NCBI ESearch
search NCBI Databases by text query (Galaxy Version 1.1)Tool Parameters
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NCBI Entrez ESearch
Responds to a text query with the list of matching UIDs in a given database (for later use in ESummary, EFetch or ELink), along with the term translations of the query.
Example Queries
Search in PubMed with the term cancer for abstracts that have an Entrez date within the last 60 days:
| Parameter | Value |
|---|---|
| NCBI Database to Use | PubMed |
| Term | Cancer |
| Datetype | Entrez Date |
| In past N Days | 60 |
Search PubMed Central for free full text articles containing the query stem cells:
| Parameter | Value |
|---|---|
| NCBI Database to Use | PubMedCentral |
| Term | Stem Cells AND free fulltext[filter] |
Search in Nucleotide for all tRNAs:
| Parameter | Value |
|---|---|
| NCBI Database to Use | Nucleotide |
| Term | biomol trna[prop] |
Search in Protein for a molecular weight range:
| Parameter | Value |
|---|---|
| NCBI Database to Use | Protein |
| Term | 70000:90000[molecular weight] |
Usage Guidelines and Requirements
Frequency, Timing, and Registration of E-utility URL Requests
In order not to overload the E-utility servers, NCBI recommends that users 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.
Minimizing the Number of Requests
If a task requires searching for and/or downloading a large number of records, it is much more efficient to use the Entrez History to upload and/or retrieve these records in batches rather than using separate requests for each record. Please refer to Application 3 in Chapter 3 for an example. Many thousands of IDs can be uploaded using a single EPost request, and several hundred records can be downloaded using one EFetch request.
Disclaimer and Copyright Issues
In accordance with requirements of NCBI's E-Utilities, we must provide the following disclaimer:
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 enter into a licensing agreement and lease the data for free from NLM. For more information on this please see http://www.nlm.nih.gov/databases/leased.html
The full disclaimer is available on their website
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