Embase for biomedical searching: Indexing and Retrieval

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Embase for biomedical
searching: Indexing
and retrieval
Dr. Ian Crowlesmith
Senior Product Manager for Content Development
October 28, 2015

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Need to Know

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• Dissection of an Embase index
• A brief history of indexing at Embase
• Focusing on drugs: in-depth indexing
- drugs, diseases and devices
- subheadings (including floating subheadings & triple links)
- trade names, manufacturers
- CAS numbers
• Other indexing highlights
- major focus terms - mapping from MEDLINE
- Emtree / backposting - automatic indexing
- check tags & limits - medical devices
- study types & topic terms - numerical indexing
Agenda
Reference: Embase Indexing guide
See:http://www.elsevier.com/__data/assets/pdf_file/0016/92104/Embase-indexing-guide-2015.pdf

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5. 5
Methods
section

6. 6
Tables

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Embase index: overview

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Embase index: detail (drug subheadings)

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Embase index: detail (disease subheadings)

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drug of major focus (A term)
drug subheading
disease treated
adverse drug reactions
comparatordrug
route by which drug was
administered
other drug subheadings
DRUG TERMS AND SUBHEADINGS

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drug of major focus (A term)
drug subheading
disease treated
adverse drug reactions
comparatordrug
route by which drug was
administered
other drug subheadings
DRUG TERMS AND SUBHEADINGS
A aclidinium bromide

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drug of major focus (A term)
drug subheading
disease treated
adverse drug reactions
comparatordrug
route by which drug was
administered
other drug subheadings
DRUG TERMS AND SUBHEADINGS
A aclidinium bromide
drug therapy
chronic obstructive lung disease

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drug of major focus (A term)
drug subheading
disease treated
adverse drug reactions
comparatordrug
route by which drug was
administered
other drug subheadings
DRUG TERMS AND SUBHEADINGS
A aclidinium bromide
drug therapy
chronic obstructive lung disease
adverse drug reaction
coughing
diarrhea
ECG abnormality
headache
pruritus
rhinopharyngitis
tooth pain

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drug of major focus (A term)
drug subheading
disease treated
adverse drug reactions
comparatordrug
route by which drug was
administered
other drug subheadings
DRUG TERMS AND SUBHEADINGS
A aclidinium bromide
drug therapy
chronic obstructive lung disease
adverse drug reaction
coughing
diarrhea
ECG abnormality
headache
pruritus
rhinopharyngitis
tooth pain
drug comparison
formoterol fumarate

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drug of major focus (A term)
drug subheading
disease treated
adverse drug reactions
comparatordrug
route by which drug was
administered
other drug subheadings
DRUG TERMS AND SUBHEADINGS
A aclidinium bromide
drug therapy
chronic obstructive lung disease
adverse drug reaction
coughing
diarrhea
ECG abnormality
headache
pruritus
rhinopharyngitis
tooth pain
drug comparison
formoterol fumarate
(route of drug administration)
inhalational drug administration

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drug of major focus (A term)
drug subheading
disease treated
adverse drug reactions
comparatordrug
route by which drug was
administered
other drug subheadings
DRUG TERMS AND SUBHEADINGS
A aclidinium bromide
drug therapy
chronic obstructive lung disease
adverse drug reaction
coughing
diarrhea
ECG abnormality
headache
pruritus
rhinopharyngitis
tooth pain
drug comparison
formoterol fumarate
(route of drug administration)
inhalational drug administration
other subheadings
clinical trial
drug dose

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DRUG TERMS AND SUBHEADINGS
B formoterol fumarate
drug therapy
chronic obstructive lung disease
adverse drug reaction
coughing
diarrhea
headache
pruritus
rhinopharyngitis
tooth pain
drug comparison
aclidinium bromide
(route of drug administration)
inhalational drug administration
other subheadings
clinical trial
drug with minor focus (B term)
drug subheading
disease treated
adverse drug reactions
comparatordrug
route by which drug was
administered
other drug subheadings

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DISEASES AND OTHER TERMS
other check tags
minor focus (B) terms
study type check tags
sex and age check tags
disease subheading
disease with major focus (A)
human study type check tag
drugs treating disease

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other check tags
minor focus (B) terms
study type check tags
sex and age check tags
disease subheading
disease with major focus (A)
human study type check tag
drugs treating disease
DISEASES AND OTHER TERMS
A chronic obstructive lung disease

