pubmed-id 1.1

Simple interface to query or scrape IDs from PubMed.

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="[e-mail]", tool="MyToolName")

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

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)

{
  "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.

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.

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",
    "..."
  ]
}

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References

• PubMed API