decs health terminology description, uses and services bireme/paho/who latin-american and caribbean...

DeCS Health TerminologyDescription, uses and services

BIREME/PAHO/WHO Latin-American and Caribbean Center on Health Sciences Information

Pan American Health OrganizationWorld Health Organization

Agenda

– DeCS/MeSH description and uses– DeCS Services– DeCS Update

Description in briefControlled vocabulary created by BIREME in 1982, fully compatible with MeSH (“Medical Subject Headings”, produced by the U.S. National Library of Medicine (NLM), is a controlled vocabulary used for indexing and recovering information in MEDLINE / Pubmed)

DeCS – the Portuguese acronym for Descritores em Ciências da Saúde (Health Sciences Descriptors)

Yearly updated (idem MeSH)

Currently available in Portuguese, Spanish and English

Composed of 16 MeSH Categories plus 4 thematic terminology categories: Public Health, Health Surveillance, Homeopathy, and Science & Health

An integrating component of the VHL and GHL - Allows meta-searching by descriptor, ie, searches multiple IS - Allows multilingual searching

DeCS/MeSH

description in briefusesdescription

categories / numberstypes of terms

descriptorssynonymsqualifierscheck-tagspublication types

characteristicstrilingualpolyhierarchicalpostcoordination precoordination

servicesfor users

documentationbrowser

helprecord view word search exact termindex view alphabetical i. kwic i. tree i.configuration

for computer applics.search by

tree codeword or termlexical similarity

lexical similarityoccurrences in VHLalphabetical ruleravailability/licensing

user supportupdatenumber of accesses

DeCS/MeSH





servicesfor users







UsesServes as a standard controlled vocabulary for indexing scientific and technical health-related literature

It groups synonymous terms into concept units

Allows searching by subject (concepts), independently of the language

the use of natural language searches in document titles, abstracts and full-texts require long/complex search expressions, loses specificity and brings less trustworthy results

Hierarchical codes allow exploding (searching) all the terms of a conceptual hierarchy (branch)

Categories descriptors synonyms

Anatomy [A] 1646 2606

Organisms [B] 3630 8420

Diseases [C] 4494 8973

Chemicals and Drugs [D] 8974 12898

Analytical, Diagnostic and Therapeutic Techniques and Equipment [E] 2552 4495

Psychiatry and Psychology [F] 918 1429

Phenomena and Processes [G] 1836 2889

Disciplines and Occupations [H] 365 357

Anthropology, Education, Sociology and Social Phenomena [I] 523 1082

Technology, Industry, Agriculture [J] 473 872

Humanities [K] 185 150

Information Science [L] 391 706

Named Groups [M] 202 343

Health Care [N] 1485 2701

Publication Characteristics [V] 150 123

Geographicals [Z] 382 323

Subtotal MeSH 25588 44370

Homeopathy [HP] 1944 1285

Science and Health [SH] 219 553

Public Health [SP] 3491 1926

Health Surveillance [VS] 828 544

Subtotal DeCS-only 4697 6115

Total 30895 50485

DeCS 2011 Categories

DeCS/MeSH





servicesfor users







DeCS only15.7%

MeSH 84.30%

DeCS version 2011 January 28

Types of DeCS/MeSH terms

Descriptor

Synonyms

Qualifiers

Check-tags

Publication Types

DeCS/MeSH





servicesfor users







Descriptor

This ise the term used in the information sources as the indexing term.

The term reflects a meaning; its use indicates the topics discussed by the

work cited.

Also known as

Index terms

Keywords,

Key terms,

Main headings,

Preferred terms and

Subject heading

DeCS/MeSH





servicesfor users







SynonymsAlso known as

Used For (UF) terms,

Cross-references or

Entry terms

They mean the same or nearly the same as the descriptor (EQV, NRW, BRD, REL).

They are used as alternate terms in search expressions, obtaining the same search result.

For the system they are considered equivalent.

DeCS/MeSH





servicesfor users







Frequently occurring health-related terms that are used for indexing in conjunction with descriptors.

This combination permits retrieving only those citations which are concerned with a particular aspect of a subject.

