MEDLINE®/PubMed® An introduction

MEDLINE®/PubMed® An introduction
This will be an introduction to MEDLINE and PubMed. PubMed for Trainers, revised Fall 2012 U.S. National Library of Medicine (NLM) and NLM Training Center

Objectives By the end of this presentation, you will be able to:
Distinguish between a MEDLINE and non-MEDLINE record in PubMed. Define: MeSH headings MeSH Major Topics MeSH Subheadings Conduct a basic PubMed search Manipulate the results’ display Move from your PubMed results to other resources Identify where to customize your use of PubMed (My NCBI) By the end of this presentation, you will be able to: Distinguish between a MEDLINE and non-MEDLINE record in PubMed. Define: MeSH headings MeSH Major Topics MeSH Subheadings Conduct a basic PubMed search Manipulate the results’ display Move from your PubMed results to other resources Identify where to customize your use of PubMed (My NCBI) PubMed for Trainers Revised 2013/03

Overview We will answer the following questions: What is MEDLINE?
What is the content of MEDLINE? Who selects MEDLINE journals? How has the scope of MEDLINE changed over time? What is included in each MEDLINE record? What are Medical Subject Headings? What is PubMed? How do you search PubMed? What are some of the features of the PubMed search? What other resources are linked from PubMed? How to customize PubMed using My NCBI We will answer the following questions: What is MEDLINE? What is the content of MEDLINE? Who selects MEDLINE journals? How has the scope of MEDLINE changed over time? What is included in each MEDLINE record? What are Medical Subject Headings? What is PubMed? How do you search PubMed? What are some of the features of the PubMed search? What other resources are linked from PubMed? How to customize PubMed using My NCBI PubMed for Trainers Revised 2013/03

What is MEDLINE? PubMed for Trainers Revised 2013/03

1964 – MEDLINE - a database of citations to biomedical journal articles. The origins of MEDLINE began over 130 years ago. The earliest indexing of medical literature began with the Catalogue of the Library of the Surgeon-General's Office. This indexing was begun to help provide health professionals access to published literature. Index Medicus, originally a set of printed indexes to journal articles, in 1964, became the database known as MEDLINE. PubMed for Trainers Revised 2013/03

Highlights of MEDLINE MEDLINE is a database of citations to published biomedical journal articles. Over 5,600 journals are currently indexed for MEDLINE. Journals must be approved by a review committee. NLM indexers use Medical Subject Headings (MeSH) to index over 50,000 articles each month. MEDLINE has over 20 million citations going back to the mid 1940s. Most of the citations are for English-language articles and include abstracts. MEDLINE is a renowned database for at least three reasons: because of the careful selection of journals by the expert review committee because of the controlled vocabulary, the Medical Subject Headings (MeSH), used to describe the literature, and because of the highly trained subject matter experts who, using MeSH, do the indexing. MEDLINE is the primary source for biomedical journal citations. It contains citations, not articles, and currently indexes articles in over 5,600 journals in 39 languages. MEDLINE currently contains over 19 million references dating back to These citations are from journals worldwide. Most records are in English or have abstracts in English. PubMed for Trainers Revised 2013/03

Who decides what journals are in MEDLINE?
The Literature Selection Technical Review Committee Made up of medical experts and librarians. Meets 3 times per year. Considers approximately 180 titles each meeting. Selects roughly 20-25% of reviewed titles. The Literature Selection Technical Review Committee (LSTRC) is a group of medical experts and librarians who meets three times a year to consider approximately 180 titles for MEDLINE. Roughly 20-25% titles reviewed are selected. Final approval is made by the Director of the National Library of Medicine. PubMed for Trainers Revised 2013/03

What criteria are used to select MEDLINE journals?
Critical elements for inclusion: Scope and coverage Quality of content Quality of editorial work Production quality Audience Types of content Critical Elements for inclusion in MEDLINE are: Scope and coverage (“core biomedical subjects”) Quality of content (validity, importance, originality, overall contribution) Quality of editorial work (objectivity, credibility, quality; explicit external peer review, disclosure of financial interests, timely correction, opportunity for comments and dissenting opinion) Production quality (quality of layout, printing , graphics) Audience (intended for health professionals) Types of content (emphasis on original research, clinical observations, analysis) Some additional journals and newsletters are selected based on NLM-initiated reviews, e.g., history of medicine, health services research, AIDS, toxicology and environmental health, molecular biology, and complementary medicine, that are special priorities for NLM or other NIH components. For more details, see the NLM Fact Sheet, MEDLINE Journal Selection, by going to the NLM Home Page, click on About the NLM, then go to the Fact Sheets. See Fact Sheet for selection criteria. PubMed for Trainers Revised 2013/03

How has the scope of MEDLINE changed over time?
Historically, MEDLINE covered the broad topic of clinical medicine. MEDLINE has expanded over time in three directions: Mainly the journal content of MEDLINE now reflects the recognition of the increasing importance of fundamental biosciences to modern medicine. Secondly the recognition of the influences on health from the interaction of individuals with their social, cultural and physical environment as well as the study of health from an economic viewpoint has led to the inclusion of social sciences, environmental health, and other interdisciplinary studies. Thirdly, MEDLINE has an increasingly global perspective. See Journals Recently Accepted for Inclusion in MEDLINE: PubMed for Trainers Revised 2013/03

MEDLINE Basic Bibliographic Citation
Journal Source Information Title of the journal article Names of the Authors First Author Affiliation Abstract published with the article Language in which the article was published Publication Type (description of the type of article, e.g., Review, Letter, etc.) Controlled Vocabulary search terms (Medical Subject Headings) One MEDLINE citation represents one journal article and is composed of fields that provide specific information about the journal article. The following information is generally provided: Journal Source Information Title of the journal article Names of the Authors First Author Affiliation Abstract published with the article Language in which the article was published Publication Type (description of the type of article, e.g., Review, Letter, etc.) Controlled Vocabulary search terms (Medical Subject Headings) The underlying structure of a MEDLINE record is built with XML elements. Elements, or sets of elements, can be indexed and made available for display, searching and linking. PubMed for Trainers

What are Medical Subject Headings?
PubMed for Trainers Revised 2013/03

Indexers assign the most specific term possible.
MeSH (Medical Subject Headings) terms are added by NLM indexers to reflect the content of the article. Here is an example of a MEDLINE record for an article about AIDS in Nigeria. Medical Subject Headings, or MeSH terms, are added by NLM indexers to provide a controlled vocabulary to describe the articles. Indexers assign the most specific term possible. Indexers assign the most specific term possible.

Mouth Mucosa/pathology Nail Diseases/immunology
Subheadings are used with MeSH headings to be more specific. Mouth Mucosa/pathology Nail Diseases/immunology Subheadings are provided with MeSH headings to describe the particular aspect of the subject discussed. In this example, note Mouth mucosa/pathology and Nail diseases/immunology. Note also that the indexer identifies the major points of the article. These are marked with an asterisk. It is the addition of these MeSH terms that make MEDLINE easy to search. * = a major concept.

What is PubMed? PubMed for Trainers Revised 2013/03

PubMed http://www.pubmed.gov/ PubMed for Trainers Revised 2013/03
PubMed is a database developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM) available on the Web. Since 1996, free access to MEDLINE has been available to the public online via PubMed, which you can find from the NLM home page or simply by typing PubMed in your browser address bar and hitting <ctrl> <enter> PubMed for Trainers Revised 2013/03

MEDLINE Licensees PubMed for Trainers Revised 2013/03
Note that PubMed is just one of many search systems available to search MEDLINE records. Among the almost 700 licensees of MEDLINE data are those who create their own search systems. The method used to index these various elements of the MEDLINE record and the search capabilities are unique to each system. In this class, we will be discussing NLM’s PubMed which uses unique indexes and search algorithms. Be aware that if you use other systems to search, you may need to use different search methods. [The search labels may be the same, but the indexes may not be.] PubMed for Trainers Revised 2013/03

What’s in PubMed? PubMed for Trainers Revised 2013/03 includes:
records for online books & chapters out of scope articles PubMed is comprised mostly of MEDLINE records. About 2% are records in process, destined to be MEDLINE records. A remaining 8% are records for out-of-scope articles, which get there in a variety of ways (you read the details in your homework due yesterday), and a very small number are records for online books and chapters. PubMed for Trainers Revised 2013/03

PubMed Record Status Tags
Note that records are added to PubMed immediately upon receipt from the publisher. This means that records recently added may be in different stages of processing. See the different status tags on these records. Only those that are “indexed for MEDLINE” <click> will have Medical Subject Headings applied. Because of this, your search isn’t restricted to just MeSH terms – your search terms are also searched in the title, abstract and other fields of the record. Click on the article title to get to the full record, to read the abstract and to access any links to the full text and to related information. PubMed for Trainers Revised 2013/03

How to Search PubMed aids drugs breast feeding PubMed for Trainers
PubMed is designed so that you can type in significant words representing the concepts of interest. You should retrieve relevant citations. No punctuation, connectors or quotation marks are needed. In fact, it is best not to use them. PubMed for Trainers Revised 2013/03

Search Results PubMed for Trainers Revised 2013/03
<click>Your results are displayed in a Summary format, 20 per page, and sorted by when they entered the database. The most recently added records appear at the top. <click> Page through your results using the navigation at the top right. <click> You can change your display options (e.g., to see multiple abstracts on one page, or change the sort order). <click> You can send records to a file, to , or save them in a collection or in your own bibliography. PubMed for Trainers Revised 2013/03

Automatic Term Mapping (ATM)
PubMed uses Automatic Term Mapping which recognizes thousands of concepts and maps to an appropriate term. ATM Checks these tables: Subjects (Medical Subject Headings) Journal Titles Authors Searches like this work because of PubMed’s Automatic Term Mapping process, which maps your search terms with the terms used in the database. Automatic Term Mapping searches for subjects, journals and authors. PubMed for Trainers Revised 2013/03

Search details PubMed for Trainers Revised 2013/03
If you look at your search details (always displayed in the right column of your results), you can see ATM in action. PubMed for Trainers Revised 2013/03

The Search Details feature lets you see how your search was mapped.
If you look at your search details (always displayed in the right column of your results), you can see ATM in action. Here you see that “aids drugs” was mapped to “anti-hiv agents,” and breast feeding mapped to “breast feeding.” To give you a taste of the sophistication of the system: When the mapped term is a pharmacological action, a special kind of MeSH term, your search is also expanded to include all of the substances that have been identified as having that action. In this example, you see “anti-hiv agents” tagged as a [Pharmacological Action]. Here are all of the substances automatically included in this search… <follow link to MeSH DB> Revised 2013/03 PubMed for Trainers

See the Difference: “aids drugs” + “breast feeding” = 3 aids drugs breast feeding = 404 (processed using ATM) But as a searcher, you don’t have to know the details. As a result of this very useful mapping, the results of your search are far better than if you had put the phrases “aids drugs” and “breast feeding” in quotes, to find just those phrases. PubMed for Trainers Revised 2013/03

Pop Quiz! PubMed for Trainers Revised 2013/03
Which is the best PubMed search (according to NLM)? “mouth cancer” tobacco men “mouth cancer” AND tobacco AND men mouth cancer tobacco men PubMed for Trainers Revised 2013/03

Citation Sensor fauci cell 2007 PubMed for Trainers Revised 2013/03
PubMed also has special algorithms to identify components of citations. If, for example, you’re searching for an article by fauci in the journal cell, published in 2007, you can enter just those terms. PubMed for Trainers Revised 2013/03

Citation Sensor PubMed for Trainers Revised 2013/03
The results highlight a specific citation match at the top in yellow. If this isn’t what you were looking for, the full results appear below that. PubMed for Trainers Revised 2013/03

Title Matcher PubMed for Trainers Revised 2013/03
Similarly, if you copy and paste a full article title into the PubMed search box, PubMed will find the citation for you using an automatic title matching program. PubMed for Trainers Revised 2013/03

How to search PubMed for Trainers Revised 2013/03
Because of these features, users should be able to use PubMed with a minimum of explanation or training. Enter the concepts you’re looking for, and explore the results. PubMed for Trainers Revised 2013/03

Abstract & Related Citations
Here you see the abstract <click> The abstract display includes the first author’s affiliation and contact information <click> Expand the Publication Types, MeSH Terms section to see how the citation was indexed <click> Related citations, which are matched based on words in the MeSH terms, title and abstract. <click> You may also be able to access to full text, depending on whether the publisher has made the full text available online for free or for a fee, and what subscriptions you have activated via your library. Note that the full text links will appear in the upper right of the abstract display. <click>

The link will take you outside of PubMed, to the full text provider’s site.
You may be asked to sign in or pay for the article.

