Introduction to Introduction to Searching Bibliographic Searching Bibliographic

DatabasesDatabasesJennifer Lyon, M.S., M.L.I.S.Jennifer Lyon, M.S., M.L.I.S.Clinical Research LibrarianClinical Research Librarian

Health Science Center LibrariesHealth Science Center LibrariesUniversity of FloridaUniversity of Florida

A A databasedatabase is an organized is an organized collection of data. collection of data.

Bibliographic databases are searched Bibliographic databases are searched through many of the same through many of the same techniques as any other databasetechniques as any other database

Focus will be on PubMed, but these Focus will be on PubMed, but these techniques apply to ANY literature techniques apply to ANY literature databasedatabase

Examples of Records and Examples of Records and FieldsFields

Record Record ##

AuthorAuthor TitleTitle PublisherPublisher Date of Date of

PublicationPublication

11 Jones KMJones KM Infectious Infectious DiseasesDiseases

WileyWiley 20012001

22 Smith BRSmith BR MedicineMedicine Cambridge Cambridge Univ. PressUniv. Press

20042004

33 Johnson Johnson ASAS

CancerCancer ElsevierElsevier 20052005

44 Bradley Bradley PLPL

AsthmaAsthma SynergySynergy 20032003

Examples of Records and Examples of Records and FieldsFields

Record Record ##

AuthorAuthor TitleTitle PublisherPublisher Date of Date of

PublicationPublication

11 Jones KMJones KM Infectious Infectious DiseasesDiseases

WileyWiley 20012001

22 Smith BRSmith BR MedicineMedicine Cambridge Cambridge Univ. PressUniv. Press

20042004

33 Johnson Johnson ASAS

CancerCancer ElsevierElsevier 20052005

44 Bradley Bradley PLPL

AsthmaAsthma SynergySynergy 20032003

RED=RECORD BLUE=FIELD PURPLE = ONE PIECE OF DATA

Searching a DatabaseSearching a DatabaseDifferent search interfaces do the same things in slightly different Different search interfaces do the same things in slightly different

waysways

Good search interfaces should provideGood search interfaces should provide– Ability to search for a specific item Ability to search for a specific item – Ability to search for related items to a Ability to search for related items to a

known itemknown item– Ability to search in a specific field or Ability to search in a specific field or

fieldsfields– Ability to combine search terms using Ability to combine search terms using

Boolean LogicBoolean Logic– Ability to retrieve search results in a Ability to retrieve search results in a

useful wayuseful way

Step-by-Step ProcedureStep-by-Step Procedure

– Asking and Parsing the QuestionAsking and Parsing the Question– Understanding Boolean LogicUnderstanding Boolean Logic– Understanding Database StructureUnderstanding Database Structure– Understanding Field SearchingUnderstanding Field Searching– Understanding Controlled VocabularyUnderstanding Controlled Vocabulary

Controlled Vocabulary vs Keyword SearchingControlled Vocabulary vs Keyword Searching

– Specialty FeaturesSpecialty Features– Putting It All TogetherPutting It All Together

Asking the Question: PICOAsking the Question: PICO

– Patient, Population or Problem Patient, Population or Problem What are the characteristics of the patient or What are the characteristics of the patient or

population? population? What is the condition or disease you are interested What is the condition or disease you are interested

in? in?

– Intervention or exposure Intervention or exposure What do you want to do with this patient (e.g. treat, What do you want to do with this patient (e.g. treat,

diagnose, observe)? diagnose, observe)?

– Comparison Comparison What is the alternative to the intervention (e.g. What is the alternative to the intervention (e.g.

placebo, different drug, surgery)? placebo, different drug, surgery)?

– Outcome Outcome What are the relevant outcomes (e.g. morbidity, What are the relevant outcomes (e.g. morbidity,

death, complications)? death, complications)?

http://healthlinks.washington.edu/ebp/pico.html

Parsing the QuestionParsing the Question

What are the main concepts in your What are the main concepts in your question?question?

Sample question: Sample question:

Does nutrition therapy improve Does nutrition therapy improve decubitus (pressure) ulcer healing in decubitus (pressure) ulcer healing in an elderly patient? an elderly patient?

Concepts: Concepts:

Nutrition therapy

Decubitus/pressure ulcers

Ulcer healing Elderly patients

Treatment efficacy

Boolean LogicBoolean Logic

A British mathematician named George A British mathematician named George Boole (1815-1864) developed an algebraic Boole (1815-1864) developed an algebraic system of logic that is now widely used in system of logic that is now widely used in computer and electronic systems including computer and electronic systems including database searching.database searching.

