PubChem's Integration with Entrez

Entrez is NCBI's primary text search and retrieval system used for PubChem's three primary databases and other major NCBI databases, including PubMed, Nucleotide and Protein Sequences, Protein Structures, Genome, Taxonomy, BioSystems, Gene Expression Omnibus (GEO) and many others.


One can search the PubChem databases through Entrez by initiating a search from the PubChem home page (, which also provides launch points to various PubChem services, tools, help documents and more. Alternatively, one can begin the search from the NCBI home page ( By default, if a specific database is not selected in the search menu, Entrez searches all Entrez databases available and lists the number of records in each database that are returned for this ‘global query’. Simply by selecting one of the three PubChem database from the global query result page, one can see the query result specific to that database.


If an Entrez search returns multiple records, they are displayed in a document summary (DocSum) report.  Below are examples of the DocSum page returned from the search of the PubChem databases for term "aspirin".


For each record in the DocSum page, some data-specific information is provided with a link to the page for that record.  The DocSum page contains controls to change the display type, to sort the results by various means, or to export the page to a file or printer. In addition, the icons and links on the right column of the DocSum page allow users to perform further analysis on the query result, to download the corresponding records, to refine or modify the search, to obtain associated records in other databases and so on.


The Entrez system features powerful options for constructing precise searches and managing results, including Entrez indices, filters, and links. 


  • Entrez indices and filters  
    Entrez indices, tied to individual records in an Entrez database, include information on particular aspects (often referred to as fields) of the records.  Entrez indices are useful for narrowing the search to a particular indexed field.
    Entrez filters, which indicate whether or not a given record in an Entrez database has a particular type of annotations, may be used to subset other Entrez searches according to this annotation type.  Importantly, Entrez filters are closely related to Entrez links in that many Entrez filters are generated by checking whether a given record in an Entrez database has an Entrez link to a record in the same or different Entrez database.


  • Entrez Cross-Links
    Entrez links are crosslinks between records in different Entrez databases or within the same Entrez database. The Entrez links provide a way to discover relevant information in Entrez databases based on a user’s specific interests. For example, one can readily obtain a list of scientific articles related to a particular molecule through an Entrez link from the corresponding compound record in PubChem to associated articles in PubMed.


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