You should avoid high-frequency hits to NCBI's web interface for any type of information retrieval. See the Guidelines for Scripting Calls to NCBI Servers. Also note that any screen-scraping of PubMed Central articles is forbidden. For any bulk searches and data retrievals you should consider NCBI API's, which bypass the web:
- Use the Entrez Programming Utilities (E-utilities) as your interface for high-frequency searching and record retrieval in the Entrez databases. Adhere to the E-utilities Usage Guidelines and Requirements.
- If your expect your BLAST® searches to exceed the limits described in the Usage Guidelines for Web service interfaces, consider using Cloud BLAST or the stand-alone BLAST applications (BLAST+).