PubMed Help

Table of Contents:

• Basic PubMed Search
• Advanced Search
  • Entering a Search Term
    • Search Fields
    • Search Modes
  • Choosing a Term in List Terms Mode
  • Your Chosen List of Terms
  • Retrieving Documents
• The Document Summary Page
  • Viewing Documents
    • Viewing Formats
  • Getting Document Neighbors and Links
  • Outside Links
• For Experts Only
  • Entering Complex Boolean Expressions
• Special Features
• For More Assistance

Basic PubMed Search

• Enter one or more search terms.
• Author names should be entered in the form Smith JB, but initials are optional.
• Journal titles may be entered in full, as valid MEDLINE abbreviations, or as ISSN numbers (see Journal Browser for more information).

Enter the term or terms that you wish to search on, separating terms by spaces, and press the return key or the Search button. This will take you immediately to the Document Summary Page, where you can review the results of your search.

Finding all terms that begin with a given text string

Note! If the use of an * character results in too long a list of terms to process efficiently (more than a hundred or so), PubMed will not perform the search and will so inform you.

Forcing PubMed to search for a phrase

Lipman DJ AND Genomics

It may happen that PubMed fails to find a phrase that you think is vital to a search. For instance, if you enter

brca 1

PubMed will not recognize that this is all one item and will search for "brca" and "1" separately. Since the latter is a numeral and is not included in the index for title and abstract fields, it will likely not find what you want. You can circumvent this by putting quotes (") around the words that PubMed is failing to recognize, e.g.

"brca 1"

PubMed does not actually perform adjacency searching, but employs a list of recognized phrases against which search terms are matched. If your search phrase is not on that list, then the individual terms are ANDed together. Use of quotes forces PubMed to check a second dictionary to identify the phrase. In addition, if you put the phrase in quotes, you are specifying that the search be performed ONLY if the phrase is recognized. Individual search terms will not be ANDed in this case.

Important! It is usually best to let Entrez do your grouping for most accurate retrieval, and to use quotes only when PubMed has failed to find anyting because of a failure to group words properly. Forcing PubMed to group words will often result in "No Documents Found". This does not mean that the phrase you are looking for does not exist; rather, it was not indexed as a group.

For Experts

All of the Advanced Search capabilities are still available in Basic mode, they are just hidden.

Advanced Search

Entering a Search Term

To access the advanced search mode in Pubmed, simply click on Advanced Search from the PubMed home page. You will then see a screen that looks like this:

• Enter one or more search terms.
• Author names should be entered in the form Smith JB, but initials are optional.
• Journal titles may be entered in full, as valid MEDLINE abbreviations, or as ISSN numbers (see Journal Browser for more information).
• Use pull-down menus to specify fields and search mode.
• Boolean search statements can also be entered directly in the search box, using AND, OR, and NOT logic operators. See Boolean Search page for more information.

Select the field and mode under which you want to search, enter the term you want to search for in the box given, and then press the Search button.