While Boole’s algebraic system can be While Boole’s algebraic system can be complex, a very simple form of Boolean complex, a very simple form of Boolean Logic is used for searching most Logic is used for searching most bibliographic databases.bibliographic databases.

Boolean OperatorsBoolean Operators

Standard Boolean Logic for database Standard Boolean Logic for database searching uses 3 relationships searching uses 3 relationships among search terms.among search terms.

ANDAND

OR OR

NOTNOT

It is both simple and powerful.It is both simple and powerful.

ANDAND

BOTH BOTH terms included in terms included in any results.any results.

If a record has only one of If a record has only one of the two terms, it will the two terms, it will not be retrieved. not be retrieved.

If the record has neither If the record has neither term, it will not be term, it will not be retrieved.retrieved.

What does this do to the What does this do to the amount of records amount of records retrieved?retrieved?

OROR

Only oneOnly one ( (NOT bothNOT both) ) of the terms are in of the terms are in the resultsthe results

‘‘OR’ will retrieve the OR’ will retrieve the record if both are record if both are included. included.

What does OR do to What does OR do to the amount of the amount of records retrieved?records retrieved?

NOTNOT

Excludes any results Excludes any results containing the containing the termterm

Records containing Records containing both will not be both will not be retrieved.retrieved.

What does NOT do What does NOT do to the amount of to the amount of records retrieved?records retrieved?

Using ORUsing OR

““OR” groupings contain terms for the same OR” groupings contain terms for the same idea/concept and are usually put in idea/concept and are usually put in parenthesisparenthesis

(term OR term OR term)(term OR term OR term) where all terms are difference ways of where all terms are difference ways of

representing the same conceptrepresenting the same concept

(faculty OR teachers OR professors)(faculty OR teachers OR professors)

(students OR learners OR pupils)(students OR learners OR pupils)

Using ANDUsing AND

““AND” groupings contain terms for different AND” groupings contain terms for different ideas/concepts and can combine OR ideas/concepts and can combine OR groupingsgroupings

Term AND (Term OR Term)Term AND (Term OR Term) where each where each represents a different conceptrepresents a different concept

heart attack AND smokingheart attack AND smoking

Diabetes AND exerciseDiabetes AND exercise

Cancer AND (treatment OR therapy)Cancer AND (treatment OR therapy)

Using NOTUsing NOT

““NOT” statements are usually put last NOT” statements are usually put last and can contain an “OR” grouping; and can contain an “OR” grouping; they are often used to get rid of a they are often used to get rid of a common subgroupcommon subgroup

Students NOT dentalStudents NOT dental

Diabetes NOT juvenileDiabetes NOT juvenile

Putting Them TogetherPutting Them Together

1.1. Identify the concepts (Parse the Identify the concepts (Parse the question)question)

2.2. List specific terms for each conceptList specific terms for each concept

3.3. Put the terms for each concept in Put the terms for each concept in an OR statements within an OR statements within parenthesesparentheses

4.4. Combine OR statements with ANDCombine OR statements with AND

5.5. Add any NOT statements to the endAdd any NOT statements to the end

Creating a Boolean SearchCreating a Boolean Search

Concept 1Concept 1

InfluenzaInfluenzaConcept 2Concept 2

Vitamin CVitamin CConcept 3Concept 3

TreatmentTreatmentConcept 4Concept 4

helpfulnesshelpfulness

InfluenzaInfluenza Vitamin CVitamin C TreatmentTreatment OutcomeOutcome

FluFlu Ascorbic acidAscorbic acid TherapyTherapy RecoveryRecovery

Orange JuiceOrange Juice ManagementManagement SuccessSuccess

QUESTION: Is Vitamin C helpful in treating the flu?