Links Between Databases
In the right column of your PubMed results, look for links to information related to the topic of the abstract(s) displayed or listed. In this example, there is sequence data linked from the record, as well as taxonomy and protein information. Follow the links to explore. PubMed for Trainers Revised 2013/03

PubMed for Trainers Revised 2013/03
Following the link to the Nucleotide database, see this glycoprotein gene sequence. As PubMed is continually improved, more related information may be available linked from PubMed records, so be sure to look around the screens, especially in areas you might think to see advertisements on commercial sites. PubMed for Trainers Revised 2013/03

Customizing PubMed Using My NCBI
My NCBI allows you to: Save records (Collections, My Bibliography) Save searches (Saved Searches) Customize your results (Filters, My NCBI Preferences) My NCBI is a feature of the NCBI databases that allows you to save records and searches, and customize your results display with filters and other options. PubMed for Trainers Revised 2013/03

My NCBI homepage PubMed for Trainers Revised 2013/03
The My NCBI homepage contains “portlets” for each functional section of My NCBI, including your saved searches, collections, bibliography, and your recent activity. Each portlet shows you a preview of the content of that section while providing access to the complete information through links. The homepage is customizable. Each section or "portlet" may be:Moved, Minimized, Restored, or Deleted. PubMed for Trainers Revised 2013/03

Register for an account
Homework: Register for a My NCBI account if you don’t already have one. Throughout the class, the instructors will point out useful features of My NCBI to use when searching PubMed To use My NCBI you need to register for an account or sign in through a partner organization. Your homework tonight includes registering for an account if you do not already have one. Throughout this class, instructors will point out handy features of My NCBI to use when searching PubMed PubMed for Trainers Revised 2013/03

PubMed Mobile Mobile-friendly version of PubMed
Minimal feature set: Small HTML, CSS, JavaScript A service that we will not be discussing in depth in this class is PubMed Mobile. PubMed mobile is a simplified version of PubMed for mobile devices. Accessing pubmed.gov from a mobile device will automatically take you to the mobile version. VIDEO: PubMed Mobile Demonstration

Online Help and Training
We will be using the PubMed Tutorials extensively in this class and we encourage you to use them in your own classes. Feedback is appreciated!

Summary The MEDLINE database of biomedical journal citations is the heart of PubMed. MEDLINE includes only good quality journals deemed important and relevant by a committee of experts. MEDLINE is available for free using PubMed, but it is also available from other database searching systems. MEDLINE is enhanced with Medical Subject Headings (MeSH), which improve access to the literature and can be used for searching. In Summary: The MEDLINE database of biomedical journal citations is the heart of PubMed. MEDLINE includes only good quality journals deemed important and relevant by a committee of experts. MEDLINE is available for free using PubMed, but it is also available from other database searching systems. MEDLINE is enhanced with Medical Subject Headings (MeSH), which improve access to the literature and can be used for searching. PubMed for Trainers Revised 2013/03

Summary (continued) Search PubMed by entering the main concepts of your search without punctuation. Your terms will automatically map to MeSH. Enter components of references (author, title, journal) to find a known article or set of articles. The full text article may be linked from the PubMed record using an icon in the upper right of the abstract display. Explore related citations and related information from the right column of your search results and the abstract display. Customize your PubMed search experience using My NCBI In Summary: Search PubMed by entering the main concepts of your search without punctuation. Your terms will automatically map to MeSH. Enter components of references (author, title, journal) to find a known article or set of articles. The full text article may be linked from the PubMed record using an icon in the upper right of the abstract display. Explore related citations and related information from the right column of your search results and the abstract display. Customize your PubMed search experience using My NCBI PubMed for Trainers Revised 2013/03

Conclusions You will now be able to:
Distinguish between a MEDLINE and non- MEDLINE record in PubMed. Define: MeSH headings MeSH Major Topics MeSH Subheadings Conduct a basic PubMed search Manipulate the results’ display Move from your PubMed results to other resources Identify where to customize your use of PubMed (My NCBI) You will now be able to: Distinguish between a MEDLINE and non-MEDLINE record in PubMed. Define: MeSH headings MeSH Major Topics MeSH Subheadings Conduct a basic PubMed search Manipulate the results’ display Move from your PubMed results to other resources Identify where to customize your use of PubMed (My NCBI) PubMed for Trainers Revised 2013/03

PubMed Searching: Automatic Term Mapping (ATM)
The following lecture provides the basics of PubMed searching. PubMed for Trainers, Winter 2013 U.S. National Library of Medicine (NLM) and NLM Training Center

Objectives By the end of this session, you should be able to:
Describe how PubMed processes a search using Automatic Term Mapping (ATM) Use Search Details to determine how PubMed processed your search Modify your PubMed search based on what you learn from Search details By the end of this session, you should understand: How to search PubMed How PubMed processes searches (Automatic Term Mapping) PubMed for Trainers Revised 2012/09

Composing Your Search Be specific
Use no punctuation (e.g., no quotation marks) Use no operators (e.g., AND) Use no tags Capitalization is unimportant To Review: When entering Search Terms: Enter significant terms in the search box (e.g., indigestion abdominal pain). Click on the Search button. Most important is to be as specific as possible. The more terms you enter, the narrower your search will be and the fewer results you’ll retrieve. Use no punctuation. PubMed will find phrases for you. Use no operators. PubMed will add AND between concepts. Use no tags. PubMed can identify topic words vs. author names vs. dates, etc. The take-home for info specialists and librarians might be: for most searches it is best to focus on TERMINOLOGY, not fancy syntax PubMed for Trainers Revised 2012/09

Here’s an example of a search for indigestion abdominal pain. Note that we are not using operators or tags. We’re letting PubMed do the work. From your results, scroll down to <> Search details in the right column to check PubMed’s translation. Click <>See more… to bring this up in a larger screen. PubMed for Trainers Revised 2012/09

ATM in Action This screen may be a lot to digest, but the important thing to note here is that PubMed is doing far more than a simple keyword search. Let’s explore the process…

ATM (cont’d) PubMed looks for: Subjects Journals Authors
In that order. PubMed uses a process called Automatic Term Mapping or ATM to parse users’ searches. PubMed matches search terms with a number of tables developed from the data in PubMed. It looks for: Subjects Journals and Authors In that order. We’ll first investigate how it finds subjects. PubMed for Trainers Revised 2012/09

MeSH (Subject) Translation Table Contains:
MeSH Headings Subheadings Publication Types Entry Term mappings (also known as synonyms) for MeSH terms Supplementary Concepts and synonyms to the Supplementary Concepts Mappings derived from the Unified Medical Language System (UMLS) To find subjects, PubMed matches search terms against the MeSH Translation Table. This table includes: MeSH Headings Subheadings Publication Types Entry Term mappings (also known as synonyms) for MeSH terms Supplementary Concepts and synonyms to the Supplementary Concepts Mappings derived from the Unified Medical Language System (UMLS) At this point you are familiar with the MeSH vocabulary, including headings, subheadings, publication types, entry terms and supplementary concepts. You may not be familiar with the Unified Medical Language System or UMLS. The UMLS is a vocabulary database that contains information about biomedical and health-related concepts, their various names, and the relationships among them. This is a system that brings together a large number of medical vocabularies from different disciplines and different purposes. It includes MeSH, and also includes, for example, SNOMED, a vocabulary of clinical terminology for health records; ICD-10, terminology used for morbidity statistics and health services billing; LOINC, a vocabulary for laboratory tests and procedures; and RxNorm, a vocabulary of pharmaceuticals. PubMed for Trainers Revised 2012/09

When a Match is Found for your Subject
If a match is found in this translation table: the term will be mapped to the appropriate MeSH term and searched as MeSH In this example, backache is mapped to Back Pain the searcher’s term and the mapped MeSH term as phrases and broken into individual words will be searched in All Fields MORE: Exception: Supplementary Concepts (substances) or MeSH Headings that include a standalone number or single character (e.g., protein c) are not broken into individual words but are searched only as phrases in All Fields. Processing now stops! PubMed for Trainers Revised 2012/09

Automatic Explosion: What you Don’t See in Search Details
What the Search Details page doesn’t show you is that, when a term is mapped to MeSH, your search also automatically includes any terms indented under that term in the MeSH hierarchy. This is called automatic explosion. Again, this is not in the Search Details***. You would need to go to the MeSH Database to find the additional terms that PubMed is including in your search. ***commonly missed pre-test question PubMed for Trainers Revised 2012/09

Some of the retrieval for the search, backache, will be records indexed with the more specific term, Low Back Pain, as in this example. PubMed for Trainers Revised 2012/09

If you enter the term hair in PubMed, what terms are automatically included in the search? Eyebrows [MeSH Terms] Eyelashes [MeSH Terms] Hair Follicle [MeSH Terms] Wool [MeSH Terms] All of the above None of the above The answer is ALL of the above. (Demo: try the search in PubMed. Look at Details. Not there! How do you know? Must go to MeSH!) PubMed for Trainers Revised 2012/09

ATM (cont’d) If PubMed doesn’t find a match in the MeSH subject table, it looks for: Subjects Journals Authors After subject terms are mapped to the MeSH table, those subject terms are not processed further. If terms are remaining in the search, PubMed then checks for journals. PubMed for Trainers Revised 2012/09

Journals Translation Table
Full journal title MEDLINE abbreviation International Standard Serial Number (ISSN) To find journals, PubMed matches search terms against the Journals Translation Table. Only FULL journal titles, MEDLINE abbreviations and ISSNs are matched. Notice my emphasis on FULL journal titles. If you enter only components of the title, PubMed will not match to the journal***. For example, entering New England as a PubMed search will NOT retrieve all citations from the New England Journal of Medicine. For this reason, PubMed includes some handy features that allow you to easily find full journal titles – We’ll get into those later. ***commonly missed pre-test question PubMed for Trainers Revised 2012/09

