Transcript biolabs

Electronic Resources Awareness
- Bytes for Biologists No.1 -
Biological Abstracts
Roger Mills
January 2003
Oxford University Library Services / IT Learning Programme
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
• BIOSIS web site
• www.biosis.org
Searching
®
Biological Abstracts
• Using SilverPlatter
About BIOSIS
 World’s
largest abstracting and
indexing service for the life sciences
 Not-for-profit
Company
 Headquartered
 European
in Philadelphia
office in York, UK
The Biological Abstracts family
 Biological Abstracts
 Biological
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
Geographical Coverage
North America (31%)
Asia, Australasia
(14%)
Europe &
Middle East (52%)
Central & S. America (2%)
Africa (1%)
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/erlclients.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 Record
TI 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 Record
MC Major Concepts: Infection-; Hematology- (Human-Medicine, Medical-Sciences);
Pharmacology-
ST Super Taxa: Adenoviridae-: Animal-Viruses, Viruses-, Microorganisms-; Hominidae-:
Primates-, Mammalia-,Vertebrata-, Chordata-, AnimaliaOR Organisms: adenovirus- (Adenoviridae-): pathogen; human- (Hominidae-): patient, adult
TN Taxa Notes: Animal-Viruses; Animals-; Chordates-; Humans-; Mammals-;
Microorganisms-; Primates-; Vertebrates-; VirusesCB Chemicals and Biochemicals: HLA-; ribavirin-: antiviral-drug
DS Diseases: adenovirus-induced hemorrhagic-cystitis [AD-HC]: urologic-disease, viraldisease
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 AU
Saito-H* in AU
nagoya 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 Information
Journals

Can be searched using field tag SO for journal
name, volume, issue, pagination, and publication
year

Journal URL included, when available

Search example
SO=bone-marrow-transplantation
SO=New-England-Journal-of-Medicine
SO=Cell-

BIOSIS Serial Sources provides a complete
journal list
Searching for Source Information
Journals

ISSN
International Standard Serial
0268-3369 in IS
Searching for Subject Information
Searching 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 Website
www.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 of
drugs for the diagnosis, prevention, or treatment of
disease in animals and humans includes drug
design, testing and clinical trials, drug
pharmacokinetics, and pharmacodynamics
studies.
Tree 1 of 1: Major Concepts
Major Concept Terms
Pharmacology
Pharmaceuticals
Pharmacognosy
Accessing the Controlled Vocabulary
(Authority File)
 From
the Term Details screen you have
several options:
 Explode
Term
 Single-Term Search
 Back
 Add to list
Searching the Subject Terms Field
[TS]
Simultaneously searches:
alternate indexing
super taxa
chemicals & biochemicals
institutions & organizations
diseases
geopolitical location
industry
taxa notes
persons
major concepts
methods & equipment
miscellaneous descriptors
registry numbers
organism names
sequence data
parts, structures & systems
time
Searching for Subject Information
Improving 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
Check application for
broader and/or narrower
terms, as well as related
terms and scope notes
Qualify search
term(s) by using
controlled
vocabulary lists
(Authority File) or
the BIOSIS
Search Guide’s
Vocabulary Guide
section
Search completed
successfully
YES
Are the search
term(s) controlled?
term? Check
synonyms and
variants
(singular/plural etc.)
YES
Carry out
search, expand
if necessary
NO
Search as non controlled
term(s) using natural
language including any
synonyms, variants
(singular/plural) etc.
Review results
and check for
relevancy
NO
Depending on your
search strategy,
include more
controlled and/or non
controlled terms to
refine/broaden your
search
Searching for Subject Information
Indexing syntax
Classifier
Key Term
Variant
Modifier
Searching for Subject Information
Indexing syntax example
Diptera
Drosophila melanogaster
fruit fly
pest
Organization of Subject Information
Descriptor fields
Sentence 1
Higher level
taxonomic terms
Sentence 2
Organisms:
Plasmodium-falciparum (Sporozoa-): parasite-; human- (Hominidae-):
host-, childroles
Taxa Notes:
Animals-; Chordates-; Humans-; Invertebrates-; Mammals-; Primates-;
Protozoans-; VertebratesDisease modifiers
Diseases:
malaria-: blood-and-lymphatic-disease, parasitic-disease
Synonyms
Chemicals &
Biochemicals
Drug modifiers
pyrimethamine-dapsone [Maloprim-]: antiparasitic-drug, antiprotozoal-drug
chemoprophylaxis-, efficacy-, side-effects; chloroquine-: antiparasitic-drug,
antiprotozoal-drug, chemoprophylaxis-, efficacy-, side-effects
Specific geographic terms
Geopolitical
Location
Tanzania- (Africa-, Ethiopian-region): Kilombero-District
Higher level geographic terms
Searching for Subject Information

Broad topics
Major Concepts
Concept Codes

Specific topics
Title
Subject Terms/Descriptors
Individual Subject Term fields
Searching for Broad Subjects
Major Concepts

Controlled terms for broad subjects emphasized by
the author

Use Controlled Vocabulary (Authority File) to locate
suitable terms

Search example
hematology in MC
medical sciences in MC
pharmacology in MC

Display example
Infection-; Hematology- (Human-Medicine, MedicalSciences); Pharmacology-
Searching for Broad Subjects
Concept 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 Subjects
Concept Codes
98 Concept Code groups can be cascaded to
three digits
 Search five-digit codes
cc15506 in CC (for Urinary System Pathology)

OR

Search Code groupings
cc155* in CC (for all Urinary System codes)
Searching for Specific Subjects
Title & Abstract

Title and Abstract are as written by the
author
 U.S.
or British spelling
 Abbreviated or spelled out forms
 Truncation
 Synonym

