NCBI provides several public APIs that allow programmatic access to many databases and tools.
Entrez Programming Utilities (E-utilities)
The E-utilities are the public API to the NCBI Entrez system and allow access to all Entrez databases including PubMed, PMC, Gene, Nuccore and Protein. The E-utilities are a suite of eight server-side programs that accept a fixed URL syntax for search, link and retrieval operations. A companion package named Entrez Direct consists of several executables that allow the E-utilities to be called directly from a UNIX command line.
BLAST URL API
The BLAST API allows developers to submit BLAST searches for processing at NCBI or cloud service provider(s) using HTTPS. The API can then check the status of submitted searches and retrieve results when ready in several formats.
PubChem Power User Gateway (PUG)
PUG is a suite of APIs for the NCBI PubChem resource, and provides programmatic access to many PubChem functions including downloads of chemical and assay data, chemical structure searches and chemical standardization. PUG offers HTTP, REST and SOAP interfaces, and also integrates with the E-utilities to provide convenient access to other NCBI databases.
PubMed Central (PMC) APIs
PMC provides several APIs that provide programmatic access to various services that deal with PMC literature content, including file validation tools, Open Access web services, and an ID convertor that interconverts PMCID's, PMID's, Manuscript ID's, and DOI's.