When a Match is Found for your Journal Title
If a journal is found, the journal is added to the search. The term is also searched in All Fields. Processing now stops. Processing now stops! PubMed for Trainers Revised 2012/09

You’re looking for citations from the journal Cell and tissue research. Which of the following searches will retrieve all citations from that journal (check all that apply and take your best guess)? Tissue research Cell and tissue research Cell Tissue Res All of the above PubMed for Trainers Revised 2012/09

ATM (cont’d) If PubMed doesn’t find a match in the journals table, it looks for: Subjects Journals Authors After subject terms and journals are searched, if terms are remaining, PubMed then checks for author names. PubMed for Trainers Revised 2012/09

Author Translation Tables
Author Index In the format: Lastname Initials: Jennings BH Full Author Translation Table Author names in natural and inverted order: Barbara H Jennings Jennings, Barbara H Investigator Index Full Investigator Translation Table To find authors, PubMed matches search terms with full author names, author names in lastname, initials format, and investigator names in both formats. Full author names are included for articles published from 2002 forward and to journals that publish using the full names of authors. They can be searched in either natural or inverted order. A more comprehensive index is the author index, which includes all author names in the format: lastname space initials Investigators are individuals who contributed to the research, but may not have participated in writing the article. The names in the Full Investigator Translation Table and the Investigator Index are formatted and searchable in the same way as the Full Author Name Table and Author Index PubMed for Trainers Revised 2012/09

When a Match is Found for an Author Name
Author’s names, for all years of publication, are included in the form of Last Name (space) Initials. Use this format for searching. If only the first initial is used, PubMed automatically truncates the author’s name to account for varying initials. If only an author’s last name is entered, PubMed will search that name in All Fields (Author field plus all other searchable fields). It will not default to the Author Index because the last name is not followed by an initial. Processing now stops. Processing now stops! PubMed for Trainers Revised 2012/09

Which will most likely retrieve all records in PubMed for articles written by William J Jusko? William Jusko Jusko, William J Jusko wj PubMed for Trainers Revised 2012/09

ATM: Searching Multiple Concepts
Searches for: Results: Action: head lice shampoo No match found Removes term on right to re-run Automatic Term Mapping process. head lice Match found in MeSH Translation Table head lice will be searched as "pediculus"[MeSH Terms] OR "pediculus"[All Fields] OR ("head"[All Fields] AND "lice"[All Fields]) OR "head lice"[All Fields] shampoo No match found in Translation Tables shampoo will be searched as shampoo[All Fields] Because of this Automatic Term Mapping process, you can search multiple concepts without worrying about syntax. Just enter your terms. Here’s an example of how PubMed processes a multiple term search. PubMed for Trainers Revised 2012/09

Combining Subjects, Journals & Authors: What does ATM Do?
You can also search combinations of subjects, authors and journals without tagging. In this example, PubMed didn’t find the full string: jennings bh signal transduction molecular cell in any index. PubMed then breaks apart the search and looks for strings: First in the subject or MeSH Table. It finds signal transduction there. Then in the journal table. It finds molecular cell there. Then in the author tables. It finds jennings bh there. For the MeSH and journal retrieval, it also searches for the terms as phrases and individually in All fields. PubMed for Trainers Revised 2012/09

No match in any of the translation tables?
Details not reflecting your intended search? If no match is found, PubMed breaks apart the phrase and repeats the automatic term mapping process until a match is found. Terms that don’t make a match will be searched in “All Fields.” Individual terms will be combined (ANDed) together. PubMed for Trainers Revised 2012/09

Phrase Searching with Quotes
Caution! Using quotes bypasses ATM & automatic explosion. If you want to search for a phrase and PubMed didn’t find it automatically, you can force a phrase search using quotes. BUT…Searching a phrase using double quotes bypasses automatic mapping to MeSH terms. For example, "heart attack" will not map to the MeSH term Myocardial Infarction, whereas, heart attack (without quotes) will. MORE: You can bypass ATM by: Using a search tag: kidney allograft [tw] Using quotes: “kidney allograft” (this will be searched in All Fields) Truncating: kidney allograft* Hyphenating will also force a phrase search, but won’t bypass ATM: e.g., Anticoagulant-drugs PubMed for Trainers Revised 2012/09

Quoted Phrase Not Found
Also: Not all phrases are recognized in PubMed, e.g., culture of health. In this case, the search results will be the same with or without quotes. With or without quotes culture of health will be searched as shown on the screen. When a quoted term is not searched as a phrase, the following message appears above the search results: Quoted phrase not found. More about the phrase index later in the class. PubMed for Trainers Revised 2012/09

Exercise Search the following in PubMed:
“health planning” health planning What is missed in the first search? Try these searches. What is missed in the first search? Answer (click to display text box of MeSH tree): quotes turn off ATM and mapping to MeSH. Mapping to MeSH includes automatic explosion, which includes all of the narrower terms indented under the MeSH term. This is the hierarchy under Health Planning, including 27 indented terms. PubMed for Trainers Revised 2012/09

Searches that Bypass Automatic Term Mapping:
Using a search tag: Gene [author] Science [journal] Forcing a phrase search with quotes: “pressure point” Using the Single Citation Matcher Using Advanced Search Use with caution! When the Automatic Term Mapping process isn’t doing what you want with your terms, you several options: Type the search tag by hand. We’ve seen the author tag and the journal tag as PubMed applies them. There are also abbreviations for each tag. You can find the full list in PubMed Help. Force a phrase search, as just shown Use the Single Citation Matcher or Advanced Search. We’ll be discussing the Advanced Search in detail later in the course. You’ll be exploring the Single Citation Matcher in tonight's’ homework. PubMed for Trainers Revised 2012/09

Summary For most PubMed searches just enter your terms and click Search. Always check Search details Automatic Term Mapping processes subjects, journals and authors, in that order. PubMed for Trainers Revised 2012/09

Summary With ATM, your MeSH terms will automatically explode to include narrower topics. The 3 ways to enter journal titles are: Full journal title MEDLINE journal title abbreviation ISSN For the most comprehensive author search, use the format lastname initials (e.g., smith ja). If necessary, bypass ATM by using: Quotations or tags Single Citation Matcher Advanced Search (to be discussed later) PubMed for Trainers Revised 2012/09

You should now be able to:
Describe how PubMed processes a search using Automatic Term Mapping Use Search Details to determine how PubMed processed your search Modify your PubMed Search depending on what you learn from Search Details Now that we’ve presented an analysis of how PubMed processes a search, you should be able to: Analyze how PubMed processes a search using Automatic Term Mapping Appraise your PubMed Search Modify your PubMed Search depending on what learn from Search Details PubMed for Trainers Revised 2012/09

Evidence-Based Medicine in PubMed
[Prep: Set up Custom Filter for docpeabody, abc123: double-blind method [mh]] PubMed for Trainers, Winter 2013 U.S. National Library of Medicine (NLM) and NLM Training Center

Objectives To explore MeSH vocabulary and PubMed features that facilitate finding evidence-based research Define the term “evidence based medicine” Identify and discuss publication types and research design vocabulary available in MeSH Introduce and examine three PubMed topic-specific searches: clinical queries; systematic reviews; and comparative effectiveness research Introduce PubMed Health The objective of this lecture is to explore MeSH vocabulary and PubMed features that facilitate and inform evidence-based research Revised February 2013

What is Evidence-Based Medicine?
The use of the current best evidence in making clinical decisions To quote David Sackett, Evidence-Based medicine is "the conscientious, explicit and judicious use of current best evidence in making decisions about the care of the individual patient. It means integrating individual clinical expertise with the best available external clinical evidence from systematic research." (David Sackett, 1996) In other words, it is the use of the current best evidence in making clinical decisions. See Sackett, D. Evidence-based Medicine - What it is and what it isn't. BMJ 1996; 312: Revised February 2013

“The best evidence is usually found in clinically relevant research that has been conducted using sound methodology.” (Sackett D, 2002) Sackett also said that the “best evidence is usually found in clinically relevant research that has been conducted using sound methodology” This quote explains the emphasis of this presentation: Methodology. While two critical components of EBM: 1. Developing a clinical question and 2. Evaluating the evidence you find Are outside of the purview of a PubMed class… Revised February 2013

What do we mean by “Evidence-Based Medicine” in the context of PubMed?
Identifying the best available evidence in the literature to inform clinical decision making using: Study characteristics (i.e., research design and methods) Reviews (including systematic reviews) of the literature We can highlight the important information you need to know about PubMed that will help you find the relevant literature. This information is regarding how we describe research methods in MeSH And how to access review literature, specifically systematic reviews. Revised February 2013

Useful Vocabulary to Describe Study Characteristics
First we’ll talk about how we describe research methods in MeSH Revised February 2013

Publication Types Describe the item being indexed rather than its topic. There are 3 main categories: Publication Components, e.g., English Abstract Publication Formats, e.g., Lectures, Letter Study Characteristics, e.g., Clinical Trial, Twin Study As we learned earlier in the class, publication types are one of the four types of MeSH terms. There are 3 main categories of publication type: Publication components, like abstract Publication formats, like review, letter, lecture, and Study Characteristics. These study characteristics are of primary interest, here. These describe the structure and procedure of the research itself. Revised February 2013

Study Characteristics (PTs)
Case Reports Clinical Conference Clinical Trial + Comparative Study Consensus Development Conference + Evaluation Studies In Vitro Meta-Analysis Multicenter Study Scientific Integrity Review Twin Study Validation Studies There are many terms under study characteristics. Some study types may be more or less of interest to your research. Here you see, for example, Clinical Trial. The plus sign indicates that terms are indented under this one. We’ll take a look at the types of clinical trials described in MeSH. Revised February 2013

Study Characteristics (PTs) Clinical Trial
Clinical Trial, Phase I Clinical Trial, Phase II Clinical Trial, Phase III Clinical Trial, Phase IV Controlled Clinical Trial Multicenter Study Randomized Controlled Trial There are terms for the 4 phases of clinical trials, as well as for controlled clinical trial, multicenter study and randomized controlled trial: All terms indented under Clinical Trial. Let me get back to the phases in just a moment. A “controlled” clinical trial involves one or more test treatments, at least one control treatment, specified outcome measures for evaluating the studied intervention, and a bias-free method for assigning patients to the test treatment. The “control” might be considered the “no-intervention” group, which might be a placebo, for example. A “randomized” trial involves the use of a mathematical technique such as a random numbers table to assign patients to the test or control treatments. Revised February 2013

Clinical Trial Phases Phase I Is it safe?
Phase II What’s the right dose? Phase III How good is it compared to the standard treatment? Phase IV Does it have any rare or long term adverse effects? Here are oversimplified example questions of what these phases are designed to answer for a fictitious drug study, just to give you an idea of what is meant by these phases. Phase I asks if the drug is safe. Phase II asks, what’s the right dose? Phase III asks how good it is compared to the standard treatment, And Phase IV asks if the drug has rare or long term adverse effects. You may also find phase 0 and phase 5 in the literature: Phases 1 through 4 are the terms currently available in MeSH. Revised February 2013

Publication Type vs. Method “as Topic”
Please note that the terms for publication types that describe research methods also exist in MeSH in the form, “method AS TOPIC,” for example, “clinical trials as topic,” as seen on this slide. Don’t confuse the publication type with the MeSH heading. An article reporting results from a clinical trial will have the PUBLICATION TYPE, clinical trial. An article discussing how clinical trials in France are funded, for example, will have the MeSH term, CLINICAL TRIALS AS TOPIC. Revised February 2013

