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Electronic Resources Awareness
Oxford University Library Services / IT Learning Programme
- Bytes for Biologists No.1 -
Biological Abstracts
Roger Mills
January 2003
Electronic Resources Awareness
Session Objectives An overview of Biological Abstracts
What it covers
How to access it
Tips for searching
Locating source material
How to get help
SearchingBiological Abstracts®
• Using SilverPlatter
About BIOSIS
World’s largest abstracting and indexing service for the life sciences
Not-for-profit Company
Headquartered in Philadelphia
European office in York, UK
The Biological Abstracts family
Biological AbstractsBiological Abstracts/RRM
(Reports, Reviews & Meetings)
BIOSIS Previews
Biological Abstracts
Comprehensive coverage ensures that life science researchers get the breadth and depth of coverage required
Specialized indexing provides a unified structure for diverse information, making search and retrieval more effective
Statistics
Approximately 360,000 records will be added in the current year
Over 5.5 million records are included from 1980 to date
OXFORD: electronic version 1985-date Print version 1926-1984
Biological Abstracts Coverage
Over 4,000 international scientific journals
Published in over 90 countries
North America (31%)
Asia, Australasia (14%)
Europe &Middle East (52%)
Central & S. America (2%)Africa (1%)
Geographical Coverage
Subject Coverage
Traditional topics: Molecular biology, Botany, Zoology,
Ecology and the Environment,Microbiology
Interdisciplinary areas Experimental, Clinical and Veterinary
Medicine, Biotechnology and Genetics,Agriculture and Nutrition, Biochemistry,Pharmacology, Public Health
Related areas Methods, Instrumentation
Specialized indexing for better retrieval
By life scientists for life scientists
Specialized indexing provides a unified structure for diverse information, making search and retrieval more effective
CAS Registry Numbers and MeSH disease terms make searches more effective
Biological Abstracts with SilverPlatter
CD-ROM [PC, Mac, Unix]
WebSPIRS
ERL [used at Oxford with WinSPIRS and WebSPIRS – client software on http://www.bodley.ox.ac.uk/erl/erl-clients.html
SilverLinker [not at Oxford]
http://www.bodley.ox.ac.uk/oxlip/
http://www.bodley.ox.ac.uk/erl/
Sample Biological Abstracts Article Record
Sample Article RecordTI Title: Successful ribavirin therapy for severe adenovirus hemorrhagic cystitis after
allogeneic marrow transplant from close HLA donors rather than distant donors.
AU Author, Editor, Inventor: Miyamura-K {a}; Hamaguchi-M; Taji-H; Kanie-T; Kohno-A; Tanimoto-M; Saito-H; Kojima-S; Matsuyama-T; Kitaori-K; Nagafuji-K; Sato-T; Kodera-Y
AD Author Address: {a} First Department of Internal Medicine, Nagoya University School of Medicine, Tsurumai-cho 65, Showa-ku, Nagoya, 466-8550, Japan
SO Source: Bone-Marrow-Transplantation. March, 2000; 25 (5): 545-548..
PY Publication Year: 2000
DT Document Type: Article
IS ISSN (International Standard Serial Number): 0268-3369
LA Language: English
LS Language of Summary: English
AB Abstract: Intravenous ribavirin was given to nine patients who had developed severe adenovirus-induced hemorrhagic cystitis (AD-HC) which was resistant to conventional therapy or where there was involvement of other organs after allogeneic BMT. Three patients recovered completely from AD-HC, two of whom had been resistant to vidarabine. All three had received sibling BMTs (2 HLA matched, 1 HLA mismatched)………..
