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Glossary

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

-A-

Abridged Index Medicus (AIM) - A National Library of Medicine® (NLM®) bibliography of articles from 120 English language clinical journals arranged in subject and author sections. It was designed for individual practitioners and libraries of small hospitals and clinics. This publication ceased following the Volume 28, Number 12 (December 1997) issue. While AIM ceased publication, it remains a subset limit within (Core clinical journals) within PubMed®.

AIDS Subset - This subset strategy was created to facilitate searching for subjects in the area of AIDS. It is based on search strategies used for creating NLM AIDSLINE® database. This subset can also be used in a search as aids [sb].

AIDSLINE® - AIDS Information Online is a database of bibliographic citations to literature covering research, clinical aspects and health policy issues about AIDS and related topics.

AIM - see Abridged Index Medicus (AIM)

Author Index - see Index

automatic explosion (explode) - In PubMed, MeSH (Medical Subject Headings) terms (as well as any subheading that is the top of a "subheading tree") are "exploded" automatically to retrieve citations that carry the specified MeSH heading (or subheading) and also retrieve citations that carry any of the more specific MeSH headings (or subheadings) indented beneath it in the Tree structure.

Automatic Term Mapping - The process used by PubMed to find a match to unqualified terms that are entered into the query box. Untagged terms are matched (in this order) against subjects using the MeSH (Medical Subject Headings) translation table, journals using the Journals translation table, and authors and investigators, using the the Full Author translation table, Author index, Full Investigator translation table and Investigator index. If a match is found in any translation table, the mapping stops. When subject or journal matches are found, the query and individual terms are also searched in All Fields. If no match is found in any tables, terms are searched in All Fields and ANDed together.

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-B-

Bioethics Subset - This subset strategy was created by NLM and the Kennedy Institute of Ethics, Georgetown University to facilitate searching for citations to articles in the area of bioethics. This subset can also be used in a search as bioethics [sb].

bookmarks - Bookmarks save the addresses of your favorite sites, so you can return to them quickly without having to retype the address. In PubMed, bookmarks are used to save search strategies. In some browsers, bookmarks are called favorites.

Bookshelf (Books) - In collaboration with authors and publishers, the National Center for Biotechnology Information (NCBI) is adapting biomedical books for the web.

Boolean - Boolean is a logic system. Using the "AND" operator between terms retrieves documents containing both terms. "OR" retrieves documents containing either term. "NOT" excludes the retrieval of terms from your search. Use "NOT" with caution.

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-C-

Clinical Queries - Specialized PubMed searches intended for clinicians to limit retrieval to articles that report research conducted with specific methodologies.

ClinicalTrials.gov - offers up-to-date information for locating federally and privately supported clinical trials for a wide range of diseases and conditions. A clinical trial (also clinical research) is a research study in human volunteers to answer specific health questions.

Complementary Medicine Subset - This subset strategy was created using terms from the Alternative Medicine branch of MeSH, as well as additional terms and names of MEDLINE journals provided by The National Center for Complementary and Alternative Medicine. It is provided to facilitate searching for subjects in the area of complementary and alternative medicine. This subset can also be used in a search as cam [sb].

Core Clinical Journals - PubMed journal subset limit consisting of the 121 English language clinical journals formerly published as the Abridged Index Medicus.

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-D-

Dietary Supplements Subset - This strategy was developed jointly by NLM and the Office of Dietary Supplements at the National Institutes of Health. It is designed to limit search results to citations from a broad spectrum of dietary supplement literature. This subset can also be used in a search as dietsuppl [sb].

-E-

Entrez - The search and retrieval system that integrates information from the National Center for Biotechnology (NCBI) databases. These databases include nucleotide sequences, protein sequences, macromolecular structures, whole genomes, and MEDLINE, through PubMed.

exploding - see automatic explosion (explode)

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-F-

favorites - see bookmarks

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-G-

GenBank® - The National Institutes of Health (NIH) genetic sequence database. GenBank is an annotated collection of all publicly available DNA sequences.