Research Design MeSH Headings: Investigative Techniques (examples)
Double-blind method (1990, Aug 1977) Matched-Pair Analysis (1992) Patient selection (1995) Random allocation (1991, 1978) In addition to publication types, there are many other research design terms in MeSH. Several of these terms are under the term “Methods” in MeSH. But there is a very large branch of the MeSH tree devoted to “Investigative Techniques” and I encourage you to explore it. I’ve included the dates here because it is important to keep in mind that these terms haven’t been around MeSH forever. If you want to look at older studies, some of these terms like “Matched-Pair Analysis” will not help you. Other terms, such as double-blind method and random allocation, have been in use since the 1970s, predating the Study Characteristics publication types, so could be useful for identifying relevant studies back almost 50 years. Revised February 2013

MeSH Pop Quiz! Revised February 2013
MEDLINE indexers use the following types of MeSH terms to describe the design of a research study: Study Characteristics publication types The Investigative Techniques branch of headings Both of the above The answer is: BOTH. If you are interested in EBM and searching for specific methodologies, it is important to familiarize yourself with BOTH the publication types and the Investigative Techniques branch of MESH (specifically, the Methods terms). Revised February 2013

Exercise Find studies comparing treatments for sleep apnea.
For a quick exercise, open the MeSH Database and explore the MeSH Study Characteristics tree. Find a publication type that will help you find studies comparing active treatments. Answer: Comparative study sleep apnea therapy Or Comparative study [pt] sleep apnea/th [majr] See: Sleep Apr 1;34(4): Comparative effects of two oral appliances on upper airway structure in obstructive sleep apnea. Revised February 2013

Clinical Queries Poll: Have you used Clinical Queries? Yes No Not Sure
Please unmute and share how you use the Clinical Queries. The Clinical Queries page is a special tool to help you take advantage of some of this vocabulary without having to research it yourself. Available on PubMed homepage; also available from the “More Resources” pull down menu at the top of the Advanced Search screen. There are 3 search filters available from this page: Clinical Study Categories Systematic Reviews Medical Genetics Enter your term(s), click Search, and choose your Category, Scope or Topic (if appropriate). Click See all to run the search in PubMed. In the context of Evidence-Based Medicine, we are specifically interested in the Clinical Study Categories and the Systematic Reviews.

Clinical Queries: Clinical Study Categories
Let’s start with the Clinical Study Categories. This specialized search query is intended for clinicians and has built-in search "filters." <>Five study categories or filters are provided: etiology diagnosis therapy prognosis clinical prediction guidelines <>Two emphasis categories or filters are provided: narrow, specific search -- will get more precise, relevant citations but less retrieval broad, sensitive search -- includes relevant citations but probably some less relevant; will get more retrieval <>Click See all to retrieve the full results in PubMed <>Click filter information to view details on how the searches are constructed

Clinical Queries: Clinical Study Categories
To show one example, here are the details for the therapy query. Note that underlying this query are the therapeutic use subheading and terms for clinical trial or, more specifically, randomized controlled trials. You can follow the link in PubMed Help to learn more about the development of these queries by R. Brian Haynes, M.D., Ph.D. at McMaster University in Canada. Revised February 2013

Systematic Reviews Defined (by NLM)
One or more questions are posed. Study results are collected. Criteria are used to include or exclude studies. Data extracted from the selected studies are combined and compared. Conclusions are made. Systematic Reviews summarize and evaluate information that can help in decision-making. What is the difference between a review and a systematic review? A review is generally considered an examination of the literature from the author's perspective A systematic review is characterized as having the following components: One or more questions or hypotheses are posed at the start of the review. Publications/study results in the subject area are collected, sometimes limited to a particular type (e.g., literature reviews, randomized controlled trials), and are often obtained from specific sources (e.g., databases, bibliographies). Criteria are used to include or exclude studies found for the actual review. This step is often referred to as the "study selection." Data extracted from the selected studies are combined and compared, or if the data cannot be combined, the strength of the evidence is assessed and used to evaluate results. Conclusions are made based on results and/or the presence or absence of supporting evidence. Revised February 2013

PMID: Here is a nice example of a systematic review. Note the components: Question posed at the start of the review. (Is there a link between depression and increase risk of stroke?) Note the named databases from which studies are collected (MEDLINE, EMBASE, PsychINFO) in the Data Sources section. Note the inclusion criteria in the Study Selection section. Note how the Data extracted was combined or “pooled.” The Conclusion, based on the results, states that there is evidence of a link.

PubMed Systematic Review query also includes:
meta-analyses reviews of clinical trials evidence-based medicine consensus development conferences guidelines, and citations to articles from journals specializing in clinical review studies. In November 2001, a Systematic Reviews search filter was added to PubMed on the Clinical Queries screen to make it easier to retrieve citations for these distinctive articles. You should note that the filter also includes: meta-analyses reviews of clinical trials evidence-based medicine consensus development conferences guidelines, and citations to articles from journals specializing in clinical review studies. Filter strategy: Revised February 2013

Exercise: Clinical Queries
Using the Clinical Queries page, find studies exploring the effect of weight loss on obstructive sleep apnea Look at the Systematic Reviews and click See all to view them in PubMed Take a moment and try the Clinical Queries page. Take a look at results for a topic of interest to you, or use the suggested topic on the slide. Try changing the Clinical Study Category and the scope from broad to narrow, and look at your Systematic Review results. Revised February 2013

Comparative Effectiveness
effectiveness [sb] As homework in preparation of this class you should have read a brief article in the MLA News that briefly describes CE. Comparative effectiveness research, also known as Patient-Centered Outcomes Research (PCOR), is the conduct and synthesis of systematic research comparing different interventions and strategies to prevent, diagnose, treat and monitor health conditions. (Federal Coordinating Council for Comparative Effectiveness Research, Because of the relationship between EBM and comparative effectiveness research, I want to point out that NLM has developed some PubMed searches that retrieve clinical comparisons of treatments or that report on treatment outcomes; again using the MeSH publication type and study design terms that we’ve discussed. Note that you can choose Clinical Studies (randomized controlled trials), Observational Studies, or Systematic Reviews, Simulations, Models To search all CE for your topic you can use effectiveness [sb] When would you use a comparative effectiveness search vs. a Clinical study category on the Clinical Queries page? First let me make it clear that there can be a great deal of overlap or a very small amount of overlap depending on what category or topic you choose. CQ – designed to help the busy clinician find a few good references that could readily be applied to patients/practice. That is, findings/information that results from good study design so is more evidence based. But also, two of the Clinical Study categories aren’t really addressed in the CER searches: etiology and diagnosis. CER is focused on comparing treatments. 2. The CER searches have been developed to help inform discussions about comparisons in treatments, devices, procedures, etc. as a starting point. What are the questions to be asked in comparing treatment approaches for different patients? The focus is on patient outcomes from these different approaches. But it’s easier to differentiate these searches if you remember that the searches we’re talking about are based on study design. One example area that the CER searches address that the Clinical Queries don’t is Observational Studies. We’re going to look at this with an example in a minute. Revised February 2013

Administrative Data/Registries/ Observational Studies
PubMed CER Searches Conceptual Structure Comparative OR Effective Clinical Studies RCTs Outcomes Cohort Administrative Data/Registries/ EHRs Observational Studies Comparative OR Effective Outcomes Systematic Reviews Systematic Reviews Simulations Modeling Health Disparities Here’s a schematic of the Comparative Effectiveness searches conceptual structure. The green bubbles represent the various search filters available. The blue bubbles represent sets of search terms combined to retrieve these general concepts. For example, the clinical studies filter is comprised of terms used to retrieve randomized controlled trials which include something about comparisons or effectiveness and something about outcomes. This is just a schematic, but the full CER search strategies are available on the NICHSR Web site at the link on the slide. You can also find it again by searching the NLM web site for “comparative effectiveness search strategies” and it should be the first option listed. (search NLM Web site for comparative effectiveness) Costs & Cost Analysis AND OR “About” CER ALL of the Above Revised February 2013

Exercise: Comparative Effectiveness Research
Use the comparative effectiveness search page to search for weight loss on obstructive sleep apnea Look at results for Observational Studies Look at results for Systematic Reviews, Simulations, Models Compare your results for CER search on Systematic Reviews with the Clinical Queries Systematic Reviews search results Try a search using the comparative effectiveness search. Try these two different filters: observational studies, and systematic reviews, simulations and models. Look at the types of studies you get for each filter. Once you’ve looked at those for a bit, compare the results for your CER systematic reviews search and the systematic reviews search you did previously using the Clinical Queries page. You should be seeing: Extensive overlap in the Sys Review searches (the results may be identical) Very different findings from the Observational Studies. Here you see the kinds of studies that CER brings out that a focus on randomized controlled trials may miss. Revised February 2013

Another EBM Resource: http://www.ncbi.nlm.nih.gov/pubmedhealth/
Full-text online collection of systematic reviews (or summaries) Curated Some not in PubMed While we’re talking about reviews and specifically systematic reviews, I want to spend just a minute to tell you about PubMed Health. PubMed Health is an online collection of systematic reviews and summaries of systematic reviews. These are made available thanks to NLM information partners like the Agency for Health Care Research and Quality and the Cochrane Collaboration (full list see Much of what is in PubMed Health is cited in PubMed, but some is not because it is not in a journal format. If you are looking for systematic reviews, you may want to search PubMed Health as well as PubMed. Revised February 2013

More about Comparative Effectiveness Research
Webinar: Comparative Effectiveness Research (from the Pacific Northwest RML): Finding Evidence for Comparing Medical Interventions (AHRQ Guide on comparative effectiveness reviews) Systematic Review Workshop: The Nuts and Bolts for Librarians (3-day workshop) Webinar: Comparative Effectiveness Research Excellent Webinar provided by the Pacific Northwest RML (October ). Ione Auston, NICHSR, gave a nice overview of comparative effectiveness research and the various initiatives as well as resources on this topic. Rose Relevo, from the AHRQ Effectiveness Health Care Program at the OHSU, Portland, OR gave a really nice presentation on conducting systematic reviews. Full text info on systematic reviews by Rose Relevo is at: click on the full text link to get to Bookshelf for full text. At about 48 minutes into the webinar, Rose mentions this 3-day workshop: Systematic Review Workshop: The Nuts and Bolts for Librarians Workshop sponsored by the Falk Library at the University of Pittsburgh each fall and summer. Revised February 2013

More about Evidence-Based Medicine
Online tutorial: lcome.htm Work by Dr. John Ioannidis (see profile in the Atlantic 0/11/lies-damned-lies-and-medical-science/8269/ and/or search PubMed for ioannidis jp) As said in the beginning, we can only intelligently cover PubMed searching, but medical librarians everywhere are involved in much more of the Evidence-Based Medicine process. Learn more about EBM by taking this online tutorial developed by Connie Schardt Duke University Medical Center Library and Jill Mayer University of North Carolina at Chapel Hill Health Sciences Library You may also be interested in the work of people like Dr. John Ioannidis (yo-NEE-dees), who has made a career of pointing out the flaws in research methodology and the interpretation of that research. Try a search for ioannidis jp in PubMed for some VERY interesting reading. Revised February 2013