AI Abstract Indicator: Y
Sample Article RecordMC Major Concepts: Infection-; Hematology- (Human-Medicine, Medical-Sciences);
Pharmacology-
ST Super Taxa: Adenoviridae-: Animal-Viruses, Viruses-, Microorganisms-; Hominidae-: Primates-, Mammalia-,Vertebrata-, Chordata-, Animalia-
OR Organisms: adenovirus- (Adenoviridae-): pathogen; human- (Hominidae-): patient, adult
TN Taxa Notes: Animal-Viruses; Animals-; Chordates-; Humans-; Mammals-; Microorganisms-; Primates-; Vertebrates-; Viruses-
CB Chemicals and Biochemicals: HLA-; ribavirin-: antiviral-drug
DS Diseases: adenovirus-induced hemorrhagic-cystitis [AD-HC]: urologic-disease, viral-disease
RN CAS Registry Number (R): 36791-04-5: RIBAVIRIN
MQ Methods and Equipment: allogeneic-marrow-transplantation: therapeutic-method
MI Miscellaneous Descriptors: clinical symptoms
AN Accession Number: 200000129172
UD Update Code: 20000425
Searching for Record Identification Information
Accession Number - reference to individual record
Search example
200000129172 in AN
AN=200000129172
Searching for Author Information Full first names appear after last names,
when available
Up to 100 author names may appear in each record
Links are provided between Author names and Author Address field
Corporate Source/Author Address includes author e-mail and URL, when available
Searching for Author Information Search example
Miyamura-K in AUSaito-H* in AUnagoya university in AD
Display example (Authors)Miyamura-K {a}; Hamaguchi-M; Taji-H; Kanie-T; Kohno-A; Tanimoto-M; Saito-H; Kojima-S; Matsuyama-T; Kitaori-K; Nagafuji-K; Sato-T; Kodera-Y
Display example (Author Address){a} First Department of Internal Medicine,
Nagoya University School of Medicine, Tsurumai-cho 65, Showa-ku, Nagoya, 466-8550, Japan
Searching for Source Information
Publication Year PY=2000 or 2000 in PY
Language LA=English or English in LA
Summary Language
LS=English or English in LS
Document Type
DT=ARTICLE
Searching for Source InformationJournals
Can be searched using field tag SO for journal name, volume, issue, pagination, and publication year
Journal URL included, when available
Search exampleSO=bone-marrow-transplantationSO=New-England-Journal-of-MedicineSO=Cell-
BIOSIS Serial Sources provides a complete journal list
ISSN International Standard Serial
0268-3369 in IS
Searching for Source InformationJournals
Searching for Subject InformationSearching natural language terms
Biological Abstracts is largely a natural language database
When searching for specific subjects, make liberal use of Free text Truncation (* or ? for single character) Abbreviations
Controlled Vocabulary (Authority File or Thesaurus)
Controlled vocabulary file [1993-]
A file built on the strengths of natural language
Available on the BIOSIS Websitewww.biosis.org/authorityfile.html
Controlled Vocabulary Thesaurus Branches
Major Concepts Organisms
New Taxon modifiers
Fossil modifiers Super Taxa Taxa Notes Diseases
Disease modifiers Parts, Structures, & Systems
Organ System modifiers
Chemicals & Biochemicals
Drug modifiers Sequence Data
Sequence type modifiers Geopolitical Location Institutions and
Organizations
Institution type modifiers
Accessing the Controlled Vocabulary
TERM DETAIL FOR: Pharmacology
SCOPE NOTE: The development or use ofdrugs for the diagnosis, prevention, or treatment ofdisease in animals and humans includes drugdesign, testing and clinical trials, drugpharmacokinetics, and pharmacodynamicsstudies.
Tree 1 of 1: Major Concepts
Major Concept Terms
PharmacologyPharmaceuticalsPharmacognosy
From the Term Details screen you have several options:
Explode TermSingle-Term Search Back Add to list
Accessing the Controlled Vocabulary(Authority File)
Searching the Subject Terms Field[TS]
Simultaneously searches:alternate indexing major concepts
super taxa methods & equipment
chemicals & biochemicals miscellaneous descriptors
institutions & organizations registry numbersdiseases organism names
geopolitical location sequence data
industry parts, structures & systems taxa notes timepersons
Searching for Subject InformationImproving Precision
Limit searches to specific fields
Turkey yields 759 hits (no field limit)
Turkey in TI,TS yields 692 hits (Title & Subject Terms)
Turkey in GE yields 399 hits (Geopolitical Location)
Turkey in OR yields 245 hits (Organism)
Controlled vs Non-controlled terms
Are the search term(s) controlled?
term? Check synonyms and
variants (singular/plural etc.)