Search example
marrow transplant in TI
ribavirin therapy in TI
transplant in AB
Searching for Specific Subjects
Parts, Structures & Systems

Contains components above the macromolecular
level (e.g. organ systems, body parts)

Controlled Vocabulary (Authority File) contains
organ system modifiers

Search example
digestive-system in PS

Display examples
cerebellum-: nervous-system;
liver-tissue: digestive-system, postmortem-
Searching for Specific Subjects
Diseases

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 example
viral-disease in DS
hemorrrhagic cystitis in DS

Display example
adenovirus-induced-hemorrhagic-cystitis
[AD-HC]: urologic-disease, viral-disease
Searching for Specific Subjects
Alternate Indexing
MeSH disease terminology
 Search example

arthritis rheumatoid in ALT

Display example
Alternate Indexing:
Arthritis,-Rheumatoid-(MeSH)
Diseases:
Rheumatoid-arthritis: connectivetissue-disease, immune-system-disease
Searching for Specific Subjects
Alternate Indexing MeSH Examples
Alternate Indexing:
Prostatic-neoplasms(MeSH)
Leukemia-(MeSH);
Neoplasms-(MeSH)
BIOSIS Diseases field:
prostate-cancer:
neoplastic-disease,
reproductivesystemdisease/male…
cancer: neoplasticdisease; leukemia:
blood-and-lymphatic
disease, neoplasticdisease
Searching for Specific Subjects
Chemicals & Biochemicals

Chemical names are as given in the paper.

Locate controlled Drug modifiers in the
Controlled Vocabulary (Authority File)

Search examples
ribavirin in CB
hla in CB

Display example
HLA-; ribavirin-: antiviral-drug
Searching for Specific Subjects
Gene Name/Organism
Gene name plus organism from which it is
isolated indexed in Chemicals &
Biochemicals field (1999- )
 Examples

human MDM2 gene (Hominidae)
rat E2A gene (Muridae)
Searching for Specific Subjects
CAS 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 Subjects
Methods and Equipment
Includes methods, apparatus or scientific
techniques studied in the item
 Search using free text terms


Search example
allogeneic marrow transplantation in MQ
therapeutic method in MQ

Display example
allogeneic-marrow-transplantation: therapeuticmethod
Searching for Specific Subjects
Sequence 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 sequence
sugar sequence
Search example
AF001177 in SD

Display example
AF001177-: GenBank-, amino-acid-sequence;
U89896-: GenBank-, amino-acid-sequence, nucleotidesequence
Searching for Specific Subjects
Time (Geologic)

Includes archeological time, climatic,
historic and geologic time periods

Search example
Paleozoic in TM

Display examples
Cambrian-: Paleozoic-; Devonian-;
Ordovician-: Paleozoic-; Silurian21st century; 18th century
Searching for Specific Subjects
Geopolitical Location

Includes country, continent and zoogeographical
regions

Check Controlled Vocabulary (Authority File) for
appropriate terms

Search example
Austria in GE
USA in TS

Display example
USA- (North-America, Nearctic-Region)
Austria- (Europe-, Palearctic-Region)
Searching for Specific Subjects
Person
 Provides
information on people
discussed in the item
 Search example
Charles Darwin in NP
Albert Einstein in NP
 Display example
Charles Darwin: biologist
Albert Einstein: inventor
Searching for Specific Subjects
Industry

Contains industry types discussed in the
item

Search examples
biotechnology industry in IN
pharmaceutical industry in IN

Display example
pharmaceutical industry
biotechnology industry
Searching for Specific Subjects
Institutions & 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 example
Monsanto Company, company/organization
Searching for Specific Subjects
Miscellaneous Descriptors

Field includes additional words and phrases
not indexed to specific fields

Search example
clinical symptoms in MI

Display example
clinical-symptoms
immune-system-activation; Meeting-Abstract
Searching for Organisms

Broad organism groups
Super Taxa
Taxa Notes
Biosystematic Codes

Specific organisms
Organisms
Title
Descriptors
Controlled Vocabulary
(Thesaurus)
Searching for Broad Organism Groups
Super 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 example
viruses in ST
hominidae in ST

Display example
Adenoviridae-: Animal-Viruses, Viruses-, Microorganisms-;
Hominidae-: Primates-, Mammalia-, Vertebrata-, Chordata-,
Animalia-
Searching for Broad Organism Groups
Taxa Notes

Common names of broad groups of organisms
Use the Controlled Vocabulary (Authority File)
to locate suitable terms
 Search examples

nonhuman mammals in TN
humans in TN

Display example
Animal-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 example
bc86215 in BC
bc02610 in BC
Searching for Specific Organisms
Organisms

Includes specific scientific or common name
followed by next higher taxonomic category
and modifying terms

Search examples
human in OR
(bottlenose dolphin* OR tursiops truncatus) in OR
adenovirus in OR

Display example
Adenovirus- (Adenoviridae-): pathogen-; human(Hominidae-): adult-, patientbottlenose-dolphin (Delphinidae-)
Searching for Specific Organisms
Organisms

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 examples
Adenovirus- (Adenoviridae-): pathogen-; human(Hominidae-): adult-, patientrat- (Muridae-): animal-model; Equus-caballus
[horse-] (Equidae-)
Searching for Specific Organisms
New 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 example
Lambrusca- (Diptera-): Tachinidae-,
description-, new-genus
Searching for Specific Organisms
Fossil 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 OR
humans in TN
Hominidae in OR [includes fossil species]

Use appropriate modifiers for gender,
developmental stages, etc…

Search example
(human NEAR female) in OR

Display example
human- (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 - SilverPlatter
1980-1992
1993-1997
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
1998Words in Title
Subject 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