1. Identify concepts and list terms

Step 2Step 2

2. Make your OR statements, one per concept

– (influenza OR flu OR orthomyxovirus)– (vitamin C OR ascorbic acid OR

ascorbate)– (treatment OR therapy OR

management)– (outcome OR recovery OR success)

Steps 3 and 4 Steps 3 and 4

3. Put “AND” between each of the OR 3. Put “AND” between each of the OR statementsstatements

(influenza OR flu) AND (vitamin C OR (influenza OR flu) AND (vitamin C OR ascorbic acid OR orange juice) AND ascorbic acid OR orange juice) AND (treatment OR therapy OR management) (treatment OR therapy OR management) AND (outcome OR recovery OR success)AND (outcome OR recovery OR success)

4. Consider any NOT statements you might 4. Consider any NOT statements you might want to add. want to add.

Note: NOT isn’t used very oftenNote: NOT isn’t used very often

Parsing a Boolean SearchParsing a Boolean Search

(emergency OR acute OR critical) (emergency OR acute OR critical) AND (treatment OR therapy OR AND (treatment OR therapy OR management OR care) AND (motor management OR care) AND (motor vehicle accident OR car crash) vehicle accident OR car crash) NOT (pedestrian OR walkingNOT (pedestrian OR walking))

What are the four concepts?What are the four concepts?What terms are used for each concept?What terms are used for each concept?Which three concepts must be included in all records Which three concepts must be included in all records

found?found?Which concept must not be included in any record Which concept must not be included in any record

found?found?

Beyond Basic BooleanBeyond Basic Boolean

Field SearchingField Searching Controlled VocabularyControlled Vocabulary

– Subject vs. Keyword SearchingSubject vs. Keyword Searching Specialty FeaturesSpecialty Features

– TruncationTruncation– Phrase searchingPhrase searching

Field SearchingField Searching

Almost all databases will provide you with Almost all databases will provide you with some ability to search a specific field or some ability to search a specific field or fields. fields.

Allows faster searchingAllows faster searching Allows more accurate searchingAllows more accurate searching

Not all databases may make all fields Not all databases may make all fields searchable. searchable.

Each search system will require a specific Each search system will require a specific format.format.

All Field vs. Specific Field All Field vs. Specific Field SearchesSearches

I would like to find articles by John Smith.I would like to find articles by John Smith.

Search all fields: John Smith Search all fields: John Smith Search Author Field only: John SmithSearch Author Field only: John Smith

I would like to find an article published in 1997.I would like to find an article published in 1997.

Search all fields: 1997Search all fields: 1997 Search Publication Date Field: 1997Search Publication Date Field: 1997

Why waste time searching for a date in the author Why waste time searching for a date in the author field or an author in the volume field?field or an author in the volume field?

Formats for Field SearchingFormats for Field Searching

Different databases provide different formats Different databases provide different formats for specifying fields.for specifying fields.

Most use field names or nicknames Most use field names or nicknames Field ‘tags’ OR ‘labels’Field ‘tags’ OR ‘labels’

which may follow a period or be placed in which may follow a period or be placed in brackets or parentheses.brackets or parentheses.

Some databases offer forms or drop-down Some databases offer forms or drop-down menus. menus.

PubMedPubMedField tags go in [] and follow termField tags go in [] and follow term

Field tags can be used within Boolean Field tags can be used within Boolean queriesqueries

PubMed Field TagsPubMed Field Tags

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.Search_Field_Descrip

[au] = author[au] = author

[ti] = title[ti] = title

[tw] = textword[tw] = textword

[tiab] = title and [tiab] = title and abstractabstract

[mh] = medical subject [mh] = medical subject headingheading

[dp] = date of publication

[la] = language

[gr] = grant number

[ta] = journal name

[ad] = affiliation

OVID databases require field tags to OVID databases require field tags to follow the term separated by a follow the term separated by a period.period.

Meharry.in and 2005.yrMeharry.in and 2005.yr

Some databases, such as the ISI’s Web Some databases, such as the ISI’s Web of Science (Science Citation Index of Science (Science Citation Index Expanded) provide forms to fill out.Expanded) provide forms to fill out.

Select Field from drop-down menu

Select Boolean Operator

Combining Field SearchesCombining Field Searches

Multiple field searches can be combined Multiple field searches can be combined using Boolean logic.using Boolean logic.

Find a 2005 article by an author named Find a 2005 article by an author named Hubble about ankle fractures.Hubble about ankle fractures.

Combine with AND:Combine with AND: 2005 in date/year field2005 in date/year field Hubble in author fieldHubble in author field Ankle fractures in title fieldAnkle fractures in title field

2005[dp] AND Hubble[au] AND ankle fractures[ti]

Final Notes on FieldsFinal Notes on Fields

Each database provides its own Each database provides its own specific fieldsspecific fields

Each database requires a specific Each database requires a specific format to designate field searchingformat to designate field searching

When searching a new database, When searching a new database, take a moment to read the help take a moment to read the help documentation; most will provide a documentation; most will provide a list of fields and how to search them.list of fields and how to search them.

