: Usage Guidelines.

Get paper references

Returns list of references from a paper:

>>> api(6798965, method="refs")

{
  "6798965": [
    "7430347",
    "..."
  ]
}

Get citations for a paper

Returns list of citations to a paper:

>>> api(6798965, method="citedin")

{
  "15356126": [
    "32868408",
    "..."
  ]
}

References

• PubMed API