PHP Entrez Tools documentation

PHP Entrez Tools (PET) is a library of PHP classes for, amongst other things, making requests to NCBI's API. The tools make it simple to construct web applications processing data from databases such as PubMed, GenBank, PubMed Central, and OMIM, by running searches and returning the results as assoc arrays.

This page contains documentation of use to those who wish to develop tools of their own, and those who wish to develop the core library further.

The Classes

NCBI tools

To produce something using the NCBI API, you will need to run a combination of eSearch and either eSummary or eFetch.

• eSearch - Retrieve a count or list of matching IDs for a search.
• eSummary - Retrieve document summaries for a list of IDs.
• eFetch - Retrieve details, abstracts, etc, for a list of IDs.
• EntrezRequest - This is called by eSearch, eSummary, and eFetch, and handles HttpRequests and file caches. You should not need to call it directly.
• XmlArray - You should not need to call this directly,

Other tools

• BioMedCentral - Retrieve a BMC publication and turn it into a useful assoc array.

 

Ready made packages

• PubmedSearch - Run a PubMed Search and put the results on your own website.