Controlled VocabularyControlled Vocabulary

A controlled vocabulary is a set of A controlled vocabulary is a set of established terms where established terms where

every term represents a single concept every term represents a single concept only one term is used for that conceptonly one term is used for that concept

Another exampleAnother example How many words could you think of for the How many words could you think of for the

idea of “cancer”?idea of “cancer”?– Cancer, tumor, malignancy, neoplasm, Cancer, tumor, malignancy, neoplasm,

sarcoma…sarcoma…

Articles in a databaseArticles in a database– Article one: “Breast tumors in young women”Article one: “Breast tumors in young women”– Article two: “Surgery for prostrate cancer.”Article two: “Surgery for prostrate cancer.”– Article three: “Diagnosing Melanoma.”Article three: “Diagnosing Melanoma.”

All three articles are about types of cancer All three articles are about types of cancer but different terms are used in titles.but different terms are used in titles.

In a controlled vocabulary ONE word (In a controlled vocabulary ONE word (i.e.,i.e., cancer) is cancer) is chosen and placed in a special field, usually called chosen and placed in a special field, usually called a subject field. a subject field.

For all three articlesFor all three articles– Article one: “Breast tumors in young women”Article one: “Breast tumors in young women”– Article two: “Surgery for prostrate cancer.”Article two: “Surgery for prostrate cancer.”– Article three: “Diagnosing Melanoma.”Article three: “Diagnosing Melanoma.”

The subject term (concept term) “cancer” is placed in The subject term (concept term) “cancer” is placed in the subject field by database indexers. the subject field by database indexers.

Now, Searching the database for cancer in the Now, Searching the database for cancer in the subject field will identify all records about the subject field will identify all records about the concept of cancer even if a different word for concept of cancer even if a different word for cancer is used. cancer is used.

Search ‘cancer-in-subject-field’ finds all three Search ‘cancer-in-subject-field’ finds all three articlesarticles

How many articles would the search ‘cancer-in-How many articles would the search ‘cancer-in-title-field’ find?title-field’ find?

Structure of Controlled Structure of Controlled VocabularyVocabulary

Broader Concepts

Narrower Concepts

More on Controlled More on Controlled VocabularyVocabulary

““Expanding” = Search includes all narrower Expanding” = Search includes all narrower terms beneath the searched termterms beneath the searched term– Some databases do it automatically, others don’tSome databases do it automatically, others don’t

““Focusing” or “Majoring” = For a given Focusing” or “Majoring” = For a given item, some subject terms are considered item, some subject terms are considered the major focus; you can select to return the major focus; you can select to return only those articles.only those articles.– Hip fracture[majr] = only give me articles where Hip fracture[majr] = only give me articles where

hip fracture is an important concepthip fracture is an important concept

Subject vs. Keyword Subject vs. Keyword SearchingSearching

Controlled vocabulary Controlled vocabulary searchingsearching

Matches terms against a Matches terms against a

specific field in the specific field in the record. record.

You need to consult a You need to consult a thesaurus (paper or thesaurus (paper or online) to find out what online) to find out what the controlled the controlled vocabulary term is for vocabulary term is for each concept. each concept.

Free-text (keyword) Free-text (keyword) searchingsearching

Some concepts have Some concepts have many synonyms. A free-many synonyms. A free-text search statement text search statement would mean "OR"ing all would mean "OR"ing all those terms togetherthose terms together

Matches terms against Matches terms against words anywhere in words anywhere in record (abstract, title, record (abstract, title, etc.). etc.).

Advantages to Controlled Advantages to Controlled VocabulariesVocabularies

Using the controlled vocabulary can make your Using the controlled vocabulary can make your search more precise and easier.search more precise and easier.

Increases the relevancy of results (fewer false Increases the relevancy of results (fewer false drops)drops)

The indexers have already done much of the work The indexers have already done much of the work for you.for you.

Searchable tree structures of terms can help you Searchable tree structures of terms can help you find new terms to use.find new terms to use.

Problems with Controlled Problems with Controlled VocabulariesVocabularies

NOT all databases use a controlled NOT all databases use a controlled vocabularyvocabulary

New concepts take time to be added New concepts take time to be added There is often a lag phase during which the There is often a lag phase during which the

newest articles aren’t indexednewest articles aren’t indexed Controlled vocabularies can contain some Controlled vocabularies can contain some

very strange things and some concepts very strange things and some concepts may not be handled well may not be handled well

The controlled vocabulary must be easily The controlled vocabulary must be easily searchablesearchable

Trying to understand what is and isn’t in a Trying to understand what is and isn’t in a particular controlled vocabulary can give particular controlled vocabulary can give you a big headache! you a big headache!