Search Fields

• Affiliation [AD, AFFL] contains the institutional affiliation and address of the primary author, and sometimes of other authors.
• All Fields [ALL] covers all searchable PubMed fields.
• Author Name [AU, AUTH] contains the list of authors for a paper in the literature. The format for author names is the last name, followed by a space and the first initial(s), without periods. For example, David J. Lipman would be Lipman DJ; James Ostell would be Ostell J . Initials may be omitted when searching.
• E. C. Number [RN, ECNO] is a number assigned by the Enzyme Commission to designate a particular enzyme. This field also includes CAS Registry Numbers.
• Journal Title [TA, JOUR] is the name of the journal where the record was published. Journal names are stored in the database in abbreviated form; for instance, the Journal of Biological Chemistry is stored as J Biol Chem . If you are not sure how a journal name is abbreviated, use List Terms mode to browse the journal titles. You may also enter the complete joujrnal name or the ISSN number in this field. A Journal Browser is also available to look up the full name, abbreviation, and ISSN number of a journal.
• Language [LA, LANG] is the language in which the article was published. Note that many non-English articles, however, do have English abstracts.
• MeSH Major Topic [MAJR] includes all MeSH Terms (see below) that are marked as being of major importance to this record by the National Library of Medicine indexers for MEDLINE.
• MeSH Terms [MH, MESH] includes all of the terms in the Medical Subject Headings, a controlled vocabulary of terms used to index MEDLINE. Each MEDLINE citation is given a group of MeSH terms that relate to the subject of the paper from which it is drawn. Frequently, MeSH terms will have an additional term, called a "subheading", which further defines how the MeSH term relates to the article it is associated with. This subheading is appended to the MeSH term, e.g. "pneumonia/diagnosis". Searching on the MeSH term (here, pneumonia) will retrieve all of the articles that use that MeSH term, whether they have subheadings or not. Use the subheading terms if you require more specificity than the MeSH term alone allows.
  Note: MeSH terms searched for using the Mesh or Mesh Major Topic fields are automatically "exploded" by PubMed; that is, all terms which are logical subsets of the term entered are included. For instance, "vision disorders" includes "blindness" . MeSH terms found using the "All Fields" search, however, are NOT exploded.
• Modification Date [MDAT] contains the date that the record was placed into PubMed, in the format year/month/day, as for Publication Date, see below.
• Page Number [PAGE] is the number of the first journal page that the article appears on.
• Publication Date [DP, PDAT] contains the date that the article was published in the format year/month/day, e.g. 1984/10/06. A year alone, (e.g. "1984") will retrieve all articles for that year; a year and month (e.g. "1984/03") will retrieve all for that month. Note that journals vary in the way the date appers, some including only year, some year plus month, some year plus month plus day. PubMed takes the date as it appears in the journal.
• Publication Type [PT, PTYP] refers to the form of presentation of an article or other work. Examples include review articles, clinical trials, randomized controlled trials, and retracted publications.
• Substance [NM, SUBS] contains the names of any chemicals associated with this record from the Chemical Abstract Service (CAS) registry and the MEDLINE Name of Substance field.
• Text Words [TW, WORD] includes all words in the title and abstract, plus indivudial words from MeSH terms and chemical substance names.
• Title Words [TI, TITL] includes only those words found in the title of a record.
• Volume [VI, VOL] is the number of the journal volume in which this article is published..
• Medline ID [UI, MUID] is the MEDLINE unique identifier of a given citation.
• PubMed ID [PMID] is the PubMed unique identifier of a given citation.

  Finding all terms that begin with a given text string

  Placing an asterisk at the end of a search term will cause PubMed to search for all terms that begin with that word; for instance bacter* will find all terms that begin with the letters bacter, e.g. bacteria, bacterium, bacteriophage, etc. Phrases that have a space in the word that occurs after the asterisk will NOT be included; for instance, "infection*" will include "infections", but not "infection control".

  Note! If the use of an * character results in too long a list of terms to process efficiently (more than a hundred or so), PubMed will not perform the search and will so inform you.

  Forcing PubMed to search for a phrase

  PubMed will do its best to find logical groupings in your input. For instance, if you enter "Lipman DJ Genomics" (without quotes), PubMed will recognize that Lipman DJ is the name of an author and will convert your search into

  Lipman DJ AND Genomics

  It may happen that PubMed fails to find a phrase that you think is vital to a search. For instance, if you enter

  brca 1

  PubMed will not recognize that this is all one item and will search for "brca" and "1" separately. Since the latter is a numeral and is not included in the index for title and abstract fields, it will likely not find what you want. You can circumvent this by putting quotes (") around the words that PubMed is failing to recognize, e.g.

  "brca 1"

  PubMed does not actually perform adjacency searching, but employs a list of recognized phrases against which search terms are matched. If your search phrase is not on that list, then the individual terms are ANDed together. Use of quotes forces PubMed to check a second dictionary to identify the phrase. In addition, if you put the phrase in quotes, you are specifying that the search be performed ONLY if the phrase is recognized. Individual search terms will not be ANDed in this case.