Example: Aphthovirus/pathogenicity, finds documents about the capacity of this virus to cause disease.

Note: Qualifiers are preceded by a slash “/” in the DeCS Search System (or Browser)

QualifiersDeCS/MeSH





servicesfor users







Check tags (or Limits)Check tags are generic terms used to limit the scope of research subjects, such as: PREGNANCY; ANIMALS (mammals: HUMANS and non-human, frequently used in basic and clinical research: CATTLE, CATS, CRICETINAE, DOGS, GUINEA PIGS, MICE, RABBITS, RATS; and CHICK EMBRYO), the genders MALE or FEMALE; the historical periods (HISTORY, ANCIENT; HISTORY, MEDIEVAL; HISTORY, 15TH CENTURY; ...HISTORY, 21ST CENTURY); and the age groups below.

The age groups are:

INFANT, NEWBORN (birth to 1 month) INFANT (1 to 23 months) CHILD, PRE-SCHOOL (2 to 5 years) CHILD (6 to 12 years) ADOLESCENT (13 to 18 years)YOUNG ADULT (19 to 24 years)ADULT (19 to 44 years)MIDDLE AGE (45 to 64 years) AGED (65 to 79 years) AGED, 80 AND OVER

DeCS/MeSH





servicesfor users







Check tags (or Limits)

NAMED GROUPS [M] Persons [M01] Abortion Applicants [M01.050] Adult Children [M01.055] Age Groups [M01.060] Adolescent [M01.060.057] Adult [M01.060.116] + Aged [M01.060.116.100] + Aged, 80 and over [M01.060.116.100.080] Frail Elderly [M01.060.116.100.540] Middle Aged [M01.060.116.630] Young Adult [M01.060.116.815] Child [M01.060.406] + Child, Preschool [M01.060.406.448] Infant [M01.060.703] + Infant, Newborn [M01.060.703.520] + Infant, Low Birth Weight [M01.060.703.520.460] + Infant, Small for Gestational Age [M01.060.703.520.460.560] Infant, Very Low Birth Weight [M01.060.703.520.460.600] + Infant, Postmature [M01.060.703.520.500] Infant, Premature [M01.060.703.520.520]

The expanded hierarchical structure with the location of the age groups in DeCS is shown below, and the check tags marked in bold face.

DeCS/MeSH





servicesfor users







Publication TypesDeCS/MeSH





servicesfor users







Terms used for describing the document format which allows another means for restricting the search result.

Examples:

Editorial, Letter, Review, Clinical Trial, Clinical Trial, Phase I, etc. (in DeCS, and in the VHL)

Types of relations

• Word (dictionaries) -> Term (thesauri) -> Concept or Conceptual unit (multilingual thesauri) -> Record or Multi-conceptual Unit (MeSH/DeCS vocabularies)

• Types of relations:– Equivalency (synonyms; intra-conceptual)– Hierarchical (Is a, part of, type of; inter-conceptual; may be intra-

record [subfields BRD, NRW, EQV, REL] or inter-records [tree code field])– Associative (non-hierarchical): of two types:

a) intra-record: language versions, scope note, historical note, abbreviations; b) inter-record: annotation, online note, consider also (reference to other greek

and latin prefixes or morphemes), reference to entry combination (postcoordination with qualifiers), see related reference, pharmacological actions, allowable [topical] qualifiers, reference to the allowed subcategories with qualifier, MeSH-Suggested descriptor, UMLS semantic type, terms in UMLS vocabularies, MeSH ID

• the relations in bold are not shown yet on the decs server.

DeCS/MeSH




types of relationscharacteristics

trilingualpolyhierarchicalpostcoordination precoordination

servicesfor users







Vocabulary Characteristics

TRILINGUAL

POLYHIERARCHICAL

POSTCOORDINATION

PRECOORDINATION

DeCS/MeSH






servicesfor users







Language versions

DeCS is trilingual (English, Spanish and Portuguese)

DeCS’ Spanish and Portuguese terms are exported to the UMLS metathesaurus (Unified Medical Language System) and distributed as Spanish MeSH and Portuguese MeSH

To date, there are 11 MeSH translations incorporated into the UMLS Metathesaurus

DeCS/MeSH






servicesfor users







PolyhierarchicalA descriptor may belong to more than one category or to several branches of the same category due to the multidisciplinary nature of many concepts.