Summary Vocabulary PubMed Clinical and Special Queries
Study Characteristics (PTs) Investigative Techniques headings PubMed Clinical and Special Queries Clinical Study Categories (Clinical Queries page) Systematic Reviews (Clinical Queries page) Comparative Effectiveness (NICHSR Web site) PubMed Health for full-text systematic reviews Summary: When we’re talking about Evidence-Based Medicine in the context of PubMed we are talking about research design and methodology. Evidence-Based Medicine can be explored in PubMed using study characteristics (research design and methods) and reviews. MeSH includes a wide variety of terms to describe study characteristics, including: the Study Characteristics publication types (e.g., clinical trial, meta-analysis, multicenter study), the Investigative Techniques branch of headings (e.g., Methods, including Matched-Pair Analysis and Random Allocation). NLM staff has worked with experts to create topic-specific searches to make finding relevant "evidence-based" literature available, including: Clinical Study Categories (Clinical Queries page) Systematic Reviews (Clinical Queries page) Comparative Effectiveness literature (NICHSR Web site) Explore PubMed health for full-text systematic reviews Revised February 2013

Searching for Drug Information In PubMed
Good morning everyone. I am Margaret and I am so happy to see you all here this morning. We are going to discuss searching PubMed for drug information. I invite you to ask questions and make comments as we go along. PubMed for Trainers Winter 2013 U.S. National Library of Medicine (NLM) and NLM Training Center

Goal: To gain familiarity with the NLM MeSH vocabulary related to chemicals and drugs and to get comfortable with searching for drug information in PubMed. Our goal this morning is for you to gain familiarity with the NLM MeSH vocabulary related to chemicals and drugs and to get comfortable with searching PubMed for chemicals and drugs. PubMed for Trainers Revised 2013/01

Objectives: By the end of this session you will be able to:
Explain how chemicals, drugs and other substances are described in MeSH. Search for drugs or chemicals in PubMed. Search using pharmacological action terms. By the end of our discussion you will be able to: Explain how chemicals and drugs are described in MeSH. Search for chemicals and drugs in PubMed. Search PubMed using pharmacological action terms. We’ll do this by addressing the following topics: Preferred vocabulary for chemicals and drugs The MeSH hierarchy for chemicals and drugs Supplementary concepts and their MeSH mappings Searching chemicals and drugs with search tags Searching pharmacological action terms PubMed for Trainers Revised 2013/01

Help, I’m not a Chemist! Revised 2013/01 First of all, let’s relax.
We don’t need to be chemists to search PubMed for chemicals and drugs because the MeSH preferred term for a chemical or drug is usually its common name. Also, there are plenty of Entry Terms to account for the different names of chemicals and drugs. Remember, the preferred term is the MeSH name for the concept and Entry Terms are synonyms to the preferred term. PubMed for Trainers Revised 2013/01

Drugs and Chemicals in MeSH
Let’s search PubMed for Aleve, a common anti-inflammatory pain reliever. A quick look at Search details shows us that Aleve is an Entry Term to Naproxen. PubMed Automatic Term Mapping (ATM) maps Aleve to the MeSH term Naproxen. PubMed for Trainers Revised 2013/01

Many Synonyms, One Preferred Name, Same Concept
Let’s look at Naproxen in the MeSH Database. Here are the Entry Terms and we find Aleve in this list. PubMed ATM maps Entry Terms to MeSH Terms so that a search for Aleve retrieves all PubMed citations indexed with Naproxen. PubMed for Trainers Revised 2013/01

Common v. Chemical Names
Mimosine 3-Hydroxy-4-oxo-1(4H) pyridinealanine C8H10N2O4 Aspirin Acetylsalicylic Acid Always exceptions … 1,2-dinitrobenzene Look at the Drug Handout Here are more examples of preferred terms. MeSH uses aspirin rather than acetylsalicylic acid. But there are always exceptions, for example 1, 2-dinitrobenzene is the preferred term (simply because there IS no common name for 1,2-dinitrobenzene!). There is additional information in the handout included with Session 4 slides. PubMed for Trainers Revised 2013/01

Exercise: Preferred Term
Develop a good PubMed search for information on Zantac. What do you think is a good PubMed search for Zantac? That’s correct. Zantac is a trade name and an Entry Term for the MeSH term Ranitidine (ran it i dean). Search this in PubMed. PubMed for Trainers Revised 2013/01

The Chemicals and Drugs Category in MeSH
Inorganic Chemicals Organic Chemicals Heterocyclic Compounds Polycyclic Compounds Macromolecular Substances Hormones, Hormone Substitutes, and Hormone Antagonists Enzymes and Coenzymes Carbohydrates Lipids Amino Acids, Peptides, and Proteins Nucleic Acids, Nucleotides, and Nucleosides Complex Mixtures Biological Factors Biomedical and Dental Materials Pharmaceutical Preparations Chemical Actions and Uses Here is the MeSH Chemicals and Drugs Branch. It is organized by classes or compound types. These chemicals and drugs are MeSH headings. Revised 2013/01

Medical Subject Headings (MeSH® Vocabulary)
MeSH Vocabulary Type Examples Headings Body Weight, Kidney, Dental Cavity Preparation, Self Medication, Brain Edema, Oseltamivir Subheadings adverse effects, genetics, contraindications, ultrastructure Publication Types Letter, Review, Practice Guideline, Twin Study Supplementary Concept Records cordycepin, albuterol-ipratopium, carbon monoxyde dehydrogenase, nocturnin This slide reviews the four types of MeSH vocabulary: Headings are biomedical subjects like body weight and brain edema and chemicals and drugs Subheadings are terms that describe specific aspects of the heading or subject like adverse effects and genetics Publication Types are terms that describe the type of article like letter to the editor or review article Supplementary Concept Records are terms that describe subjects that are not included as Headings. Most supplementary concepts are substances. When we say substances please think chemicals and drugs. Chemicals and drugs are either MeSH Headings or Supplementary Concept Records. The Headings are found in the Chemicals and Drugs Category that we just looked at. MeSH Headings are updated once per year. By contrast, Supplementary Concept Records are added and changed throughout the year. This allows us to add new chemicals and drugs to the MeSH vocabulary as they are published in the literature. This keeps PubMed searching uniform and up to date. PubMed for Trainers Revised 2013/01

Supplementary Concepts
Let’s search PubMed for the antidepressant metapramine. Search details shows that metapramine is a supplementary concept. PubMed for Trainers Revised 2013/01

Supplementary Concepts (cont.)
Now let’s look at the MeSH Database record for metapramine. Supplementary Concept Records have definitions, Date introduced, Previous Indexing and Entry Terms. Each supplementary concept is mapped to a MeSH Heading. Notice Heading Mapped to: Dibenzazepines. In this way MeSH associates metapramine with Dibenzazepines. When an indexer adds metapramine to a MEDLINE/PubMed record, Dibenzazepines is automatically added. PubMed for Trainers Revised 2013/01

Supplementary Concepts (cont.)
Notes for Slides 13 and 14 Let’s take a look at the MeSH headings and Substances on a MEDLINE/PubMed record for an article about metapramine. We see metapramine and Dibenzazepines. When you search PubMed for Dibenzazepines, you’ll get all the citations indexed with metapramines. Supplementary concepts do not have subheadings and cannot be indicated as major topics. However, the Headings Mapped to: can have subheadings and can be indicated as major topics. You can search the Heading Mapped to: with subheadings to get at a specific aspect of the SCR. For example, the search Dibenzazepines/pharmacokinetics AND metapramine retrieves results about the pharmacokinetics of metapramine. You can also search the Heading Mapped to: as a major topic to retrieved results in which the SCR is a major topic of the articles. PubMed for Trainers Revised 2013/01

Dibenzazepines/pharmacokinetics AND metapramine
Mapped to MeSH Dibenzazepines/pharmacokinetics AND metapramine PubMed for Trainers Revised 2013/01

MeSH Heading v. SCRs: Why Both?
MeSH Headings Supplementary Concepts Located in hierarchy Subheadings Updated annually Pharmacologic Actions Entry Terms Not located in hierarchy no explosion No subheadings Updated weekly Pharmacologic Actions Entry Terms Heading Mapped To Can become MeSH Heading In this side-by-side comparison we see that there are differences between MeSH Headings and Supplementary Concepts. Trainers should understand these differences. Searchers may not have to know all of them. PubMed for Trainers Revised 2013/01

SCRs Are… Updated Weekly Update SCR’s Revised 2012/10
Notes for Slides 16, 17, and 18 Searchers should know that SCRs are updated weekly, they don’t have subheadings, and they are not in the hierarchy and therefore do not explode. Searchers should know that SCRs are mapped to MeSH headings and that the MeSH headings can be used to help focus an SCR search. PubMed for Trainers Revised 2012/10

SCRs Do Not… Take Subheadings PubMed for Trainers Revised 2012/10

SCRs Are Not… In the MeSH Hierarchy. No explosion! Revised 2012/10

Exercise: Headings, Subheadings and Supplementary Concepts
What MeSH Heading/Subheading combination would be applied to a citation for an article about the synthesis of sordarin? What search would retrieve only highly relevant citations on this topic? What MeSH Heading/Subheading combination would be applied to a citation for an article about the synthesis of sordarin? Indenes/chemical synthesis What search might retrieve highly relevant citations on this topic? Indenes/chemical synthesis AND sordarin PubMed for Trainers Revised 2013/01

Searching Tip: Use Tags Sparingly
Use [mh] for drugs that you know are MeSH Headings: oseltamivir [mh] dibenzazepines [mh] You can use [nm] for drugs that are Supplementary Concepts OR MeSH Headings: metapramine [nm] dibenzazepines [nm] water [nm] BUT headings will not explode if searched with [nm]. It’s best to search by common names without tags. For searchers who want to use tags, here are some tips: If it’s a MeSH heading use [mh] If it’s a Supplementary concept use [nm]. If you search a MeSH heading with the [nm] tag you are turning off automatic explosion. This is equivalent to searching with the tag [mh:noexp]. If drug/chemical is an Supplementary Concept and you use [mh] you’ll get zero – example royal jelly[mh] PubMed for Trainers Revised 2013/01

Best way to search for a drug: No tags
Results (# records) Xanthophylls [nm] 2000 Xanthophylls [mh] 2923 Xanthophylls 3166 Let’s look at Xanthophylls, a MeSH heading. Xanthophylls[nm] turns off automatic explosion retrieving citations with the term Xanthophylls but none of its narrower terms. Xanthophylls[mh] retrieves citations with the term Xanthophylls and any of its narrower terms. Xanthophylls without search tags allows PubMed ATM to map to the MeSH heading, explode the MeSH heading and search for xanthophylls in the title and abstract, for example. PubMed for Trainers Revised 2013/01

Pharmacological Action Terms
The way a chemical or drug behaves in the body A pharmacologic action is how a chemical or drug behaves in the body. MeSH chemical and drug records include information on the drug’s action. In MeSH these are called Pharmacological Action terms and they are MeSH terms. PubMed for Trainers Revised 2013/01

Pharmacological action terms
[DEMO]: MeSH record for aspirin Let’s look at Aspirin. Aspirin is known to have these five actions. If an article is about aspirin as a platelet aggregation inhibitor, the indexer will add both MeSH terms to the citation: Aspirin and Platelet Aggregation Inhibitors. Indexers have been using pharmacologic action headings in this way since For a targeted search about a drug and its pharmacological action, search the drug and the action with the [mh] search tag. PubMed for Trainers Revised 2013/01