Genome database - The Entrez Genome database at the National Center for Biotechnology (NCBI) contains the whole genomes for over 600 organisms. The genomes represent both completely sequenced organisms and those for which sequencing is in progress. All three main domains of life - bacteria, archaea, and eukaryota - are represented, as well as many viruses and mitochondria.

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History of Medicine Subset - This subset strategy was created by NLM History of Medicine Division to facilitate searching for subjects in the history of medicine. This subset can also be used in a search as history [sb].

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-I-

Index - An alphabetical listing of the terms found on database records and the number of records on which the terms are found. In PubMed there are several indexes including an All Fields Index as well as indexes for specific search fields including Author Name, Title Word, and Text Word indexes among others.

Index Medicus® - A bibliographic listing of references to current articles from over 3,500 of the world's biomedical journals. Included are subject and author sections and a separate Bibliography of Medical Reviews. MEDLINE's print counterpart.

In Process - records currently being reviewed for quality control and the addition of MeSH indexing terms. These records carry the notation [PubMed - in process].

ISSN - International Standard Serial Numbers - A unique code used for identifying serial publications, such as periodicals, newspapers, annuals, journals and monographic series.

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-J-

Journals Translation Table - The PubMed Journals Translation Table is an alphabetical list of full journal titles, MEDLINE journal title abbreviations, and International Standard Serial Numbers (ISSNs).

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-L-

LinkOut® - Allows publishers, aggregators, libraries, biological databases, sequence centers, and other Web resources to display links to their sites on items from the Entrez databases (including PubMed). These links can take you to the provider's site to obtain the full-text of articles or related resources, e.g., consumer health information. There may be a charge to access the text or information.

Loansome Doc® - A feature of PubMed for users to order documents found in MEDLINE. It is available to users in the United States and any country outside of the United States.

LocatorPlus® (locatorplus.gov) - NLM catalog of books, journals, and audiovisuals with holdings, availability, MARC records, and more.

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-M-

Medical Subject Headings - see MeSH

MEDLINE® - The National Library of Medicine premier bibliographic database that contains references to journal articles in life sciences with a concentration on biomedicine.

MedlinePlus® - The National Library of Medicine MedlinePlus is a Web-based database designed to assist you in locating authoritative health information. It contains pages of carefully selected links to Web resources including dictionaries, directories, organizations, news sources and health topics.

MeSH® - The National Library of Medicine controlled vocabulary thesaurus.

MeSH Major Topic - The MeSH concepts that are the main points of the article.

MeSH Translation Table - The PubMed MeSH Translation Table is an alphabetical list of MeSH Terms, Subheadings, See-References for MeSH Terms, Unified Medical Language System mappings, and Names of Substances and synonyms to the Names of Substances.

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-N-

narrower term - A term that is more specific in meaning than the more general term it is related to in a hierarchical structure.

NLM Catalog (nlmcatalog.nlm.nih.gov) - An Entrez database providing an alternate way to search books, journals, audiovisuals, electronic, and other materials with links to LocatorPlus holdings and availability.

Nucleotide database - Contains nucleotide sequence data from GenBank, the European Molecular Biology Laboratory (EMBL), and the DNA Database of Japan (DDBJ), the members of the tripartite international collaboration of sequence databases. Sequence data is also incorporated from the Genome Sequence Data Base (GSDB) and patent sequences are incorporated through arrangements with the U.S. Patent and Trademark Office (US PTO), and via the collaborating international databases from other international patent offices.

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-O-

OLDMEDLINE - citations without abstracts that were originally printed in hardcopy indexes published from 1946 through 1965.

OMIM - The Online Mendelian Inheritance in Man. A catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and provided through NCBI. The database contains information on disease phenotypes and genes, including extensive descriptions, gene names, inheritance patterns, map locations and gene polymorphisms.