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other check tags
minor focus (B) terms
study type check tags
sex and age check tags
disease subheading
disease with major focus (A)
human study type check tag
drugs treating disease
DISEASES AND OTHER TERMS
A chronic obstructive lung disease
drug therapy
aclidinium bromide, formoterol*

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other check tags
minor focus (B) terms
study type check tags
sex and age check tags
disease subheading
disease with major focus (A)
human study type check tag
drugs treating disease
DISEASES AND OTHER TERMS
A chronic obstructive lung disease
drug therapy
aclidinium bromide, formoterol*
B randomized controlled trial
B controlled study
B crossover procedure
B double blind procedure
B phase 2 clinical trial
B multicenter study

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other check tags
minor focus (B) terms
study type check tags
sex and age check tags
disease subheading
disease with major focus (A)
human study type check tag
drugs treating disease
DISEASES AND OTHER TERMS
A chronic obstructive lung disease
drug therapy
aclidinium bromide, formoterol*
B randomized controlled trial
B controlled study
B crossover procedure
B double blind procedure
B phase 2 clinical trial
B multicenter study
B major clinical study

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other check tags
minor focus (B) terms
study type check tags
sex and age check tags
disease subheading
disease with major focus (A)
human study type check tag
drugs treating disease
DISEASES AND OTHER TERMS
A chronic obstructive lung disease
drug therapy
aclidinium bromide, formoterol*
B randomized controlled trial
B controlled study
B crossover procedure
B double blind procedure
B phase 2 clinical trial
B multicenter study
B major clinical study
B adult
B female
B male
B human

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other check tags
minor focus (B) terms
study type check tags
sex and age check tags
disease subheading
disease with major focus (A)
human study type check tag
drugs treating disease
DISEASES AND OTHER TERMS
A chronic obstructive lung disease
drug therapy
aclidinium bromide, formoterol*
B randomized controlled trial
B controlled study
B crossover procedure
B double blind procedure
B phase 2 clinical trial
B multicenter study
B major clinical study
B adult
B female
B male
B human
B bronchodilatation
B forced expiratory volume
B forced vital capacity
B powder inhaler
B drug dose comparison
B evening dosage
B morning dosage

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DEVICE TRADE NAMES WITH LINKED
MANUFACTURER NAMES
drug trade name & drug manufacturer
name & country code
clinical trial number repository & clinical
trial number
device trade name & device
manufacturer name & country code (for
2 devices)
CLINICAL TRIAL NUMBERS
DRUG TRADE NAMES WITH LINKED
MANUFACTURER NAMES

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DRUG TRADE NAMES WITH LINKED
MANUFACTURER NAMES
foradil
Novartis CHE
DEVICE TRADE NAMES WITH LINKED
MANUFACTURER NAMES
drug trade name & drug manufacturer
name & country code
clinical trial number repository & clinical
trial number
device trade name & device
manufacturer name & country code (for
2 devices)
CLINICAL TRIAL NUMBERS

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DEVICE TRADE NAMES WITH LINKED
MANUFACTURER NAMES
DRUG TRADE NAMES WITH LINKED
MANUFACTURER NAMES
foradil
Novartis CHE
Genuair
Almirall ESP
Aerolizer
Novartis CHE
drug trade name & drug manufacturer
name & country code
clinical trial number repository & clinical
trial number
device trade name & device
manufacturer name & country code (for
2 devices)
CLINICAL TRIAL NUMBERS

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CLINICAL TRIAL NUMBERS
DRUG TRADE NAMES WITH LINKED
MANUFACTURER NAMES
foradil
Novartis CHE
DEVICE TRADE NAMES WITH LINKED
MANUFACTURER NAMES
Genuair
Almirall ESP
Aerolizer
Novartis CHE
drug trade name & drug manufacturer
name & country code
clinical trial number repository & clinical
trial number
device trade name & device
manufacturer name & country code (for
2 devices)
ClinicalTrials.gov
NCT01120093

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Embase index (summary)
PubMed indexing
for the same record

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Embase indexing principles
1. TRANSLATE
To bring the semantic richness of medical terminology
within your grasp: mapping many synonyms to a single
(natural language) preferred terminology
2. EXPAND
To expose and summarize the information in biomedical
articles beyond title and abstract: discovering in-depth
data about drugs, diseases and medical devices
3. FOCUS
To identify the key concepts hidden within those articles –
what they are really about – providing you with a toolkit to
find answers beginning with comprehensive searches