Example: Ethics belongs to the F, K and N categories

F = Psychiatry and Psychology; K = Humanities; N = Health Care

DeCS/MeSH






servicesfor users







Related documents in the VHL

Postcoordination

• Descriptor + Descriptor• Descriptor + Qualifier • Descriptor + Check tag• Descriptor + Publication Type

The act of coordinating two or more concepts at the moment of searching for literature with the objective of narrowing the scope of a subject. The DeCS/MeSH vocabulary permits four types of terminological postcoordination.

DeCS/MeSH






servicesfor users







Examples:

•Arthritis, Rheumatoid + Immunity, Innate/immunol VHL VHL2

•Antibiotic Prophylaxis + Bacitracin/ther use VHL VHL2

•Arthritis, Rheumatoid + Immunity, Innate/immunol + Female VHL VHL2

•Anti-bacterial Agents + Clinical Trial, Phase IV VHL VHL2(*)

(*)In the new VHL search system, hyfenated term searches is being implemented.

Precoordination

There are two types of precoordination:

1) Descriptor1/qualifier use Descriptor2

Example 1: PREGNANCY

PREGNANCY/complications use “PREGNANCY COMPLICATIONS”

Example 2: KIDNEY

KIDNEY/transplantation use “KIDNEY TRANSPLANTATION”

2) Descriptor1 AND Descriptor2 use Descriptor3

Example: KIDNEY

TRANSPLANTATION and KIDNEY use “KIDNEY TRANSPLANTATION”

DeCS/MeSH






servicesfor users







DeCS Services

• DeCS Server (DeCS Search)

http://decs.bvs.br/I/homepagei.htmhttp://decs.bvsalud.org/I/homepagei.htm

- for users• Search by Words• Search by Index

- Alphabetic- Keywords in Context (KWIC)- Tree (hierarchical navigation or tree code)

DeCS/MeSH






servicesfor users







VHL>HEALTH TERMINOLOGY

DeCS ServerDeCS/MeSH






servicesfor users

browserhelprecord view word search exact termindex view alphabetical i. kwic i. tree i.configuration




user supportupdatenumber of accessesdocumentation

DeCS Server

DeCS/MeSH






servicesfor users






Search by Word

Word or Term

Result for “Osteoporosis”

DeCS/MeSH






servicesfor users






Search by Word

Exact Descriptor

Result for “Osteoporosis”

DeCS/MeSH






servicesfor users






Search By Index

Alphabetical Index

Result for “osteoporosis”

DeCS/MeSH






servicesfor users






Search By Index

“Keywords in Context” Index


DeCS/MeSH






servicesfor users






Search By Index

Tree Index

Category Titles

DeCS/MeSH






servicesfor users






Search By Index

Tree Index


DeCS/MeSH






servicesfor users






Some descriptors ommited in order to fit slide

DeCS/MeSH






servicesfor users






Search By Index

Tree Index

Result for “Surgical

Procedures, Operative”

Click a descriptor to open its full

record

Full record

view

“Surgical Procedures, Operative”

previous page was its hierarchical

view

DeCS/MeSH






servicesfor users

browserhelprecord view word search exact termindex view alphabetical i. kwic i. tree i.index2record view





Occurrences in VHLDeCS/MeSH






servicesfor users


occurrences in VHLlexical similarityoccurrences in VHLalphabetical ruleravailability/licensing




Lexical Similarity

DeCS/MeSH





servicesfor users


occurrences in VHLlexical similarityalphabetical ruleravailability/licensing




Lexical Similarity

Alphabetical ruler

DeCS/MeSH





servicesfor users


occurrences in VHLlexical similarityalphabetical ruleravailability/licensing




DeCS Services• DeCS XML Server (XML format)

http://decs.bvs.br/vmxi.htm

– for computer applications

• Search by descriptor tree code http://decs.bvs.br/cgi-bin/mx/cgi=@vmx/decs?lang=i&tree_id=B01.150.900.649.801.400.112.199.120.510.550