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-P-

Phrase List - PubMed Phrase List is an alphabetical list of several hundred thousand phrases created from MeSH Terms, Unified Medical Language System Terms, and Names of Substances.

PMID - The unique identifier assigned to a record when it enters PubMed.

PopSet database - Contains sequences submitted as a set from a population, phylogenetic or mutation study describing events such as evolution and population variation.

Protein database - Contains protein sequence data from the translated coding regions from DNA sequences in GenBank, the European Molecular Biology Laboratory (EMBL), and the DNA Database of Japan (DDBJ) as well as protein sequences submitted to Protein Information Resource (PIR), SWISSPROT, Protein Research Foundation (PRF), and Protein Data Bank (PDB).

Publication Types - Describe the type of material the article represents (e.g., Review, Clinical Trial, Retracted Publication, Letter).

Publisher-supplied citations - PubMed citations received electronically from publishers. These citations carry the notation [PubMed - as supplied by publisher].

PubMed Central® - NLM digital archive of life sciences journal literature. Access to this literature is free and unrestricted.

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-Q-

qualified terms - Terms that are entered into the PubMed query box with a search field tag (e.g., [mh]).

query box - The active box at the top of every PubMed page where search terms are entered.

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-R-

Related Citations - A PubMed feature that uses a word-weighted algorithm to compare words from the title, abstract, and MeSH headings to calculate a set of PubMed citations that are closely related to the selected article.

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-S-

selectively indexed journal - A multidisciplinary journal for which the National Library of Medicine (NLM) selects only the articles that pertain to biomedicine and the life sciences for indexing for the MEDLINE database.

Space Life Sciences Subset - This subset strategy was developed by NLM and the NASA SPACELINE Office and is intended to retrieve citations of interest to those working in the field of space life sciences research. This subset is not available on the PubMed Filters page but can be used in a search as space [sb].

stopwords - A list of common or general terms (e.g., prepositions, and articles) that are not retrieved when searching PubMed because they appear in too many records.

Structure database - The Molecular Modeling Database (MMDB) contains experimentally-determined, three-dimensional protein structures.

subheadings - Qualifiers used by NLM for indexing in conjunction with MeSH (Medical Subject Headings) for MEDLINE. Subheadings are used to further describe a particular aspect of a MeSH concept.

Systematic Reviews - This strategy is intended to retrieve citations identified as systematic reviews, meta-analyses, reviews of clinical trials, evidence-based medicine, consensus development conferences, guidelines, and citations to articles from journals specializing in review studies of value to clinicians. This subset can be used in a search through the Clinical Queries screen or as systematic [sb].

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-T-

Taxonomy database - Indexes over 55,000 organisms that are represented in the sequence databases with at least one nucleotide or protein sequence. The Taxonomy Browser can be used to view the taxonomic position or retrieve sequence and structural data for a particular organism or group of organisms.

Toxicology Subset - This subset strategy was created by NLM Specialized Information Services to facilitate searching for subjects in the area of toxicology. This subset can also be used in a search as tox [sb].

TOXNET® - The National Library of Medicine TOXNET provides access to a cluster of databases on toxicology, hazardous chemicals, and related areas.

truncation - The use of a symbol to search only part of a term to retrieve variant endings of that term. The truncation symbol in PubMed is "*."

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-U-

UMLS® - see Unified Medical Language System (UMLS)

Unified Medical Language System® (UMLS) - The National Library of Medicine project to develop and distribute multi-purpose, electronic "Knowledge Sources" and associated lexical programs.

unqualified terms - Terms that are entered into the PubMed query box without a search field tag (e.g., [mh]).

-V-

Veterinary Science Subset - This strategy was created to facilitate searching for veterinary medicine and animal health literature. It includes a wide range of subject search terms and journal titles.  This subset can also be used in a search as veterinary [sb].

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