Demo in PubMed – search aspirin AND platelet aggregation inhibitors[mh]
For example, a targeted search for aspirin as a platelet aggregation inhibitor, search aspirin AND platelet aggregation inhibitors[mh] . Here are the MeSH terms on one of the results. PubMed for Trainers Revised 2013/01

Pharmacological Action Terms
But we do more with pharmacological action terms than just use them as MeSH headings. We can see this when we search the MeSH Database for a pharmacological action term. Two records are retrieved; one is the MeSH Heading record and the other is the Pharmacological Action record. PubMed for Trainers Revised 2013/01

The MeSH Heading Record
This is the MeSH Heading record for Platelet Aggregation Inhibitors. A search for this MeSH heading tagged with [mh] retrieves all MEDLINE/PubMed citations with this MeSH heading. Search PubMed from MesH. PubMed for Trainers Revised 2013/01

Drug AND MeSH Heading Revised 2013/01
So now if we wanted to find citations to articles about aspirin as a platelet aggregation inhibitor we add aspirin to the search. Notice that I’ve tagged the pharmacological action term with the [mh] tag. I could also tag the chemical term [mh] as well. When searching an action and a drug, tag the action with the [mh] tag. PubMed for Trainers Revised 2013/01

Pharmacological Action Record
Let’s look at the Platelet Aggregation Inhibitors [Pharmacological Action] record. This record is very different from the MeSH Heading record and from other records we’ve looked at so far. It is a list of all the chemicals and drugs in MeSH identified as platelet aggregation inhibitors. PubMed for Trainers Revised 2013/01

MeSH Record vs. PA Record
A concept / topic PA record: A tool (list of drugs with that PA) The MeSH record of a pharmacological action is the concept or topic. The Pharmacological Action record is a tool that gathers all the chemicals and drugs having that action. PubMed for Trainers Revised 2013/01

Disease AND Pharmacological Action [pa]
What happens when we search PubMed with this PA record? Notice the search tag is [Pharmacological Action]. The search results include all citations indexed with the MeSH heading Platelet Aggregation Inhibitors or with any of the chemicals and drugs having the action. That is any of the chemicals or drugs listed in the PA record tool. Or said another way, all citations indexed with any of these chemicals and drugs. Plus all the citations indexed with the MeSH heading. This is useful, for example, when I want to find citations to articles about venous thromboembolism and platelet aggregation inhibitors. I don’t have to hunt around for all the chemicals and drugs with this action because I know that they are already collected for me in the Platelet Aggregation Inhibitors [Pharmacological Action] record. Add venous thromboembolism[mh] to PubMed search. When searching an action and a disease, tag the action with the [pa] tag. PubMed for Trainers Revised 2013/01

PubMed ATM maps untagged searches to both the MeSH heading and the [Pharmacological Action] term.

Review – 2 Ways to Use PAs 1. Drug AND Pharmacological Action – tagged [mh] Example: lithium carbonate AND antidepressive agents [mh] retrieves articles about lithium carbonate as an antidepressive agent. 2. Disease AND Pharmacological Action – tagged [pa] panic disorder AND antidepressive agents [pa] retrieves articles about any antidepressive chemical or drug and panic disorder. To review, when searching for the action of a specific drug, tag the action term with [mh]. When searching for an action involved with a disease, tag the action term with [pa]. PubMed for Trainers Revised 2013/01

Teachback In groups of 2 or 3, explain to each other when and why you would use the [mh] or [pa] tags to search for pharmacologic actions with a drug or disease. Use these examples: Find articles about Bismuth or Magnesium Hydroxide used as antacids. Find articles about treating GERD or Heartburn with antacids. In groups of 2 or 3, explain to each other when and why you would use the [mh] or [pa] tags to search for pharmacologic actions with a drug or disease. Use these examples: Find articles about Bismuth or Magnesium Hydroxide used as antacids. Find articles about treating GERD or Heartburn with antacids. PubMed for Trainers Revised 2012/02

Exercise: Pharmacological Actions
Recently there has been some interest in thalidomide as an angiogenesis inhibitor. How might you search to find relevant records? Question: Recently there has been some interest in thalidomide as an angiogenesis inhibitor. How might you search to find relevant records? thalidomide AND angiogenesis inhibitors [mh] PubMed for Trainers Revised 2013/01

Summary You should now be able to:
Explain how chemicals, drugs and other substances are described in MeSH. Search for drugs or chemicals in PubMed. Search using pharmacological action terms. Use common names and don’t tag. When searching for specific aspects of supplementary concepts use the Heading Mapped to: to narrow the search. You can add subheadings and restrict to major topic. Use pharmacological action terms to narrow drug and disease searches. Questions? PubMed for Trainers Revised 2013/01

PubMed Nuts and Bolts PubMed for Trainers, Winter 2013
This presentation is about the “nuts and bolts” that make up PubMed. This information is important for you, as a trainer, but not intended for end-users. The purpose is to give you a glance at the back-end of the PubMed system, and point out resources that you can use to look up details about MEDLINE/PubMed data, fields and searching. PubMed for Trainers, Winter 2013 U.S. National Library of Medicine (NLM) and NLM Training Center

Goals Locate details and history about the information included in MEDLINE/PubMed records and Search the fields of MEDLINE/PubMed records efficiently. Your objective is to find detailed and specific information on what is included in MEDLINE/PubMed records and to search the fields of those records efficiently. PubMed for Trainers Revised 2012/12

Objectives After this session participants will be able to use:
the MEDLINE/PubMed Field Elements Descriptions documentation to find details about the MEDLINE data the search tags table in PubMed Help to find searchable fields and learn how to search those fields the Advanced Search page Search Builder to explore PubMed’s indexes the NLM Catalog Journal search to find journals and build journal sets for searching in PubMed History to combine searches PubMed for Trainers Revised 2012/12

The point of the following slides:
MEDLINE/PubMed data structure can vary by field MEDLINE/PubMed data inclusion has varied over time PubMed indexing can vary by field BUT you can search easily because there are tools at your disposal to: Get details about MEDLINE/PubMed data View PubMed indexing Shortcut to the data you need MEDLINE/PubMed data structure can vary by field. Data inclusion has varied over time for some fields. PubMed indexing varies by field. But you can search easily because there are tools to: Get details about the data View the indexing for every field and combination of fields and shortcut to the data you need. PubMed for Trainers Revised 2012/12

Part I: The Data PubMed for Trainers Revised 2012/12
First let’s talk about the data itself. PubMed for Trainers Revised 2012/12

Fields Records PMID 23082700 TITLE
Eosinophils in the gastrointestinal tract AUTHOR Straumann A LANGUAGE English SOURCE Acta Gastroenterol Belg Sep;75(3):310-5 Fields PMID TITLE Changing antimicrobial resistance pattern AUTHOR Jain S LANGUAGE English SOURCE J Assoc Physicians India May;60:27-8, 33 Records PMID TITLE Gut bacteria and antimicrobial resistance AUTHOR Kanerva M LANGUAGE Finnish SOURCE Duodecim. 2012;128(17): Like any other database, PubMed records are divided into fields of data. Each field represents a particular piece of information about the article (e.g., title, author, language, source). PubMed for Trainers Revised 2012/12

MEDLINE FORMAT WITH FIELD LABELS (Tags)
PMID OWN - NLM STAT- MEDLINE DA DCOM IS (Electronic) IS X (Linking) VI Suppl 2 UCTN DP TI - Eosinophilic enteritis presenting as a perforated duodenal ulcer. PG - E358-9 AD - Department of Internal Medicine, King Fahad Specialist Hospital, Dammam, Saudi Arabia. FAU - Issa, H AU - Issa H FAU - Bseiso, B AU - Bseiso B FAU - Al-Salem, A H AU - Al-Salem AH LA - eng PT - Case Reports PT - Journal Article DEP PL - Germany TA - Endoscopy JT - Endoscopy JID RN - Eosinophilic enteropathy SB - IM MH - Adult MH - Duodenal Ulcer/complications/*etiology/surgery MH - Enteritis/*complications/*diagnosis/drug therapy MH - Eosinophilia/*complications/*diagnosis/drug therapy MH - Gastritis/*complications/*diagnosis/drug therapy MH - Humans MH - Intestinal Obstruction/*etiology/therapy MH - Male MH - Peptic Ulcer Perforation/*etiology/surgery EDAT- 2011/11/10 06:00 MHDA- 2012/03/10 06:00 CRDT- 2011/11/10 06:00 PHST- 2011/11/08 [epublish] AID /s [doi] PST - ppublish SO - Endoscopy. 2011;43 Suppl 2 UCTN:E Epub 2011 Nov 8. MEDLINE FORMAT WITH FIELD LABELS (Tags) You’ve seen the typical MEDLINE record. This is what it looks like in MEDLINE format, with field labels. PubMed for Trainers Revised 2012/12

Data structure varies by field
Author [au] or Grant [gr] or Date fields Highly structured vs. Affiliation [ad] NOT structured OR standardized Abstract [ab] Sometimes partially structured Most PubMed fields are highly structured and/or standardized. However, some fields are not. Let’s look at some examples. PubMed for Trainers Revised 2012/12

Highly Structured MEDLINE Field Examples:
Author [au] Lastname initials suffix Examples: AU – Smith AB 3rd AU – McCrary SV Date fields [EDAT], [MHDA] etc. YYYY/MM/DD HH:MM EDAT – 2003/01/02 04:00 MHDA – 2005/08/03 09:00 Grant Number [gr] Number/code/agency/country Examples: GR - LM0577/LM/NLM NIH HHS/United States GR /Wellcome Trust/United Kingdom Author names are in MEDLINE in the following format: Last name followed by a space and up to the first two initials followed by a space and a suffix abbreviation, if applicable, all without periods or a comma after the last name. Dates are entered in a specific date format: YYYY/MM/DD Grant number also has a specific format. Grants are entered in up to four parts (see slide). For any of these highly structured fields, all of parts of the fields are searchable. But if you want to be specific, you need search following the specific structure of the data. PubMed for Trainers Revised 2012/12

An Unstructured MEDLINE Field Example: Affiliation [ad]
An example of an unstructured field is Affiliation. Here’s are several examples of how the same institution was entered. it shows some of the variation in how people enter institution names and addresses. Because of the variation, you need to be “creative” in searching. <click> Perhaps, like in this example, by combining pieces of data you’d expect authors to include. SPECIAL NOTE: Only affiliation of FIRST author is included in PubMed PubMed for Trainers Revised 2012/12

Over time, MEDLINE data inclusion has varied
Examples: Author policy “New” fields: Full author name (2002-) Grant number (1981-) Location Identifier (2008-) “Old” fields (no new data): Gene Symbol ( ) Number of References (-2010) While changes in what data is included in a MEDLINE record are uncommon, they have happened. [Because of technology, policy, new data available?] This, of course, is important to know if you want to search these fields of the record. Here are some examples. The author policy changed over time. In the past, we limited the number of authors. We no longer do this. Other fields have been added since the beginning of MEDLINE (see slide). And we have stopped adding data for others (see slide). [More information: … ] PubMed for Trainers Revised 2012/12