Qualify search term(s) by using
controlled vocabulary lists
(Authority File) or the BIOSIS
Search Guide’s Vocabulary Guide
section
Search as non controlled term(s) using
natural language including any
synonyms, variants (singular/plural) etc.
Check application for broader and/or narrower terms, as well as related terms and scope notes
Review results and check for
relevancy
Search completed successfully
Depending on your search strategy, include more
controlled and/or non controlled terms to refine/broaden your
search
Carry out search, expand
if necessary
YES
YES
NO
NO
ModifierKey Term
Variant
Classifier
Searching for Subject InformationIndexing syntax
Drosophila melanogasterDrosophila melanogaster
fruit flyfruit fly
DipteraDiptera
pestpest
Searching for Subject InformationIndexing syntax example
Organization of Subject InformationDescriptor fields
Organisms: Plasmodium-falciparum (Sporozoa-): parasite-; human- (Hominidae-): host-, child-
Taxa Notes: Animals-; Chordates-; Humans-; Invertebrates-; Mammals-; Primates-;Protozoans-; Vertebrates-
Diseases: malaria-: blood-and-lymphatic-disease, parasitic-disease
Chemicals & pyrimethamine-dapsone [Maloprim-]: antiparasitic-drug, antiprotozoal-drugBiochemicals chemoprophylaxis-, efficacy-, side-effects; chloroquine-: antiparasitic-drug,
antiprotozoal-drug, chemoprophylaxis-, efficacy-, side-effects
Geopolitical Tanzania- (Africa-, Ethiopian-region): Kilombero-DistrictLocation
Sentence 1 Sentence 2
Higher level taxonomic terms
roles
Disease modifiers
Synonyms
Specific geographic terms
Higher level geographic terms
Drug modifiers
Searching for Subject Information
Broad topicsMajor ConceptsConcept Codes
Specific topicsTitleSubject Terms/DescriptorsIndividual Subject Term fields
Searching for Broad SubjectsMajor Concepts
Controlled terms for broad subjects emphasized by the author
Use Controlled Vocabulary (Authority File) to locate suitable terms
Search examplehematology in MC medical sciences in MCpharmacology in MC
Display exampleInfection-; Hematology- (Human-Medicine, Medical-
Sciences); Pharmacology-
Searching for Broad SubjectsConcept Codes
Five-digit codes representing broad topics in the life sciences [used 1969-1992]
Consult the BIOSIS Search Guide for a complete list of Concept Codes
Concept Code names can be searched using CN
Searching for Broad SubjectsConcept Codes
98 Concept Code groups can be cascaded to three digits
Search five-digit codescc15506 in CC (for Urinary System Pathology)
OR Search Code groupings
cc155* in CC (for all Urinary System codes)
Searching for Specific SubjectsTitle & Abstract
Title and Abstract are as written by the author U.S. or British spelling Abbreviated or spelled out forms Truncation Synonym
Search examplemarrow transplant in TIribavirin therapy in TI
transplant in AB
Searching for Specific SubjectsParts, Structures & Systems
Contains components above the macromolecular level (e.g. organ systems, body parts)
Controlled Vocabulary (Authority File) contains organ system modifiers
Search exampledigestive-system in PS
Display examplescerebellum-: nervous-system; liver-tissue: digestive-system, postmortem-
Searching for Specific SubjectsDiseases
Search for human, animal, or plant diseases, disorders or pathologies
Controlled Vocabulary (Authority File) contains controlled disease modifiers
Corresponding MeSH term will appear in the Alternate Indexing field
Search exampleviral-disease in DShemorrrhagic cystitis in DS
Display exampleadenovirus-induced-hemorrhagic-cystitis [AD-HC]: urologic-disease, viral-disease
Searching for Specific SubjectsAlternate Indexing
MeSH disease terminology Search example
arthritis rheumatoid in ALT Display example
Alternate Indexing: Arthritis,-Rheumatoid-(MeSH)
Diseases: Rheumatoid-arthritis: connective-
tissue-disease, immune-system-disease
Searching for Specific SubjectsAlternate Indexing MeSH Examples
BIOSIS Diseases field:prostate-cancer: neoplastic-disease, reproductive-system-disease/male…cancer: neoplastic-disease; leukemia: blood-and-lymphatic disease, neoplastic-disease
Alternate Indexing:
Prostatic-neoplasms- (MeSH)
Leukemia-(MeSH); Neoplasms-(MeSH)
Searching for Specific SubjectsChemicals & Biochemicals
Chemical names are as given in the paper.