  Important! It is usually best to let Entrez do your grouping for most accurate retrieval, and to use quotes only when PubMed has failed to find anyting because of a failure to group words properly. Forcing PubMed to group words will often result in "No Documents Found". This does not mean that the phrase you are looking for does not exist; rather, it was not indexed as a group.

  Expert users of PubMed can, if they wish, enter a full boolean expression in the term box. See Entering a Complex Boolean Expression below.

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  Search Modes

  WWW PubMed allows you to enter terms for searching in several different ways.
  
  • In List Terms mode, when you enter a term, PubMed displays the list of available terms for that field, starting at the first term which begins with the characters that you entered. You can then select one or more terms to add to your search. For example, to see the text terms beginning with "pneum", you would enter "pneum" in the term box, select "Text Terms" and "List Terms", then press Search . List Terms Mode thus allows you to browse through the terms in any given field. This can be very useful if you are not sure how something is spelled.
  • In Automatic mode, the term or terms that you enter are immediately added to your search. If you enter more than one word, PubMed will look for a phrase with the terms entered. If no phrase is found the terms will be ANDed for your query results. If PubMed groups or fails to group the words you entered properly, you can place one or more words in quotes (") to force PubMed to group them as you wish.

  Choosing a Term in List Terms Mode

  If a term is entered in the term box using List Terms Mode and the Search button pressed, a list of the terms that begin with the characters entered in the term box will be presented. For instance, if "pneum" were entered (with the field selector on "All Fields"), the resultant list might look like this :

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  Add Term(s) to Query :

  Search Field: Affiliation All Fields Author Name E. C. Number Issue Journal Name Language MeSH Major Topic MeSH Terms Page Number Publication Date Publication Type Substance Name Text Word Title Word Volume MEDLINE ID PubMed ID Search Mode: Automatic List Terms
  Enter Terms:

  Enter one or more author last names, text words, or other keywords. To search for all terms that begin with a given word, place an asterisk (*) at the end of the word. Journal Titles must be MEDLINE abbreviations; Author names must be in the form LastName Initial(s), e.g. Smith BJ. The initials can be omitted. Detailed Help is available.

  Clear All

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  Available terms for the field All Fields (Number of Records)
  
  (Scroll List Up) pneum (2) pneuma (8) pneuma tonometer (3) pneumabort (3) pneumabort k (3) pneumacystoides (1) pneumadin (3) pneumallergen (4) pneumallergens (8) pneumallergerns (1) pneumangiographic (1) pneumania (1) pneumaniae (1) pneumapathia (1) pneumaperitoneum (1) pneumarthography (1) pneumarthro (1) pneumarthro computed (1) pneumarthro ct (1) pneumarthrocentesis (1) pneumarthrocomputerized (1) pneumarthrography (1) pneumarthrosis (3) pneumascos (3) pneumat (2) pneumathorax (3) pneumatially (1) pneumatic (2545) pneumatic antishock garments (13) pneumatic compression (243) pneumatic compression boots (12) pneumatic driven (2) pneumatic foam (1) pneumatic hydraulic (6) pneumatic hydrostatic (1) pneumatic operated (1) pneumatic powered (2) pneumatic pump (16) pneumatic retinopexy (87) pneumatic sac type (1) pneumatic splints (6) pneumatic stockings (5) pneumatic to electric (1) pneumatic to electrical (1) pneumatic tool (5) pneumatic tourniquets (25) pneumatic tube (29) pneumatic tube systems (2) pneumatic type (3) pneumatically (256) pneumatically actuated (24) pneumatically applied (1) pneumatically assisted (20) pneumatically driven (95) pneumatically induced (1) pneumatically sprung (1) pneumaticity (1) pneumaticos (1) pneumaticos sg (1) pneumatics (7) pneumaticum (2) pneumatikakis (4) pneumatikakis g (4) pneumatikos (3) pneumatikos j (3) pneumatisation (56) pneumatisations (1) pneumatische (1) pneumatischen (1) pneumatised (16) pneumatization (323) pneumatizationas (1) pneumatized (105) pneumatizes (1) pneumato (3) pneumato entericus (1) pneumato ophthalmitis (1) pneumatoamperically (1) pneumatoamperometric (1) pneumatocele (179) pneumatocele a (13) pneumatocele osteoma (1) pneumatoceles (75) pneumatoceles lung (1) pneumatocephalon (1) pneumatocephalus (6) pneumatocoele (10) pneumatocoeles (10) pneumatocyst (6) pneumatocysts (3) pneumatocytes (4) pneumatogram (2) pneumatograms (1) pneumatography (1) pneumatology (2) pneumatoma (1) pneumatometer (1) pneumatometra (1) pneumatomucocele (1) pneumatonograph (26) (Scroll List Down)