Exercise: MEDLINE/PubMed Elements (the data)
Explore the MEDLINE/PubMed Elements documentation Google MEDLINE, Go to MEDLINE/PubMed Resources Guide Under Data Structure, choose Detailed Field/Data Element Descriptions Look at the author policy Compare these two records: PMID and PMID So how would you find details like these about the data in a MEDLINE/PubMed record? You’d go to our documentation. Let’s use this documentation: Google MEDLINE Find the MEDLINE/PubMed Resources Guide This Guide is a comprehensive list of all NLM-produced MEDLINE and PubMed documentation. See the Detailed Field/Data Element Descriptions. Try this exercise. [Can we come up with an exercise that would highlight data that IS included in MEDLINE, that people may not be aware of?] PubMed for Trainers Revised 2012/12

Part II: Indexing PubMed for Trainers Revised 2012/12
Now that we’ve looked at the data itself, let’s look at how that data is made searchable. PubMed for Trainers Revised 2012/12

Indexes Records AUTHOR INDEX Jain 23029718 Jain S Kanerva 23033785
Kanerva M PMID TITLE Changing antimicrobial resistance pattern AUTHOR Jain S LANGUAGE English SOURCE J Assoc Physicians India May;60:27-8, 33 TITLE INDEX antimicrobial antimicrobial resistance bacteria changing gut gut bacteria pattern resistance PMID TITLE Gut bacteria and antimicrobial resistance AUTHOR Kanerva M LANGUAGE Finnish SOURCE Duodecim. 2012;128(17): From each field, PubMed produces an Index. An index represents the data and access points to, for example, all the author fields of all the records. On this slide you see two examples: An author index and a title index. Here you can see that the fields can be parsed to create an index. In other words, strings of characters or words and phrases can be copied from the field in each record to create an index. PubMed for Trainers

Search Tags antimicrobial [ti] TITLE INDEX antimicrobial 23029718
antimicrobial resistance changing eosinophils gastrointestinal gastrointestinal tract pattern resistance antimicrobial [ti] PMID TITLE Changing antimicrobial resistance pattern AUTHOR Jain S LANGUAGE English SOURCE J Assoc Physicians India May;60:27-8, 33 Because of this indexing, you can use search tags to specify which index you want to search in PubMed. In this example, I’ve shown how you can tag with [ti] to specify that you want to retrieve all records with the word “antimicrobial” in the title field. The title index enables this search. PMID TITLE Antimicrobial resistance in the ICU AUTHOR Soman R LANGUAGE English SOURCE J Assoc Physicians India May;60:9. PubMed for Trainers Revised 2012/12

Search Tags Search specific PubMed fields using tags.
Syntax is term [tag], e.g.: Warning! Using search tags turns off Automatic Term Mapping (ATM) By now you understand that there is nothing complicated about using PubMed search tags. You know that... Search fields can be specified using search tags in a PubMed search. The search term should appear before the search tag in square brackets; e.g.: lung [mh] And you know that… Using search tags will turn off Automatic Term Mapping (ATM) … PubMed for Trainers Revised 2012/12

Search Tags (Look in PubMed Help)
All PubMed Search indexes are not created equal You also know that you can find the complete list of search tags in PubMed Help: Search Field Descriptions and Tags And perhaps, especially from your homework, you are appreciating the fact that <click> All PubMed search indexes are not created equal PubMed for Trainers Revised 2012/12

Article Title [ti] [ti] can be used to search for words and phrases in the title field NOT for the entire title For example, you’ve learned that [ti] can be used to search for words and phrases in the title field NOT for the entire title The entire title is rarely included in the title index, therefore is rarely searchable as an unbroken string So you need to break up the title to search it this way, e.g., <click> air pollution [ti] blood pressure [ti] traffic [ti] PubMed for Trainers Revised 2012/12

Journal Title [ta] [ta] can be used to search for the exact title or MEDLINE title abbreviation NOT for extracted words or phrases Conversely, the journal index includes ONLY full journal titles (is not parsed) -- along with MEDLINE title abbreviations and ISSNs -- and cannot be searched with elements of the journal title. PubMed for Trainers Revised 2012/12

Combined Index TITLE INDEX antimicrobial 23029718 23082700
antimicrobial resistance changing eosinophils ABSTRACT INDEX achievement acinetobacter aeruginosa amikacin changing eosinophils TITLE/ABSTRACT INDEX achievement acinetobacter aeruginosa amikacin antimicrobial antimicrobial resistance changing eosinophils Combined Index PubMed has some combined indexes. These are indexes created from multiple fields. A very obvious one is the Title/Abstract index. PubMed for Trainers Revised 2012/12

Title/Abstract [tiab]
[tiab] finds words and numbers included in the title, abstract, and other abstract of a citation. [tiab] is often used by searchers to find topic- related keywords, BUT: [tiab] does NOT find terms from the subject fields of PubMed records. [tiab] can be used to search for words and numbers included in the title, abstract, and other abstract of a citation. [tiab] is often used by searchers to find topic-related keywords, however, it fails to find terms from the subject fields of PubMed records. You looked at quality of life [majr] NOT quality of life [tiab] To explore the limitation of this search. PubMed for Trainers Revised 2012/12

Text word [tw] includes: Title Abstract MeSH headings & subheadings
Publication Types Other Terms field Chemical Names of Substances Secondary Source Identifier Personal Name as Subject The text word index is another example of an index that combines searchable fields. Text Word was created to avoid the problems of the tiab index: to include the subject-related fields in PubMed. MORE: Secondary Source Identifier field contains information of other data sources, databanks and accession numbers of molecular sequences discussed in the article. The field is composed of a source followed by a slash followed by an accession number. EX: genbank/af113832[si] Personal Name as Subject searches for citations about a named individual. The name is searched in the conventional author searching format: lastname + initial(s). NOTE: Personal Name as Subject field is not available from the Search Builder on the Advanced Search page. PubMed for Trainers Revised 2012/12

Building Phrase Indexes in PubMed
A speech analyzer identifies new noun phrases from the title and abstract fields of PubMed The phrase is added if it: occurs at least 3 times in the database contains at least 1 alphabetic character has at most 6 words Phrases are added to the PubMed indexes twice per month During our very first session we pointed out that not every phrase in PubMed is searchable. We saw the example “hourly injection.” While new citations are added to PubMed every day, Tuesday through Friday, not every phrase from these citations are indexed and therefore searchable immediately. Phrases are added to the PubMed title and abstract indexes twice per month To be added to the indexes, a phrase must: occur at least 3 times in the database contain at least 1 alphabetic character have at most 6 words See "MedPost: a part-of-speech tagger for bioMedical text" PubMed for Trainers Revised 2012/12

Explore the Indexes Searchable indexes are accessible from the Search Builder on the PubMed Advanced Search page. To find what phrases are indexed in any searchable field of PubMed, go to PubMed Advanced Search and explore the indexes. Click on the field or combined index you want to explore. PubMed for Trainers Revised 2012/12

Explore the Indexes (continued)
Type the beginning of the word or phrase you want to see. Click Show index list. PubMed for Trainers Revised 2012/12

Exercise: PubMed Indexes
Using only the Show Index feature of the PubMed Advanced Search Builder, answer the following questions: How many PubMed records are for articles in Esperanto? Is the phrase “finger to nose” indexed in PubMed? PubMed for Trainers Revised 2012/12

Part III: The Tools PubMed for Trainers Revised 2012/12

Part III: The Tools Previously covered: Next up:
MEDLINE/PubMed Elements Page Table of Search Tags in Help Index on Advanced Search Builder Next up: NLM Catalog Journal Search Search History features We’ve already covered three important tools you need to fully understand MEDLINE/PubMed data and how to search it: The Elements page, the Table of Search Tags, and the Advanced Search Search Builder. Now let’s look at two more tools that may be useful in your searches: The NLM Catalog Journal search, and your Search History. URLs: PubMed for Trainers Revised 2012/12

NLM Catalog Journal Search
In your homework you explored using the Single Citation Matcher to search by journal name. The NLM Catalog Journal search allows you to find journals using partial journal titles or topics as well as ISSN or MEDLINE journal title. It also allows you to build sets or collections of journals to search in PubMed. [DEMO: Search International Journal of Oncology Show links back to PubMed Show Add to search builder. Go back to search page, click on More Resources > Browse…Subject Terms Select Neoplasms Select Find Related Data > PubMed] PubMed for Trainers Revised 2012/12

The Journal search page has an autocomplete feature, if you’d like to search by title. PubMed for Trainers Revised 2012/12

The catalog record has extensive information about the journal, including the dates of indexing. The catalog record page also has a PubMed search builder, to use to find the citations from this journal. PubMed for Trainers Revised 2012/12

PubMed Search Results: All citations from the International Journal of Oncology

Also on the NLM Catalog Journal search page under More Resources you can find a page that allows you to find MEDLINE journals by broad subject terms. PubMed for Trainers Revised 2012/12

Broad Subject Terms PubMed for Trainers Revised 2012/12
Follow the links on this page to run an NLM Catalog search for journals with these broad subject terms applied. For example, click N to get to Neoplasms. PubMed for Trainers Revised 2012/12

Find Related Data PubMed for Trainers Revised 2012/12
Under Find related data you can select PubMed to retrieve all citations from all journals found in this search. PubMed for Trainers Revised 2012/12

Combining Searches in History
Now that we’ve added a large retrieval set to our Search History, let’s see how to use that set to build a search. The Search History feature allows you to: Run previous searches by clicking on the Items found column or by typing the search history number into the search box. Add previous searches to the search builder by clicking Add Or use previous searches by activating the menu, accessible by clicking on the search history number. <click> The History feature on the Advanced Search page allows you to re-run or combine previous searches. PubMed for Trainers Revised 2012/12

Combining searches in History (cont.)
Use neoplasms journals search and add: angiogenesis AND (high-fat OR dietary fat) PubMed for Trainers Revised 2012/12

Exercise Use the NLM Catalog Journal Broad Subject Terms to find MEDLINE journals about audiology. Search for all citations in PubMed from these audiology journals. Using History, combine the audiology journal search with a search for cochlear implants. Limit your search to those that are included in the Systematic Reviews subset. PubMed for Trainers Revised 2012/12

Summary After this session participants will be able to use:
the MEDLINE/PubMed Field Elements Descriptions documentation to find details about the MEDLINE data the search tags table in PubMed Help to find searchable fields and learn how to search those fields the Advanced Search page Search Builder to explore PubMed’s indexes the NLM Catalog Journal search to find journals and build journal sets for searching in PubMed History to combine searches PubMed for Trainers Revised 2012/12

Searching for Disease Information in PubMed: Building Searches with MeSH
PubMed for Trainers, Winter 2013 U.S. National Library of Medicine (NLM) and NLM Training Center

Objectives: Build a PubMed search using the MeSH Database.
Recognize and identify how NLM indexers assign terms to MEDLINE records, with a focus on disease and treatment terms. Apply indexing rules to improve your search technique. Create searches by “free-floating” subheadings. Enhance your search by using subject populations terms. Locate, and when appropriate, search using the AIDS and Cancer subject subsets. PubMed for Trainers Revised 2012/12

