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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