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  After each term is the number of articles that the term appears in.
  To pick one or more of the terms in the list of available terms, highlight them and press Select; the terms will then be added to your search. If you picked more than one term you will retrieve articles that contain either of the two terms.

  If the term that you want to select is not in the scrolling list of terms, you can scroll up or down further by selecting Scroll List Up/Down from the list, then pressing Select. If you want to look at another list of terms altogether, simply reenter the new term in the term box as before and press Search.

  Your Chosen List of Terms

  As you enter or select terms, the terms will be added to your search and also placed into a list at the bottom of your screen; this list is called the Chosen List. For example, if you had entered the term "pneumonia", and then entered "cytomegalo*", the Chosen List would look like this (the middle part of the form is omitted for brevity) :

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  Modify Current Query :

  
  Term (Total Records)
  pneumonia[ALL] (35538) cytomegalo* [ALL] (16000)
  for the Intersection (AND) Union (OR) Difference (BUTNOT) Range of the selected terms.
  

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  PubMed automatically calculates the intersection of the terms you enter and displays the resultant search statement at the top of the screen, calculating the number of records to retrieve. The terms included in the search are highlighted in the Chosen List. Once you have entered terms of interest, you can do any of the following:
  • If the number of documents is reasonably small, press the Retrieve button to see a listing of the records your search has chosen; see Retrieving Documents below.
  • Select and/or deselect terms in the chosen list until the terms you wish to include in the search are highlighted, then press the Search button. The system will then create a new search statement based upon only the highlighted terms, according to the type of search you have selected. Here is what each of the search types do:
    • Intersection (AND): only those records that contain all of the terms specified are returned by the search. This is abbreviated to '&' in the search statement.
    • Union (OR): those records that contain any of the terms specified are returned. This is abbreviated to '|' .
    • Difference (BUTNOT): those records that contain the uppermost term but not any of the lower terms are returned. This is abbreviated to '-' .
    Terms or expressions which are combined using the Search button are grouped into a single entity and placed on a separate line in the Chosen List. This permits you to combine terms flexibly in many ways.
    Note that the Retrieve button will continue to retrieve your old search until you tell the system to update your search using the Search button.

  Retrieving Documents

  When the number of documents that satisfy your query is reasonably small, press the Retrieve button to view them. This produces a listing containing each document's title, author, and publication year. This listing is called the Document Summary Page, and is discussed in detailed below.
  If the number of documents that your query retrieves is large, a box will appear indicating the maximum number of articles that will be displayed at a time. You can change this number to whatever is suitable. If you cannot or do not choose to display all of the articles that your search has found, the articles you do see will be the more recent ones in the database.

  The Document Summary Page

  Once you have pressed the Retrieve button, PubMed will display a listing of information on the documents that your search has found. This permits you to browse through the retrieved list of documents easily. Once you have determined which documents in the list are of interest, you can view them individually or as a group.

  Viewing Documents

  Each document can be viewed in any of several formats. The best way to decide what format best suits you for any given purpose is to experiment with them and see what they look like.

