Download [Extra Quality] Ace Utilities
Luca Iknokinok
The Entrez Programming Utilities (E-utilities) are a set of nine server-side programs that provide a stable interface into the Entrez query and database system at the National Center for Biotechnology Information (NCBI). The E-utilities use a fixed URL syntax that translates a standard set of input parameters into the values necessary for various NCBI software components to search for and retrieve the requested data. The E-utilities are therefore the structured interface to the Entrez system, which currently includes 38 databases covering a variety of biomedical data, including nucleotide and protein sequences, gene records, three-dimensional molecular structures, and the biomedical literature.
To access these data, a piece of software first posts an E-utility URL to NCBI, then retrieves the results of this posting, after which it processes the data as required. The software can thus use any computer language that can send a URL to the E-utilities server and interpret the XML response; examples of such languages are Perl, Python, Java, and C++. Combining E-utilities components to form customized data pipelines within these applications is a powerful approach to data manipulation.
This chapter first describes the general function and use of the eight E-utilities, followed by basic usage guidelines and requirements, and concludes with a discussion of how the E-utilities function within the Entrez system.
In order not to overload the E-utility servers, 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. Failure to comply with this policy may result in an IP address being blocked from accessing NCBI. If NCBI blocks an IP address, service will not be restored unless the developers of the software accessing the E-utilities register values of the tool and email parameters with NCBI. The value of tool should be a string with no internal spaces that uniquely identifies the software producing the request. The value of email should be a complete and valid e-mail address of the software developer and not that of a third-party end user. The value of email will be used only to contact developers if NCBI observes requests that violate our policies, and we will attempt such contact prior to blocking access. In addition, developers may request that the value of email be added to the E-utility mailing list that provides announcements of software updates, known bugs and other policy changes affecting the E-utilities. To register tool and email values, simply send an e-mail to vog.hin.mln.ibcn@seitilitue including the desired values along with the name of either a developer or the organization creating the software. Once NCBI establishes communication with a developer, receives values for tool and email and validates the e-mail address in email, the block will be lifted. Once tool and email values are registered, all subsequent E-utility requests from that software package should contain both values. Please be aware that merely providing values for tool and email in requests is not sufficient to comply with this policy; these values must be registered with NCBI. Requests from any IP that lack registered values for tool and email and that violate the above usage policies may be blocked. Software developers may register values of tool and email at any time, and are encouraged to do so.
Since December 1, 2018, NCBI has provided API keys that offer enhanced levels of supported access to the E-utilities. Without an API key, any site (IP address) posting more than 3 requests per second to the E-utilities will receive an error message. By including an API key, a site can post up to 10 requests per second by default. Higher rates are available by request (vog.hin.mln.ibcn@seitilitue). Users can obtain an API key now from the Settings page of their NCBI account (to create an account, visit ). After creating the key, users should include it in each E-utility request by assigning it to the api_key parameter.
If you use the E-utilities within software, NCBI's Disclaimer and Copyright notice ( ) must be evident to users of your product. Please note that abstracts in PubMed may incorporate material that may be protected by U.S. and foreign copyright laws. All persons reproducing, redistributing, or making commercial use of this information are expected to adhere to the terms and conditions asserted by the copyright holder. Transmission or reproduction of protected items beyond that allowed by fair use (PDF) as defined in the copyright laws requires the written permission of the copyright owners. NLM provides no legal advice concerning distribution of copyrighted materials. Please consult your legal counsel. If you wish to do a large data mining project on PubMed data, you can download a local copy of the database at _medline.html.
When constructing URLs for the E-utilities, please use lowercase characters for all parameters except &WebEnv. There is no required order for the URL parameters in an E-utility URL, and null values or inappropriate parameters are generally ignored. Avoid placing spaces in the URLs, particularly in queries. If a space is required, use a plus sign (+) instead of a space:
The E-utilities access the core search and retrieval engine of the Entrez system and, therefore, are only capable of retrieving data that are already in Entrez. Although the majority of data at NCBI are in Entrez, there are several datasets that exist outside of the Entrez system. Before beginning a project with the E-utilities, check that the desired data can be found within an Entrez database.
Each Entrez database refers to the data records within it by an integer ID called a UID (unique identifier). Examples of UIDs are GI numbers for Nucleotide and Protein, PMIDs for PubMed, or MMDB-IDs for Structure. The E-utilities use UIDs for both data input and output, and thus it is often critical, especially for advanced data pipelines, to know how to find the UIDs associated with the desired data before beginning a project with the E-utilities.
The core of Entrez is an engine that performs two basic tasks for any Entrez database: 1) assemble a list of UIDs that match a text query, and 2) retrieve a brief summary record called a Document Summary (DocSum) for each UID. These two basic tasks of the Entrez engine are performed by ESearch and ESummary. ESearch returns a list of UIDs that match a text query in a given Entrez database, and ESummary returns DocSums that match a list of input UIDs. A text search in web Entrez is equivalent to ESearch-ESummary. EGQuery is a global version of ESearch that searches all Entrez databases simultaneously. Because these three E-utilities perform the two core Entrez functions, they function for all Entrez databases.
The E-utilities are useful when used by themselves in single URLs; however, their full potential is realized when successive E-utility URLs are combined to create a data pipeline. When used within such pipelines, the Entrez History server simplifies complex retrieval tasks by allowing easy data transfer between successive E-utility calls. Listed below are several examples of pipelines produced by combining E-utilities, with the arrows representing the passing of db, WebEnv and query_key values from one E-utility to another. These and related pipelines are discussed in detail in Chapter 3.
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