Creating a Web Link to the Entrez Databases

Retrieve PubMed Citations

Base URL: http://www.ncbi.nlm.nih.gov/pubmed

To retrieve results in HTML or text format use PubMed Unique Identifiers (PMID).

• Retrieval parameters:

  • report=display format (AbstractPlus is the default display.)

  • format=text (HTML is the default format.)

  • tool=resource

  • email=address

Example:

Retrieve by PMID in AbstractPlus:

http://www.ncbi.nlm.nih.gov/pubmed/18276894,18276893

Retrieve by PMID in MEDLINE text format:

http://www.ncbi.nlm.nih.gov/pubmed/18276894,18276893?report=medline&format=text

Search PubMed

• Search parameters:

  • term=search terms (PubMed Help)

  • report=display format

  • dispmax=number of items to display if other than 20

  • tool=resource

  • email=address

Example:

PubMed antioxidant chocolate citations

http://www.ncbi.nlm.nih.gov/pubmed?term=antioxidant+chocolate

• activating Limits (PubMed Help):

  • cmd_current=Limits

  • pmfilter_filter name = filter value

• turning off Limits

  • pubmedfilters=true

Examples:

PubMed:
PubMed hay fever citations published in 2006, display the first 50:
http://www.ncbi.nlm.nih.gov/pubmed?term=hay+fever+AND+2006[pdat]&dispmax=50

PubMed citations on AZT limited to the AIDS subset:
http://www.ncbi.nlm.nih.gov/pubmed?term=azt&cmd_current=Limits&pmfilter_Subsets=AIDS

To turn off PubMed Limits and search for hay fever displayed in the Citation format:
http://www.ncbi.nlm.nih.gov/pubmed?term=hay+fever&pubmedfilters=true&report=citation

PubMed citations for the Text Word p21 and MeSH term Humans in the LinkOut display format:
http://www.ncbi.nlm.nih.gov/pubmed?term=p21[tw]+AND+humans[mh]&report=externallink

PubMed Feature Pages

• Limits: /limits

• Preview/Index: /index

• History: /history

• Clipboard: /clipboard

• Details: /details

Retrieve

Base URL: http://www.ncbi.nlm.nih.gov/sites/entrez

To retrieve results in HTML or text format use unique identifiers (primary IDs). Use Search to retrieve by accession numbers.

• HTML retrieval parameters:

  • cmd=retrieve

  • db=database

  • list_uids=id,id,id

  • dopt=display format

  • tool=resource

  • email=address

Example:

Gene Full Report for GeneIDs 40048 & 847

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=gene&list_uids=40048,847&dopt=full_report

• text retrieval parameters:

  • cmd=text

  • db=database

  • uid=id&uid=id&uid=id

  • dopt=display format

Example:

Protein sequence records in text format for GIs 9367031, 729567, 586553
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=text&db=protein&dopt=genpept&uid=9367031&uid=729567&uid=586553

Search

Use search to create a web link for terms with or without Boolean operators. “Escape” spaces by converting them to plus signs (+), e.g., Biochem Soc Trans should be Biochem+Soc+Trans.

You may also use Details to generate a search URL.

Base URL: http://www.ncbi.nlm.nih.gov/sites/entrez

• search parameters:

  • cmd=search

  • db=database

  • term=search terms (Entrez Help)

  • doptcmdl=display format

  • dispmax=number of items to display if other than 20

  • tool=resource

  • email=address

Example:
Protein records for AAC72193[accn] in the GenPept display:
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=protein&term=AAC72193[accn]&doptcmdl=GenPept

Nucleotide records for COMT sequences in the Brief display:
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=nucleotide&term=comt&doptcmdl=brief

OMIM:
OMIM records for the FBN1 gene in the Detailed display:
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=omim&term=fbn1[gene]&doptcmdl=detailed

Link

Display the related records (neighbors) or Entrez links for records using the unique identifiers (primary IDs), you may not use accession numbers.

Base URL: http://www.ncbi.nlm.nih.gov/sites/entrez?

• link parameters:

  • dbFrom=database searched (URL parameter is case sensitive)

  • db=database to retrieve links

  • from_uid=id

  • tool=resource

  • email=address

Examples:

Related Article citations for PubMed PMID 10495220:
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=link&db=pubmed&dbFrom=pubmed&from_uid=10495220

Nucleotide links from PubMed PMID 10492167:
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=link&db=nucleotide&dbFrom=pubmed&from_uid=10492167

PubMed links from Nucleotide GI 47717105:
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=link&db=pubmed&dbFrom=nucleotide&from_uid=47717105

Tool

A string with no internal spaces that identifies the resource that is using Entrez links. This argument is used to help NCBI provide better service to third parties generating Entrez queries from programs. As with any query system, it is sometimes possible to ask the same question different ways, with different effects on performance. NCBI requests that developers sending batch requests include a constant 'tool' argument for all requests using the utilities.

Example: tool=resource

Email Address

If you choose to provide an email address we will use it to contact you if there are problems with your queries or if we are changing software interfaces that might specifically affect your requests. If you choose not to include an email address you can sign up for utilities-announce to receive general announcements.

Example: email=name@institution.org