  To view a single document in PubMed, select the link at the top of the document. This will show you the document in default Citation format, which includes journal citation, article title, authors, affiliation or address, abstract, MeSH terms and chemical substances, and the MEDLINE and PubMed unique identification numbers.

  To view several documents at once, select the documents you wish to view by selecting their checkboxes. If you want to view all of the documents on the page, there is no need to select any of them. Then pick the type of report you want from the pull down menu at the top of the screen and press Display.

  Viewing Formats

  Viewing formats available include:

  For PubMed articles:

  • Citation report - Journal Citation, Title, Authors, Address or Affiliation, Abstract, MeSH terms, chemical substances, MEDLINE and PubMed unique identifiers.
  • Abstract report - Journal Citation, Title, Authors, Address or Affiliation, and Abstract.
  • MEDLINE report - Traditional two-character tagged field MEDLINE format for the full record. This is the format to use for downloading records into bibliographic management software packages.
  • ASN.1 report - A structured format for the full record, in which each data element is explicitly represented.

  Getting Document Neighbors and Links

  One of the most helpful features of PubMed is the ability to find documents that are similar to a document you are interested in. These related documents are called neighbors. For more details on what neighbors are, how they are calculated, and how to use them, see Special Features below.

  To retrieve the neighbors or links for a given record or set of records, the procedure is the same as for viewing records, above. Select the document(s) using the checkboxes on the left (select nothing to see them all). Then select the type of link you want from the pull down menu at the top of the screen and click the display button.

  Outside Links to Journals

  Some Documents have links to the WWW site for the specific journal in which the full text of the article is published. This will appear as a named journal button at the top of the article report.

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  For Experts Only

  This section explains features of PubMed that may be of interest to users with very specific needs. Most users do not need to be familiar with the items in this section.

  Entering Complex Boolean Expressions

  A search can be performed by specifying the terms to search, their fields, and the boolean operations to performs on them, all at once. Use the following syntax :
  • term [field] operator term [field] ....(etc)

  term is the term string that you wish to search on. All of the terms that begin with a given string can be searched on by appending an * to the end of the term.
  For example, "baker*[auth]" would find all of the author names that begin with 'baker'.

  field is the PubMed field designation, where AD=affiliation, ALL=all fields, AU=author, TA=journal title, MAJR=MeSH Major Topic, MH=MeSH terms, MDAT-modification date, PAGE=page number, PDAT=publication date, PT=publication type, NM=substance name, TW=text words, TI=title words, and VI=volume.

  operator is any of :

  • AND (for intersection)
  • OR (for union)
  • NOT (for difference).
  Note : Boolean expressions are normally processed left to right. If you wish part of your boolean expression to be processed out of order, enclose it in parentheses.

  An Example of a boolean expression : Find the articles in the Journal of Biological Chemistry that contain the term "p21" in their text :

  p21 [TW] AND J Biol Chem [TA]

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  Special Features

  What makes PubMed more powerful than many services is that most of its records are linked to other records, both within a given database and between databases. Links within a database are called "neighbors".

  PubMed neighbors are determined by comparing the Text and MeSH terms of each article, using a powerful algorithm that determines just how well the article matches every other article. The best matches for any article are saved, and you can retrieve them using the "Related Articles" button at the top of the article report.

  What this means is that if you find one or a few documents that match what you are looking for, using the "MEDLINE neighbors" on the pulldown menu will find a great many more documents that are likely to be relevant, in order from most useful to least. This allows you to find what you want with much greater speed and accuracy: instead of having to flip through thousands of documents to assure yourself that nothing germane to your query was missed, you can find just a few, then look at their neighbors.

  Try this feature out and see how it works for you; you may well wonder how you got along without it!

  In addition, some documents are linked to others for reasons other than computed similarity. For instance, if a nucleotide or protein sequence was published in a PubMed article, the two will be linked to one another.

  For More Assistance

  If you have found a bug or are still confused, please e-mail to info@ncbi.nlm.nih.gov and we will be happy to assist you.