• Search by word or term http://decs.bvs.br/cgi-bin/mx/cgi=@vmx/decs?lang=e&words=Macaca mulatta

• Search by lexical similarity (via trigrams)http://trigramas.bireme.br/cgi-bin/mx/cgi=@1?collection=DeCSi&text=cardiovascula&maxrel=10&minsim=0.30&xml

• Ocorrences of the DeCS concept in the BVS information sourceshttp://bases.bireme.br/cgi-bin/mxlindG4.exe/cgi=@iah/decs?db=LILACS&db=MEDLINE&&db=EQUIDAD&db=WHOLIS&k1=SP1&k2=SP1&count=10

DeCS/MeSH





servicesfor users

browserhelprecord view word search exact termindex view alphabetical i. kwic i. tree i.

occurrences in VHLlexical similarityalphabetical ruler




Documentation• VHL > Health terminology > About DeCS

• VHL > Health terminology > DeCS news > DeCS 2011 edition

• VHL > Health terminology > DeCS news > DeCS previous editions

DeCS/MeSH





servicesfor users

browserhelprecord view word search exact termindex view alphabetical i. kwic i. tree i.

occurrences in VHLlexical similarityalphabetical ruler

for computer applics.documentation

search by tree codeword or termlexical similarity


Accesses to DeCS in the Regional VHL site

DeCS 2007 - http://logs.bireme.br/cgi-bin/awstats.pl?month=01&year=2007&output=main&config=decs2007-bvsalud-org DeCS 2008 - http://logs.bireme.br/cgi-bin/awstats.pl?month=01&year=2008&output=main&config=decs2008-bvsalud-org DeCS 2009 - http://logs.bireme.br/cgi-bin/awstats.pl?month=01&year=2009&output=main&config=decs2009-bvsalud-org DeCS 2010 - http://logs.bireme.br/cgi-bin/awstats.pl?month=01&year=2010&output=main&config=decs2010-bvsalud-org DeCS 2011 - http://logs.bireme.br/cgi-bin/awstats.pl?month=01&year=2011&output=main&config=decs2011-bvsalud-org

DeCS Update

• Besides the annual update occurring in DeCS as a consequence of the modification and creation of MeSH terms by NLM and user suggestions by use of the DeCS User Support page, a new category will be added to DeCS following the criteria published in the “DeCS Update Guide”

– Lack of a controlled terminology for indexing documents in a health science domain not covered or not fully expressed by DeCS/MeSH;

– Validation of the proposed terminology by the DeCS Technical Committee;

• New concepts may be added to DeCS also under the criteria published in the “DeCS Update Guide”:

– Ocurrence in the literature– Scope note, with source– Suggested MeSH Concept(s)

MeSH homepagehttp://www.nlm.nih.gov/mesh

UMLS homepagehttp://www.nlm.nih.gov/research/umls/umlsmain.html

DeCS homepagehttp://decs.bvs.br/I/homepagei.htm or http://decs.bvsalud.org/I/homepagei.htm

DeCS description and useshttp://decs.bvs.br/I/decswebi2011.htm http://decs.bvsalud.org/I/decswebi2011.htm

Serviços XML DeCS:http://decs.bvs.br/vmxi.htm http://decs.bvsalud.org/vmxi.htm

Guidelines for DeCS Updating http://bvsmodelo.bvsalud.org/php/level.php?lang=en&component=27&item=1http://bvsmodelo.bvsalud.org/download/decs/DeCS-UpdateGuide.pdf

This presentation: http://decs.bvs.br/presentations/DeCS2011_en.ppt

Bibliography

Terminology

• UMLS Unified Medical Language System– NLM initiative that mantains a Metathesaurus with more than 140

vocabularies related to health, a semantic web and lexical management tools

– Annual update

• MSH = MeSH• MSHSPA = Spanish MeSH = DeCS• MSHPOR = Portuguese MeSH = DeCS

• SNOMED-CT Systematized Nomenclature of Medicine, Clinical Terms • LOINC Logical Observation Identifier Names and Codes• MedDRA Medical Dictionary for Regulatory Activities Terminology• CPT Physicians Current Procedural Terminology• HL7 Hospital Language Level 7• …