Building a Search in the MeSH Database
Let’s use the MeSH Database to find the MeSH term for autism and then search PubMed for relevant citations. Enter the term, autism, in the search box and click the Search button. From the results we see that the preferred term is Autistic Disorder. Click on the term to get to the full record. PubMed for Trainers Revised 2012/12

Building a Search in the MeSH Database (cont.)
Select PubMed, PubMed – Major Topic from the links menu in the right column to run a PubMed search with that term. Use Clinical Queries to run your topic search on the Clinical Queries page. PubMed for Trainers Revised 2012/12

Let’s use the MeSH Database to build a search strategy for a search for citations about the treatment of autism which requires the use of a subheading. Use the checkboxes to select subheadings. Click on the Subheadings link to see a list of subheading definitions. Note that you can use these checkboxes to restrict to a major topic or to not include indented terms (not “explode” the term). The PubMed Search Builder appears to the right of your MeSH Database results. It allows you to build PubMed searches with multiple MeSH terms and/or specifications. - Select the therapy subheading from the Full display screen. - Select Add to search builder. PubMed for Trainers Revised 2012/12

To add additional terms to this strategy, continue searching the database and add terms to the PubMed search builder. Let’s adjust our search to specifically look for articles discussing the treatment of autism using computer-assisted therapy. Note: The default Boolean operator used when adding terms to the search builder is “AND.” You can change this using the dropdown to the right of the Add button. Now, the search is built and is ready to be run in PubMed. Click the Search PubMed button below the PubMed search builder: PubMed for Trainers Revised 2012/12

Exercise Use the MeSH Database and the PubMed search builder to find articles discussing multiple sclerosis as the main focus of the article. Narrow your results to those citations also discussing sarcoidosis. Use the MeSH Database and the PubMed search builder to find articles discussing multiple sclerosis as the main focus of the article. Narrow your results to those citations also discussing sarcoidosis. PubMed for Trainers Revised 2012/12

MEDLINE Indexing: From the Indexer’s point-of-view

Indexing: Specificity
Indexers use the hierarchy to find the most specific MeSH heading. Example: Chronic hepatitis B Hepatitis B, Chronic (not Liver diseases or Hepatitis or Hepatitis B) Search tip: Use the most specific term appropriate for searching. PubMed for Trainers Revised 2012/12

Indexing: Depth of Indexing
For most research articles, every concept substantively discussed should be covered by at least one MeSH heading Negative results (i.e. supporting the null hypothesis) are indexed if discussed For articles discussing many subjects, general headings (but as specific as possible) may be used to group related concepts rather than indexing them individually More: Some items, such as review articles, letters, and editorials, are indexed “non-depth,” meaning: All major topics are indexed All minor concepts required for complete coordination of the major topics are indexed. PubMed for Trainers Revised 2012/12

Indexing: Rule of Three
If more than 3 related concepts are discussed in an article, the more general MeSH heading under which they are all treed is usually indexed. The specific headings may be indexed, but not as major topics. Example: Article discusses infections by Helicobacter pylori, Clostridium difficile, peptostreptococci , and vancomycin-resistant enterococci indexed with BACTERIAL INFECTIONS Article discusses infections by Helicobacter pylori, Clostridium difficile, peptostreptococci , and vancomycin-resistant enterococci indexed with BACTERIAL INFECTIONS (example PMIDs , ) PubMed for Trainers Revised 2012/12

Required (if applicable) Headings
Some headings are considered for every article (“check tags”) Include: Species (including Humans) Sex Age groups (for humans) Also historical time periods and pregnancy Usually are indexed even if merely mentioned, unlike other MeSH headings Many of these check tags identify characteristics of the population being studied, so can be very useful for searching. More: - For review articles used only if the main point of the article - Humans is not selected for institutions, e.g., clinics, hospitals - Some check tags (Animals, Humans, Male, Female, In Vitro, Comparative Study, and research support terms) can never be designated as the main point of the article PubMed for Trainers Revised 2012/12

Required (if applicable) Headings
Search tip: Use terms for species, sex and age in your search if appropriate. PubMed for Trainers Revised 2012/12

Indexing: When a Concept isn’t Found
If an exact heading does not exist, indexers use the most specific heading available. Example: Ashi points in acupuncture Acupuncture points Example PMID PubMed for Trainers Revised 2012/12

Exercise How would an article about preventing heart diseases in women be indexed for MEDLINE? How would an article about preventing heart diseases in women be indexed for MEDLINE? [Discuss female and human check tags.] PubMed for Trainers Revised 2012/12

Indexing: Coordination
Because most concepts cannot be adequately described with a single MeSH term: indexers use a combination of the appropriate: MeSH headings, subheadings, and other terms to index a concept as specifically as possible. This is called coordination. PubMed for Trainers Revised 2012/12

Indexing: Coordination
We will discuss four types of coordination: Subheading Multiple headings Multiple subheadings Pre-coordinated headings We’ll discuss 4 types of coordination: One subheading Multiple headings Multiple subheadings Pre-coordinated headings PubMed for Trainers Revised 2012/12

Indexing: Coordination (Using Subheadings)
Coordination can be done using a subheading to describe a specific aspect of a topic. Example: Radiographic imaging of a lung tumor. Lung Neoplasms/radiography PubMed for Trainers Revised 2012/12

Indexing: Coordination (Using Multiple Headings)
Coordination can be done using two or more headings. Mucinous adenocarcinoma of the ovary Adenocarcinoma, Mucinous Ovarian Neoplasms PubMed for Trainers Revised 2012/12

Indexing: Coordination (Using Two or More Subheadings)
Coordination can be done using two or more subheadings. /drug therapy on a disease term /therapeutic use on a drug term Example: Treatment of HIV infections with HIV protease inhibitors. HIV Infections/drug therapy HIV Protease Inhibitors/therapeutic use /drug therapy on disease term /therapeutic use on drug/substance term Do not need to necessarily search with both subheadings especially if adding additional concepts. This shows that good indexing allows for great flexibility in searching. Hiv infections/drug therapy [mh] AND hiv protease inhibitors [mh] Will give you fine results, as will: Hiv infections [mh] AND hiv protease inhibitors/therapeutic use [mh] But for greatest specificity, use both: Hiv infections/drug therapy [mh] AND hiv protease inhibitors/therapeutic use [mh] One example that shows that good indexing allows for great flexibility in searching. PubMed for Trainers Revised 2012/12

Exercise: Coordinated Indexing
Use the MeSH Database and the PubMed search builder to find article discussing prostate cancer as the main focus of the article. Narrow your results to those involving treatment by leuprolide. Use the MeSH Database and the PubMed search builder to find article discussing prostate cancer as the main focus of the article. Narrow your results to those involving treatment by leuprolide. PubMed for Trainers Revised 2012/12

Indexing: Coordination (Using Two or More Subheadings)
/secondary on the site to which a cancer has metastasized /secondary on the histologic/tissue type term /pathology on the primary/original organ neoplasm term Example: Liver Neoplasms/secondary metastasized site Adenocarcinoma/secondary tissue type Colonic Neoplasms/pathology primary/original site Neoplasms metastasis Metastasis means the movement of cancer from one organ to another – the tissue type is the same in both organs. The subheading /secondary is used on the site to which the tumor has gone/ You can also use /secondary on the histologic or tissue type term if relevant. The indexers will also use the /pathology subheading on the primary or original organ neoplasm site term if relevant to the article. The broad MeSH term of Neoplasm Metastasis for general articles about the process of metastasis. PubMed for Trainers Revised 2012/12

Indexing: Coordination (Using a Pre-coordinated Heading)
Coordination can be done using a "pre-coordinated" MeSH heading which combines two concepts into one. Example: Staphylococcal pneumonia Pneumonia, Staphylococcal Rather than: Pneumonia (or Pneumonia, Bacterial) Staphylococcal Infections PubMed for Trainers Revised 2012/12

Exercise: Coordinated Indexing
What MeSH term(s) would indexers use to describe osteoarthritis of the knee? PubMed for Trainers Revised 2012/12

“Free-Floating” Subheadings
It may be useful to search a subheading unattached to a Heading. Examples from homework: breast neoplasms[mh] AND trends[sh] hypertension [majr] AND toxicity [sh] [sh] allows you to search the subheading attached to any MeSH heading PubMed for Trainers Revised 2012/12

Useful Vocabulary to Describe Study Populations

Persons Category Abortion Applicants Friends Sexual Partners
Adult Children Homebound Persons Siblings Age Groups + Homeless Persons + Single Person Alcoholics Jehovah's Witnesses Spouses Athletes Legal Guardians + Students + Caregivers Medically Uninsured Survivors + Child, Abandoned Men + Terminally Ill Child, Exceptional + Mentors Tissue Donors + Child of Impaired Parents Minors Transients and Migrants Child, Orphaned Multiple Birth Offspring + Veterans Child, Unwanted Occupational Groups + Visitors to Patients Consultants Parents + Voluntary Workers + Crime Victims + Patients + Vulnerable Populations Criminals Population Groups + Women + Disabled Persons + Prisoners Drug Users Refugees Emigrants and Immigrants Research Personnel + Famous Persons Research Subjects PubMed for Trainers Revised 2012/12

Age Groups Adolescent Adult Child Infant Aged Middle Aged Young Adult
Aged, 80 and over Frail Elderly Middle Aged Young Adult Child Child, Preschool Infant Infant, Newborn + PubMed for Trainers Revised 2012/12

Population Groups Continental Population Groups Ethnic Groups
African Continental Ancestry Group + American Native Continental Ancestry Group + Asian Continental Ancestry Group + European Continental Ancestry Group Oceanic Ancestry Group Ethnic Groups African Americans Arabs Asian Americans Gypsies Hispanic Americans + Inuits Jews PubMed for Trainers Revised 2012/12

Exercise: Study Populations
Use the MeSH Database and PubMed to find ways to encourage elderly black Americans to follow treatment programs for type 2 diabetes. Some useful MeSH: Aged African-Americans Diabetes Mellitus, Type 2 Patient compliance PubMed for Trainers Revised 2012/12

AIDS and Cancer Subsets
Subsets are on Filters sidebar but also searchable with tags Strategies can be found at (use PubMed Help) aids [sb] developed from AIDSLINE work cancer [sb] developed with the National Cancer Institute All strategies reviewed at least annually Created using subject expert search strategies, including MH, TW, and journal titles. They are comprehensive and can easily focus a search. The strategies are reviewed annually. Demo: Enter fatigue in search box and use either the AIDS or Cancer subject subset from the Filters sidebar. PubMed for Trainers Revised 2012/12

Summary Find and combine terms for your PubMed search using the MeSH Database. Identify subheadings to describe specific aspects of the topic of interest for better results. Restrict your search to MeSH major topic for higher relevancy. Find the most specific term available to describe topics of an article. Indexers use the most specific term, you should too. Search terms for species, sex, age, historical time period and pregnancy when applicable. These terms are added by indexers. Consider using these for searching. PubMed for Trainers Revised 2012/12

Summary Coordinate multiple headings to describe complex topics. For example: disease/drug therapy and drug/therapeutic use Try “free-floating” a subheading to search for the subheading applied to any heading. Enhance your search by using subject populations terms. Locate, and when appropriate, search using the AIDS and Cancer subject subsets. PubMed for Trainers Revised 2012/12

Questions? Questions? PubMed for Trainers Revised 2012/12

MEDLINE®/PubMed® An introduction

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