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Embase history of indexing
Excerpta
Medica
1947 1963
Controlled
vocabulary
2
1
Emtree +
subheadings
1987
3
Item
types
1990
4
RCTs
Additional
check tags
1993
5 Automatic
indexing
2009
6
Medical
devices
2012
7
Searchable
triple
indexing
2015
8
1
2
3
4
5
6
7
8
First 9 independent abstract journals with natural language indexing
Indexing unified into a controlled vocabulary, with synonyms
Tree structure added based on MeSH: birth of Emtree
Introduction of 8 item types (aka publication types)
Extension of check tags with the first of several new EBM terms
Conference abstracts & In-process records automatically indexed
Addition of >3000 new medical device terms + 4 new subheadings
Searchable triple indexing introduced for 5 drug triples + 2 device triples

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Embase indexing: the video
Ref: http://www.elsevier.com/solutions/embase-biomedical-research

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Drugs & diseases1: in-depth indexing
Embase Indexing Guide, section 5.3.3
“Drug terms are index terms used for all drugs and chemicals: not only
therapeutic drugs, but also endogenous compounds, laboratory chemicals
and environmental chemicals or toxins. It is important to realise that “drugs”
as described in Embase may refer to any chemical entity.”
 All significant mentions are indexed *
 New drugs as candidate terms *
 CAS registry numbers generated
 All generic drug names in Emtree
 Emtree updated 3x per year *
 Indexed with subheadings *
 Key subheadings indexed as triples
 Drug trade names also indexed
 Also drug manufacturer names
1 and (since 2014) also devices * applies to disease terms as well as drugs
New drugs as candidate terms

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Using Emtree to find new drugs
Reference: http://www.news-sentinel.com/apps/pbcs.dll/article?AID=/20121115/NEWS/121119726/-1/LIVING

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Finding new drugs (1): Identifying the drug class

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Finding new drugs (2): Searching using the drug class

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Finding new drugs (2): Searching using the drug class

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Finding new drugs (2): Searching using the drug class

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Finding new drugs (3): Identifying candidate terms

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Finding new drugs (3): Identifying candidate terms
Which companies
make these drugs ?

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Indexing of drug trade names and manufacturer names

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Searching drug trade names and manufacturer names

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Searching drug, disease and device subheadings

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Drug subheadings: searching using triple links

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Drug subheadings: searching using triple links

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Floating subheadings

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Floating subheadings

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• Dissection of an Embase index
• A brief history of indexing at Embase
• Focusing on drugs: in-depth indexing
- drugs, diseases and devices
- subheadings (including floating subheadings & triple links)
- trade names, manufacturers
- CAS numbers
• Other indexing highlights
- major focus terms - mapping from MEDLINE
- Emtree / backposting - automatic indexing
- check tags & limits - medical devices
- study types & topic terms - numerical indexing
Agenda: what have we covered so far?
Reference: Embase Indexing guide
See:http://www.elsevier.com/__data/assets/pdf_file/0016/92104/Embase-indexing-guide-2015.pdf

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Major focus index terms

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Major focus index terms

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Major focus index terms

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Major index terms: history over 25 years

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Introducing Emtree: the Embase thesaurus
Ref: https://www.elsevier.com/solutions/embase-biomedical-research/embase-
coverage-and-content

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Emtree releases

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Emtree terms added and changed in September 2015

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Emtree changed terms  backposted to older records

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Embase records with backposted Emtree terms

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Embase records with backposted Emtree terms

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Check tags
Embase Indexing Guide, section 5.3.2 & Appendix 2
“Check tags … represent a special group of general terms whose definitions
are described by scope notes, and which are assigned by indexers using a
check list to ensure the highest possible consistency of indexing.”
Category Examples
Item types article, review, letter, editorial,conference abstract
Human study
types
human, major clinicalstudy, case report, human experiment,
human cell
Animal study
types
nonhuman,animalmodel, animalexperiment, animalcell
Sex and age male, female, newborn, child, adolescent,adult, aged
Clinical trials &
EBM
randomized controlledtrial, meta analysis, doubleblind
procedure, systematic review, diagnostic test accuracy study

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Searching with check tags

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Searching with check tags
Identical results

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Searching for animal studies
humans animals
humans
AND
animals
neither humans nor animals

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Searching for animal studies
[humans]/lim [animals]/lim
[humans/lim
AND
[animals]/lim
NOT ([humans]/lim OR [animals]/lim)
To search for animals only:
[animals]/lim NOT [humans]/lim

