• To Full-Page Images: Direct access to the full-page image database is now permitted without first conducting a search on the full-text database. Such access is now possible by using a URL of the form:

http://patimg1.uspto.gov/.piw?Docid=0nnnnnnn&idkey=NONE

or

http://patimg2.uspto.gov/.piw?Docid=0nnnnnnn&idkey=NONE

where “nnnnnnn” is the seven-digit patent number (right-justified with leading zeroes). The first URL, to patimg1.uspto.gov, is used if the patent number’s last two (low-order) digits are in the range 00 to 49; the second URL, to patimg2.uspto.gov, is used if the patent number’s last two digits are in the range 50 to 99.

For example, “http://patimg1.uspto.gov/.piw?Docid=01234501&idkey=NONE” would retrieve patent number 1,234,501;

“http://patimg2.uspto.gov/.piw?Docid=01234567&idkey=NONE” would retrieve patent number 1,234,567.

When a patent image is retrieved by this method, clicking on the link showing an up-arrow “Full-Text” will no longer take the user to the full text page.

1, Use a Perl tool PubCrawler: http://pubcrawler.gen.tcd.ie/pubcrawler_pod.html

2, or write a program using Perl/PHP curl, Java HttpUnit

• Search by PMID, example: http://www.ncbi.nlm.nih.gov/pubmed/18418893
• Search by Author, example: http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Bonnet%20JE%22%5BAuthor%5D
• Search by Keywords, example: http://www.ncbi.nlm.nih.gov/pubmed?term=antioxidant%20chocolate
• get Abstract: http://www.ncbi.nlm.nih.gov/entrez/queryd.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=18461658&itool=pubmed_docsum
• get Related Articles: http://www.ncbi.nlm.nih.gov/entrez/queryd.fcgi?itool=pubmed_Abstract&db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=18276748

3, Or use EUtiles: eutilities are available from http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html

EFetch for Literature Databases (PubMed, PubMed Central (PMC), Journals, OMIM)

EFetch: Retrieves records in the requested format from a list of one or more UIs or the user’s environment.

EFetch documentation is also available for the sequence and other molecular biology, and Taxonomy databases.

• Base URL: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?

  ---

  URL parameters: (NOTE: Utility parameters may be case sensitive. Use lower case characters in all parameters except forWebEnv.

  Database

  db=[pubmed|pmc|journals|omim]

  pubmed – Journal publishers hold the copyright on the abstracts in PubMed. NLM provides no legal advice concerning distribution of copyrighted materials.
  pmc – PubMed Central contains a number of articles classified as “open access” for which you may download the full text as XML. For the remaining articles in PMC you may download only the abstracts as XML. See the PMC Open Access page for a description of open access terms and the list of open access journals in PMC.
  omim – The OMIM ^TM database including the collective data contained therein is the property of the Johns Hopkins University, which holds the copyright thereto. There are restrictions on use.

  Web Environment: Value previously returned in XML results from ESearch and EPost and used with EFetch in place of a primary UI result list.
  

  WebEnv=WgHmIcDG], etc.

  Query_key: The value used for a history search number or previously returned in XML results from ESearch or EPost.
  

  query_key=6

  Note: WebEnv is similar to the cookie that is set on a user’s computers when accessing PubMed on the web. If the parameter usehistory=y is included in an ESearch URL both a WebEnv (cookie string) and query_key (history number) values will be returned in the results. Rather then using the retrieved PMIDs in an ESummary URL you may simply use the WebEnv and query_key values to retrieve the records. WebEnv will change for each ESearch query.

  Tool: A string with no internal spaces that identifies the resource which is using Entrez links (e.g., tool=flybase). 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.

  tool=

  E-mail 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 we cannot provide specific help to you, but you can still sign up for utilities-announce to receive general announcements.
  

  email=

  Record Identifier: UIs required if WebEnv is not used.

  id=11877539, 11822933,11871444

  Display Numbers: Used when the results from EPost or ESearch are maintained in the user’s environment. The maximum number of retrieved records is 10,000.
  

  retstart=x (x= sequential number of the first id retrieved – default=0 which will retrieve the first record)
  retmax=y (y= number of items retrieved – default=20)

  Retrieval Mode:
  

  retmode=output format

  Current values:
  

  xml (not journals)
  html
  text
  asn.1 (not journals)

  Use your web browser’s View Page Source function to display results in xml retrieval mode.

  Retrieval Type:

  rettype=output types based on database

  Current values:
  

  uilist
  abstract (not omim)
  citation (not omim)
  medline (not omim)
  full (journals and omim)

  Not all Retrieval Modes are possible with all Retrieval Types.

  PubMed Options:

  	uilist	abstract	citation	medline
  xml	x	x*	x*	x*
  text	x	x	x	x
  html	x	x	x	x
  asn.1	n/a	x*	x*	x

  x = retrieval mode available
  *returned retrieval type is the complete record in the retrieval mode
  n/a – not available

  OMIM Options: (not case sensitive)

  	uilist (MIM numbers)	docsum	synopsis (Clinical synopsis)	variants (Allelic Variants)	detailed	ExternalLink
  xml	x	x*	x*	x*	x*	x*
  text	x	x	x	x	x*	x*
  html	x	x	x	x	x*	x*
  asn.1	x*	x*	x*	x*	x*	x*

  x = retrieval mode available
  *returned retrieval type is the complete record in the retrieval mode
  n/a – not available

  Examples:
  In PubMed display PMIDs 12091962 and 9997 in html retrieval mode and abstract retrieval type:
  http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=12345,9997&retmode=html&rettype=abstract

• Get one article’s abstract from PubMed using PMID:

• http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=18324973&retmode=html&rettype=abstract

  In PubMed display PMIDs from history statement in html retrieval mode and medline retrieval type (where x is replaced by WebEnv and query_key values):
  http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&WebEnv=xxxx&query_key=x&retmode=html&rettype=medline

  In PubMed display PMIDs in xml retrieval mode:
  http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11748933,11700088&retmode=xml

  In Journals display records for journal IDs 22682,21698,1490:
  http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=journals&id=22682,21698,1490&rettype=full

  In PubMed Central display xml (only retmode available for pmc) for ID 212403:
  http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=212403

  In OMIM show the full record for MIM number 601100 as XML:
  http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=omim&id=601100&retmode=xml&rettype=full

• Search PubMed by author:

  http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retstart=0&retmax=100&usehistory=y&retmode=xml&term=Sten%20H%20Vermund[author]

  Search PubMed by keyword:

  http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retstart=0&retmax=100&usehistory=y&retmode=xml&term=polymerase

4, or SOAP: http://www.ncbi.nlm.nih.gov/entrez/query/static/esoap_help.html

References:

http://plindenbaum.blogspot.com/2007/06/i-will-not-spam-nature-network-with.html

http://java.sun.com/developer/EJTechTips/2004/tt0730.html

http://www.cpan.org/authors/id/V/VA/VALSALAM/bibAddPubMed-0.2

Technorati : Pubmed search PHP Perl Java

Creating a Web Link to the Entrez Databases

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.

PubMed

• 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.

Retrieve PubMed Citations

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

To retrieve results in HTML ortext 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

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

Other Entrez Databases

• retrieve records in HTML or Text format using unique identifiers
• search with terms
• link to related records or neighbors

Retrieve

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

To retrieve results in HTML ortext 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: name@institution.org

Display Formats

Display Formats for Sample Entrez Databases

Note: Scripts/programs that import XML should use E-Utilities.

Technorati : Entrez NCBI PubMed