Section Contents

Searching by using the MeSH database

Searching for journals in the Journals database

Using the Text version of PubMed

Creating a Web link to search PubMed

Using the E-utilities programming tools

Using the Batch Citation Matcher

Using Batch Entrez

MeSH (Medical Subject Headings) is NLM's controlled vocabulary thesaurus used for indexing MEDLINE articles. The MeSH Database is available from the Search menu or the sidebar.

Use the MeSH database to find MeSH terms including Subheadings, Publication Types, Supplementary Concept Records (substance names) and Pharmacological Actions - and build a PubMed search strategy. The MeSH database can be searched by MeSH term, MeSH Entry Term, Subheading, Publication Type, Substance Name, or words within a MeSH Scope Note. Subheadings and Publication Types are included in the MeSH term searches.

Please see the following MeSH Database animated tutorials:

• Searching with the MeSH Database
• Combining MeSH Terms
• Subheadings and other features of the MeSH Database

What are the Suggestions? The database displays MeSH or Entry Term suggestions based on an algorithm that compares letter combinations in words. You can use the MeSH or Entry Term suggestion link to go directly to a record. A new set of suggestions will be displayed based on the selected term.

More information about the MeSH database:

• Search results are displayed in relevance-ranked order, therefore, when a user’s search exactly matches a MeSH Term, that Term is displayed first.
• Click the MeSH term from the Summary display or choose Full from the Display menu to view additional information and search specifications, such as Subheadings, Restrict Search to Major Topic headings only or Do Not Explode this term.
• Year Introduced is the year the term was added to the MeSH. If more than one year is shown, the term was available for indexing back to the earliest year noted. Articles are indexed using the vocabulary in place at the time of indexing, therefore, the Year Introduced for a term and the date of publication of a citation indexed with that term may not agree.

The MeSH database Links menu includes the following links:

• PubMed - retrieves citations for the MeSH term in PubMed.
• PubMed – Major Topic – retrieves citations for the MeSH terms as a Major Topic of the article in PubMed.
• Clinical Queries - enters the MeSH term in the Clinical Queries search box.
• NLM MeSH Browser - links to the NLM MeSH Browser for more information about the MeSH term.

The display menu option PubMed Links retrieves PubMed citations for the selected MeSH terms or the MeSH terms displayed on the page.

Search Box: The MeSH database provides a Search Box that can be used to build a PubMed search. From any display format:

1. Click the MeSH term check box, including specifications if using the Full display, e.g., Subheadings.
2. Use the Send to menu to select one of the following:
3. Search Box with AND
4. Search Box with OR
5. Search Box with NOT
6. To add additional terms to this strategy, continue searching the database and add terms to the Search Box using the Send to Search Box feature.
7. When you have completed your search click Search PubMed.

The Journals Database includes information about the journals in PubMed and the other NCBI databases.

What are the Suggestions? In addition to the search results, this database provides suggestions. The suggestions are based on an algorithm that scores the relatedness of phrases included in a user's journal query. Click on a journal under Suggestions to go directly to a specific journal record.  Suggestions are generated from an index (multi) that is a combination of indices which may result in a journal being repeated in the list of suggestions.

Searching in the Journals database:

1. Enter the full or partial journal name in the search box
2. Click Go.
3. Click the journal title for a specific journal, or choose Full from the Display menu, to view additional information.

Building a PubMed search for multiple journals:

1. Run a search and use the check boxes to select the journals.
2. Select Search box with OR from the Send to menu.
3. To add additional journals continue searching the database and adding the journals to the Search Box using the Send to Search Box feature, and then click Search PubMed.

Note: To search PubMed for all journals displayed in a journal search choose PubMed Links from the Display menu.

More information about the Journals database:

• The Journals database includes journals in the other NCBI databases as well as PubMed. To limit journal searches to only PubMed journals or currently indexed MEDLINE journals, click these check boxes in Limits.
• Click the NLM ID to link to journal information in the NLM Catalog.
• If a journal includes parentheses or brackets, e.g., J Hand Surg [Am], enter the abbreviation or title without the special characters, j hand surg am.
• Search results are displayed in alphabetical order except when a user's search exactly matches a journal title, then that title will display first.

Untagged journal terms are searched in all fields. The following tags are also available to limit your search to a specific field:

Some or all of the journal issues are printed on acid-free paper. Search as acidfree.

The last year of the publication. To enter a date range, insert a colon (:) between each date, e.g., 1996:1998 [eyr].

Search for journals that are currently indexed for MEDLINE with currentlyindexed and those that are not currently indexed with notcurrrentlyindexed. Search for the version of the journal indexed as currentlyindexedprint or currentlyindexedelectronic.

Used for internal processing at NLM.

To search for an indexed for journal subset, enter in the search box jsubset?, where ? represents the subset value. Click the Limits tab to search for subsets.

Search for selectively or fully indexed journals as: currentindexingtreatmentfull or currentindexingtreatmentselective.

The International Organization for Standardization (ISO) journal abbreviation.

The ISSN number for the journal.

Search for all print or electronic ISSNs as print[is] or electronic[is].

The language the journal is published. Click the Limits tab to search by language.

The NLM Integrated Library System alpha-numeric identifier for the journal.

Indicates the journal's country of publication.

Search for journals currently in PubMed Central (PMC) as: journals pmc[sb] and for forthcoming PMC journals as: journalspmcforthcoming.

The first year of the publication. To enter a date range, insert a colon (:) between each date, e.g., 1996:1998 [syr].

Subject terms are assigned by NLM for MEDLINE journals to describe a journal’s overall scope. The complete list of subject terms is available

To search for journals included in a specific database, enter journals xxx[sb], where xxx is the database, e.g., journals nuccore[sb]

The full journal title.

The journal title abbreviation.

Other journal resources include:

• The list of PubMed journals with links to full-text
• A list of all journals that are included in PubMed by FTP in the Uncompressed GNU Zip, UNIX Compress, or PKZIP format
• The List of Serials Indexed for Online Users
• The List of Journals Indexed in Index Medicus
• The NLM Catalog database

Click Text version on the PubMed sidebar.

The Text version is helpful for users who require special adaptive equipment to access the Web. It provides basic PubMed search and retrieval functionality.

Text Version Help is available.

See Creating a Web Link to the NCBI Databases and Add PubMed to Your Web Site for more information.

Entrez Programming Utilities are tools that provide access to data outside of the regular Web search interface. This may be helpful for retrieving search results for future use in another environment.

The Batch Citation Matcher, available from the PubMed sidebar menu, allows you to retrieve the PubMed IDs for many articles all at once. This feature requires that you enter the bibliographic information (journal, volume, page, etc.) in a format outlined in the Batch Citation Matcher online help.

Use Batch Entrez to upload a file of PMIDs directly to PubMed.