Locate controlled Drug modifiers in the Controlled Vocabulary (Authority File)
Search examplesribavirin in CBhla in CB
Display exampleHLA-; ribavirin-: antiviral-drug
Searching for Specific SubjectsGene Name/Organism
Gene name plus organism from which it is isolated indexed in Chemicals & Biochemicals field (1999- )
Exampleshuman MDM2 gene (Hominidae)
rat E2A gene (Muridae)
Searching for Specific SubjectsCAS Registry Numbers®
CAS Registry Numbers assigned to chemicals, followed by chemical name
Search example
36791-04-5 in RN Display example
36791-04-5: RIBAVIRIN
Searching for Specific SubjectsMethods and Equipment
Includes methods, apparatus or scientific techniques studied in the item
Search using free text terms
Search exampleallogeneic marrow transplantation in MQtherapeutic method in MQ
Display exampleallogeneic-marrow-transplantation:
therapeutic- method
Searching for Specific SubjectsSequence Data
Sequence Data includes databank accession numbers or other macromolecular sequence information
Controlled Vocabulary (Authority File) includes three sequence type terms: amino acid sequence
nucleotide sequencesugar sequence
Search exampleAF001177 in SD
Display exampleAF001177-: GenBank-, amino-acid-sequence; U89896-: GenBank-, amino-acid-sequence, nucleotide-sequence
Searching for Specific SubjectsTime (Geologic)
Includes archeological time, climatic, historic and geologic time periods
Search example Paleozoic in TM
Display examplesCambrian-: Paleozoic-; Devonian-;
Ordovician-: Paleozoic-; Silurian-
21st century; 18th century
Searching for Specific SubjectsGeopolitical Location
Includes country, continent and zoogeographical regions
Check Controlled Vocabulary (Authority File) for appropriate terms
Search example
Austria in GE
USA in TS
Display exampleUSA- (North-America, Nearctic-Region)Austria- (Europe-, Palearctic-Region)
Searching for Specific SubjectsPerson
Provides information on people discussed in the item
Search exampleCharles Darwin in NPAlbert Einstein in NP
Display exampleCharles Darwin: biologistAlbert Einstein: inventor
Searching for Specific SubjectsIndustry
Contains industry types discussed in the item
Search examplesbiotechnology industry in INpharmaceutical industry in IN
Display examplepharmaceutical industrybiotechnology industry
Searching for Specific SubjectsInstitutions & Organizations
Contains information on named companies discussed in the item, and the type of institution discussed
Controlled Institution Type Modifiers Search example
Monsanto in NC
Display exampleMonsanto Company,
company/organization
Searching for Specific SubjectsMiscellaneous Descriptors
Field includes additional words and phrases not indexed to specific fields
Search exampleclinical symptoms in MI
Display exampleclinical-symptomsimmune-system-activation; Meeting-
Abstract
Searching for Organisms
Broad organism groupsSuper Taxa Taxa NotesBiosystematic Codes
Specific organismsOrganismsTitleDescriptors
Controlled Vocabulary(Thesaurus)
Searching for Broad Organism GroupsSuper Taxa
Higher level taxonomic terms that allow searching broad categories of organisms using hierarchical scientific names
Use the Controlled Vocabulary (Authority File) to locate appropriate terms
Search exampleviruses in SThominidae in ST
Display exampleAdenoviridae-: Animal-Viruses, Viruses-,
Microorganisms-; Hominidae-: Primates-, Mammalia-, Vertebrata-, Chordata-, Animalia-
Searching for Broad Organism GroupsTaxa Notes
Common names of broad groups of organisms
Use the Controlled Vocabulary (Authority File) to locate suitable terms
Search examplesnonhuman mammals in TNhumans in TN