VHL – Search result

GHL – Search result

UMLS - Unified Medical Language System. UMLS 2007AC.Source vocabularies in Portuguese, Spanish and English

144181 LAT POR 2%

85002 MedDRA Portuguese Medical Dictionary for Regulatory Activities Terminology (MedDRA), Portuguese Edition, 10.01,33%

54706 MeSH PortugueseDescritores em Ciencias da Saude (Portuguese translation of the Medical Subject Headings), 2007 0,85%

3750 WHO Adverse Reaction Terms Portuguese WHOART, Portuguese Translation, 1997 0,06%723 ICPC 1993 Portuguese ICPC, Portuguese Translation, 1993 0,01%

1529152 LAT SPA 24%

1314755 SNOMED Terminos Clinicos SNOMED Terminos Clinicos (SNOMED CT), Edicion en Espanol, Distribucion Internacional, Abril de 200720,53%133122 MedDRA Spanish Medical Dictionary for Regulatory Activities Terminology (MedDRA), Spanish Edition, 10.02,08%

69814 MeSH SpanishDescriptores en Ciencias de la Salud (Spanish translation of the Medical Subject Headings), 2007 1,09%

7632 CPT SpanishPhysicians' Current Procedural Terminology, Spanish Translation, 2001 0,12%

3106 WHO Adverse Reaction Terms Spanish WHOART, Spanish Translation, 1997 0,05%723 ICPC 1993 Spanish ICPC, Spanish Translation, 1993 0,01%

4729723 LAT ENG 74%

1068718 SNOMED Clinical Terms SNOMED Clinical Terms, 2007_07_31 16,69%665494 MeSH Medical Subject Headings, 2008_2007_08_27 10,39%395895 NCBI Taxonomy NCBI Taxonomy, 2007_07_02 6,18%381858 RXNORM RxNorm Vocabulary, 07AB_070831F 5,96%347568 Read Codes Clinical Terms Version 3 (CTV3) (Read Codes), 1999 5,43%179590 LOINC Logical Observation Identifier Names and Codes, 221 2,80%164179 SNOMED Intl 1998 SNOMED International, 1998 2,56%159353 NCI Thesaurus National Cancer Institute Thesaurus, 2007_05E 2,49%114641 OMIM Online Mendelian Inheritance in Man, 2007_03_19 1,79%100821 Metathesaurus Names UMLS Metathesaurus 1,57%92913 Digital Anatomist University of Washington Digital Anatomist, 1.7.3 1,45%86235 MedDRA Medical Dictionary for Regulatory Activities Terminology (MedDRA), 10.01,35%81799 ICPC2-ICD10 Thesaurus ICPC2 - ICD10 Thesaurus, 200412 1,28%76081 HUGO, 2004 HUGO Gene Nomenclature, 2007_01 1,19%75848 National Drug Data File National Drug Data File Plus Source Vocabulary, 2007_08_10 1,18%64519 FDA National Drug Code Directory Metathesaurus FDA National Drug Code Directory, 2007_08_10 1,01%57966 Multum Multum MediSource Lexicon, 2007_08_01 0,91%49764 Gene Ontology Gene Ontology, 2007_02_01 0,78%44274 SNOMED 1982 SNOMED-2, 2 0,69%38608 ICD-9-CM ICD-9-CM, 2008 0,60%37926 National Drug File - Reference Terminology National Drug File - Reference Terminology, 2004_01 0,59%26448 Physician Data Query Physician Data Query, 2007_02 0,41%25891 ICD-10 Austral Mod International Statistical Classification of Diseases and Related Health Problems, 10th Revision, Australian Modification, January 2000 Release0,40%25546 National Drug File Veterans Health Administration National Drug File, 2007_07_24 0,40%22775 CRISP Thesaurus CRISP Thesaurus, 2006 0,36%22186 Read Codes Synth Read thesaurus, Synthesized Terms, 1999 0,35%21180 Universal Medical Devices Nomenclature UMDNS: product category thesaurus, 2008 0,33%20685 Alcohol and Other Drug Thesaurus Alcohol and Other Drug Thesaurus, 2000 0,32%19254 UMLS ICD-9-CM Terms Metathesaurus additional entry terms for ICD-9-CM, 2008 0,30%17654 CPT Current Procedural Terminology, 2007 0,28%