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Searching for animal studies
animal:de
OR
invertebrate'/exp OR 'amphibia'/exp OR 'fish'/exp OR 'boreoeutheria'/exp OR 'afrotheria'/exp OR
'dermoptera'/exp OR 'glires'/exp OR 'scandentia'/exp OR 'sauropsid'/exp OR 'laurasiatheria'/exp OR
'ungulate'/exp OR 'reptile'/exp OR 'cercopithecidae'/exp OR 'marsupial'/exp OR 'monotremate'/exp OR
'prosimian'/exp OR 'tarsiiform'/exp OR 'hylobatidae'/exp OR 'xenarthra'/exp OR 'platyrrhini'/exp OR
'chimpanzee'/exp OR 'gorilla'/exp OR 'homo neanderthalensis'/exp OR 'cephalochordata'/exp OR
'hyperotreti'/exp OR 'urochordata'/exp OR 'ambulacraria'/exp OR 'coelomata'/exp OR
'protostomia'/exp OR 'pseudocoelomata'/exp OR 'coelenterate'/exp OR 'mesozoa'/exp OR
'placozoa'/exp OR 'porifera'/exp OR 'juvenile animal'/exp OR 'male animal'/exp OR 'female
animal'/exp
OR
primate'/de OR 'haplorhini'/de OR 'mammal'/de OR 'catarrhini'/de OR 'simian'/de OR 'ape'/de OR
'amniote'/de OR 'tetrapod'/de OR 'vertebrate'/de OR 'chordata'/de OR 'deuterostomia'/de OR
'bilateria'/de OR 'therian'/de OR 'hominid'/de OR 'euarchontoglires'/de OR 'placental mammals'/de
This is how the limit is constructed:
Do NOT use: ‘animal’/exp as this includes humans !!!

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Searching for animal studies

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Study types and topic terms
 From Emtree facet “Types of article or study”
 Include many more terms than check tags
 As from 2011: including “Topic terms”
Topic terms: 10 terms ending with (topic)
Topic terms were introduced in 2011 to differentiate
between study types indexed when the article is the
primary report for an RCT (for example), and articles in
which that term is only a topic that is discussed.

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MEDLINE records in Embase
• Almost 9m records in Embase are licensed from NLM
• MeSH terms from these records are mapped to Emtree
• See the White Paper: Coverage of MEDLINE in Embase
“When MeSH terms are mapped to
Emtree, subheadings are mapped
to Embase subheadings.
Since not all MeSH subheadings
have an exact Emtree equivalent,
some of them generate Emtree
terms rather than subheadings.”

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MEDLINE records in Embase: mapping of MeSH headings

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Differences between indexing in Embase and MEDLINE

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Heading

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Differences between indexing in Embase and MEDLINE

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Automatic indexing in Embase
When do we index automatically?
1. When data is limited to TI, AB
(conference abstracts)
2. When data is provisional
(articles in press, in process records)
How is it done?
1. Term recognition
(e.g. mapping of synonyms => PTs)
2. Morphological variants
(e.g. plural => singular )
2. Term-specific rules
(e.g. for “human”)
Not included:
• subheadings
• candidate terms

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Medical devices
 Emtree coverage expanded from 900 devices (in 2012) to over 3000 devices (in 2015)
 Medical devices have been indexed in over 2 million records in Embase (1947-2015)
 Four new subheadings (incl. two with triple links) were introduced for devices in 2014

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Medical devices: searching using triple links

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Numerical indexing
 CAS registry numbers
 Molecular sequence numbers
 Clinical trial registration numbers
873054-44-5:rn (ivacaftor)
GU372418:ms (a 16s-rRNA gene)
NCT00568503:cn (QAX028 trial)

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Numerical indexing: clinical trial registration numbers
(for record #2)

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Numerical link: Embase to ClinicalTrials.gov

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Numerical link: Embase to the NCBI Nucleotide database

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Embase Indexing and Retrieval: Summary
Translate Expand Focus
 Every record in Embase is indexed to help you identify the
records you need to find biomedical answers.
 Embase indexing focuses on drugs, diseases and (medical)
devices: these concepts are indexed in-depth.
 Essential support is provided by tools such as Emtree back-
posting, check tags, major focus terms and numerical indexing.

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Embase for biomedical
searching: Indexing
and retrieval
Dr. Ian Crowlesmith
Senior Product Manager for Content Development
October 28, 2015
Thank you for
your attention