This user guide provides instructions on creating a Web link or bookmark to PubMed and the other Entrez databases.
Users intending to send frequent queries or retrieve large numbers of records from Entrez should use the Entrez Programming Utilities (E-Utilities). Users must comply with the User Requirements to prevent overloading NCBI systems.
Retrieve PubMed citations in HTML or Text format using PubMed IDs (PMID)
Search PubMed with terms
PubMed Link to related records
PubMed Feature Pages
NLM currently leases PubMed journal citations, at no charge.
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 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
Limits: /limits
Preview/Index: /index
History: /history
Clipboard: /clipboard
Details: /details
retrieve records in HTML or Text format using unique identifiers
search with terms
link to related records or neighbors
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
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
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:
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
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
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
Display Formats for Sample Entrez Databases
Note: Scripts/programs that import XML should use E-Utilities.
Database | Display Format | |
PubMed | DocSum, Brief, Abstract, AbstractPlus, Citation, MEDLINE, XML, ASN1, ExternalLink | |
Nucleotide | DocSum, Brief, GenBank, ASN1, FASTA, ExternalLink, XML, Graph, fasta_xml, gbc_xml | |
OMIM | Detailed, Synopsis, Variants, ASN1, XML, ExternalLink | |
Gene | DocSum, Full_Report, ASN1, XML, Gene_Table, ExternalLink | |
Protein | DocSum, Brief, GenPept, ASN1, FASTA, ExternalLink, XML, graph, fasta_xml, gpc_xml | |
Genome | DocSum, Brief, ASN1, ExternalLink, XML, Protein Table, cDNA FASTA, Protein FASTA, Structural RNA Table, Contig Table | |
Structure | DocSum, Brief | |
PopSet | DocSum, Brief, ASN1, ExternalLink | |
Taxonomy | DocSum, Brief, TxUidList, TxInfo, TxTree, ExternalLink, XML |