Terms from the concept Chagas Disease in UMLS(*)

Concept Lang Source Code Atom Terms

C0041234 ENG S SY DXplain NOCODE A0464898 TRYPANOSOMIASIS, BRAZILIAN

C0041234 ENG P HT ICD-10 B57 A0400508 Chagas' disease

C0041234 ENG S PT ICPC2-ICD10 Thesaurus MTHU015997 A4442003 Chagas

C0041234 ENG S PT ICPC2-ICD10 Thesaurus MTHU075877 A4463974 trypanosomiasis; Trypanosoma cruzi

C0041234 ENG S FN MEDCIN 30909 A13616328 Chagas disease (diagnosis)

C0041234 ENG S OL MedDRA 10043043 A1593326 T.cruzi

C0041234 POR S LT MedDRA Portuguese 10044706 A11221735 Infecção por Tripanosoma cruzi

C0041234 POR S OL MedDRA Portuguese 10043043 A11251454 T. cruzi

C0041234 POR S PT MedDRA Portuguese 10001935 A6444745 Tripanossomíase americana

C0041234 SPA S LT MedDRA Spanish 10044706 A11332881 Infección por Trypanosoma cruzi

C0041234 SPA S OL MedDRA Spanish 10043043 A11324281 T. Cruzi

C0041234 SPA S PT MedDRA Spanish 10001935 A6480674 Tripanosomiasis americana

C0041234 ENG S EN MeSH D014355 A6993502 American Trypanosomiasis

C0041234 ENG S DEV MeSH D014355 A12076600 CHAGAS DIS

C0041234 ENG P MH MeSH D014355 A0037270 Chagas Disease

C0041234 ENG S EP MeSH D014355 A0129064 Trypanosomiasis, South American

C0041234 POR P MH MeSH Portuguese D014355 A9108554 Doença de Chagas

C0041234 POR S EP MeSH Portuguese D014355 A9135991 Tripanossomose Sul-Americana

C0041234 SPA S MH MeSH Spanish D014355 A9175701 Enfermedad de Chagas

C0041234 SPA S EP MeSH Spanish D014355 A9212182 Tripanosomiasis Sudamericana

C0041234 ENG P PN Metathesaurus Names NOCODE A10758873 Chagas Disease

C0041234 ENG S FNNational Drug File - Reference

Terminology C6234 A14943357 Chagas Disease [Disease/Finding]

C0041234 ENG S SY SNOMED Clinical Terms 77506005 A3005830 Chagas-Mazza disease

C0041234 ENG S PT SNOMED Clinical Terms 77506005 A2969364 Infection by Trypanosoma cruzi

C0041234 ENG S FN SNOMED Clinical Terms 77506005 A3511349 Infection by Trypanosoma cruzi (disorder)

C0041234 SPA S SY SNOMED Terminos Clinicos 77506005 A5574227 enfermedad de Chagas

C0041234 SPA P PT SNOMED Terminos Clinicos 77506005 A5780116 infección por Trypanosoma cruzi

C0041234 SPA S FN SNOMED Terminos Clinicos 77506005 A5780115 infección por Trypanosoma cruzi (trastorno)

C0041234 SPA S SY SNOMED Terminos Clinicos 77506005 A6267248 tripanosomiasis americana

C0041234 SPA S SY SNOMED Terminos Clinicos 77506005 A6267259 tripanosomiasis sudamericana (*)UMLS2007AC; strings English, Spanish, Portuguese; strings type PF/Y

decs health terminology description, uses and services bireme/paho/who latin-american and caribbean...

Documents

health surveillance

public health

tree codeword

categoriesdecsmesh description

longcomplex search expressions

mesh categories

briefcontrolled vocabulary

standard controlled