Display exampleAnimal-Viruses; Animals-; Chordates-; Humans-; Mammals-; Microorganisms-; Nonhuman-mammals; Primates-; Vertebrates-; Viruses-
Searching for Broad Organism Groups Biosystematic Codes
Five-digit codes representing broad organism groups
Search examplebc86215 in BCbc02610 in BC
Searching for Specific OrganismsOrganisms
Includes specific scientific or common name followed by next higher taxonomic category and modifying terms
Search exampleshuman in OR(bottlenose dolphin* OR tursiops truncatus) in ORadenovirus in OR
Display exampleAdenovirus- (Adenoviridae-): pathogen-; human-
(Hominidae-): adult-, patient-
bottlenose-dolphin (Delphinidae-)
Searching for Specific OrganismsOrganisms
Non controlled modifiers are linked to the organism name and may include race, gender, developmental stages, roles etc.
Search organism linked to modifiers using the NEAR Search examples
(human NEAR patient) in OR(acarina NEAR new-species) in OR(rat NEAR animal model) in OR
Display examplesAdenovirus- (Adenoviridae-): pathogen-; human-
(Hominidae-): adult-, patient-rat- (Muridae-): animal-model; Equus-caballus [horse-] (Equidae-)
Searching for Specific OrganismsNew Taxon Modifiers
Controlled terms representing newly classified taxonomic groupings
Use the Controlled Vocabulary (Authority File) to identify suitable terms
Search example (diptera NEAR new-genus) in OR
Display exampleLambrusca- (Diptera-): Tachinidae-,description-, new-genus
Searching for Specific OrganismsFossil Modifiers
Identifies the organism as fossil
Three Controlled Vocabulary (Authority File) terms
Search example (coniferopsida NEAR paleobotany NEAR new-species) in OR
Display example Sigmaphyllum-tasmanensis (Coniferopsida-): new-species, paleobotany-
Benefits of Organism Indexing
Improves search relevancy and precision
Controlled Vocabulary (Authority File) search commands facilitate searching broader and narrower organism groups
Controlled Vocabulary (Authority File) facilitates searching for new taxa and identifying fossil species
Searching for Humans Search for humans as:
human in ORhumans in TNHominidae in OR [includes fossil species]
Use appropriate modifiers for gender, developmental stages, etc…
Search example(human NEAR female) in OR
Display examplehuman- (Hominidae-): female-, patient-,
child-
Search Tips for Drugs/Chemicals Use the Controlled Vocabulary (Authority File)
to identify controlled drug modifiers for drug actions
Include as many drug modifiers as appropriate The most specific modifier is applied in the
record Use the link operator between the drug name
and modifier to specify particular actions Use synonyms and variants including trade
names for complete retrieval Consider using registry number
Field enhancements - SilverPlatter1980-1992 1993-1997 1998-
Words in the title
Added Keywords
Descriptor field
Concept Codes
Biosystematic Codes
Words in Title
Subject Terms (TS)
- Major Concepts
- Organisms
- Super Taxa
- Taxa notes
- Geopolitical Location
- Miscellaneous Descriptors
- Registry Numbers
- Chemicals & Biochemicals
- Sequence Data
- Industry
- Time
Words in TitleSubject Terms (TS) - Major Concepts - Organisms - Super Taxa - Taxa Notes - Geopolitical Location - Miscellaneous Descriptors - Registry Numbers - Chemicals & Biochemicals - Sequence Data - Methods & Equipment - Industry - Time - Parts, structures & systems - Diseases - Institutions & Organizations - Persons
Search principles
Pose the question
Identify the main topics
Determine how to search the main topics
Carry out the search
Review results and modify if necessary