Combining Subject and Combining Subject and Keyword SearchingKeyword Searching

To be comprehensive, it is often helpful To be comprehensive, it is often helpful to combine subject and keyword to combine subject and keyword searchingsearching

(diabetes mellitus[mh] OR diabetes[tw])(diabetes mellitus[mh] OR diabetes[tw])

(sickle cell anemia[mh] OR sickle cell (sickle cell anemia[mh] OR sickle cell anaemia[ti])anaemia[ti])

Don’t forget…Don’t forget…

Boolean logic to combine termsBoolean logic to combine terms Use of other search fields in Use of other search fields in

combination with subject termscombination with subject terms

A Complex Search:A Complex Search:

(head[mh] OR head[tw]) AND (wound (head[mh] OR head[tw]) AND (wound and injuries[mh] OR trauma[ti] OR and injuries[mh] OR trauma[ti] OR injury[ti]) AND 2005[dp] AND injury[ti]) AND 2005[dp] AND English[la]English[la]

Some Specialty FeaturesSome Specialty Features

TruncationTruncation Phrase searchingPhrase searching Neighboring and other rarer Boolean Neighboring and other rarer Boolean

operatorsoperators

TruncationTruncation

What about including the singular and plural versions What about including the singular and plural versions of words as well as other word variations?of words as well as other word variations?

For example: For example: therapy, therapies, therapeutics, therapy, therapies, therapeutics,

You could combine them all in an OR relationship: You could combine them all in an OR relationship:

(therapy OR therapies OR therapeutics OR (therapy OR therapies OR therapeutics OR therapeutic)therapeutic)

But an easier way is by the use of truncation. But an easier way is by the use of truncation. therap*therap*

Each database handles truncation in a unique way. Each database handles truncation in a unique way. The ‘*’ and ‘$’ are the most common wildcard symbols.The ‘*’ and ‘$’ are the most common wildcard symbols.

More on TruncationMore on TruncationSome examples:Some examples:

Bacter$Bacter$Proc*Proc*Vir?Vir?Staph?Staph?

Be cautious when truncating! Be cautious when truncating!

If the word stem is too short, there may be too many If the word stem is too short, there may be too many possible variations and you might pick up possible variations and you might pick up unrelated terms. unrelated terms.

For example, using proc* for finding procaine-like For example, using proc* for finding procaine-like drugs will also include words like proceedings and drugs will also include words like proceedings and process.process.

Phrase SearchingPhrase Searching Sometimes you want to force the database Sometimes you want to force the database

to search for a set of words in exact orderto search for a set of words in exact order““fever of unknown origin”fever of unknown origin”

Most databases will accept a phrase in Most databases will accept a phrase in quotes. quotes.

BUT…some do not handle phrases well and BUT…some do not handle phrases well and will automatically break them up – usually will automatically break them up – usually ‘AND’-ing the terms‘AND’-ing the terms

Check how the database handles phrase Check how the database handles phrase searching before doing it!searching before doing it!

Limits OptionsLimits Options

Many databases provide “limits” pages Many databases provide “limits” pages that make it easier for you to select that make it easier for you to select common options such as language, common options such as language, article type, publication dates, human article type, publication dates, human or animal, gender, age groups, etc. or animal, gender, age groups, etc.

Each database’s limits options are Each database’s limits options are uniqueunique

Most limits can be done ‘by hand’ Most limits can be done ‘by hand’ using field tags, but sometimes limit using field tags, but sometimes limit pages save timepages save time

PubMed Limits PagePubMed Limits Page

Step-By-Step Search Step-By-Step Search ConstructionConstruction

1.1. State the question State the question 2.2. Identify the concepts in the questionIdentify the concepts in the question3.3. For each concept, determine keywords and For each concept, determine keywords and

subject termssubject terms4.4. Specify field tags after terms if neededSpecify field tags after terms if needed5.5. Combine terms for the same concept with “OR” Combine terms for the same concept with “OR”

in parenthesisin parenthesis6.6. Combine “OR” statements with ANDCombine “OR” statements with AND7.7. Put any NOT terms at the endPut any NOT terms at the end

Keep track of your searches, how many articles Keep track of your searches, how many articles were found total, and how many you selected were found total, and how many you selected as relevantas relevant