Zoology 305 Library Databases/Indexes Lab Goals for session: 1) Meet your librarian Kevin Messner 2) Understand tools for journal literature searches, as well as other library resources (e.g. the catalog) 3) Learn search techniques for 3 literature indexes Biological Abstracts/BIOSIS MEDLINE/PubMed Science Citation Index/Web of Science 4) How to get to the articles you find in the indexes

Accessing these slides and other resources -> Resources by Subject -> “Biology” or “Zoology” -> Click the “Course Guides” tab for these slides

Zoology 305 Library Databases/Indexes Lab Library Databases/Indexes Lab Counts as a regular lab grade -- should be a straightforward assignment Counts as a regular lab grade -- should be a straightforward assignment Complete assignment sheet and turn in before you leave Complete assignment sheet and turn in before you leave Graded sheet will be returned to you Graded sheet will be returned to you

Concepts to look for today How to access our library’s databases and articles How to access our library’s databases and articles Search methods and tips Search methods and tips contents of a literature database record contents of a literature database record interpreting a citation interpreting a citation searching particular components of citations searching particular components of citations truncation truncation combining sets combining sets finding “more like this” finding “more like this”

What’s an Index? Library Catalogs vs. Indexes Look for the title “Genome variation in the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti” in our catalog. Look for the title “Genome variation in the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti” in our catalog. What kind of catalog search to use? What kind of catalog search to use? Do we have this? Do we have this?

Library Catalog vs Indexes Catalog -- a database of the titles the library has in its (print and electronic) collection Catalog -- a database of the titles the library has in its (print and electronic) collection Includes the titles of magazines and journals, but not the individual articles within those magazines and journals Includes the titles of magazines and journals, but not the individual articles within those magazines and journals Index -- a database of literature, usually in a particular field like biology or medicine Index -- a database of literature, usually in a particular field like biology or medicine Includes and allows searches for particular journal articles Includes and allows searches for particular journal articles Many items recorded in an index are not held in your library Many items recorded in an index are not held in your library

Why these three indexes? Key tools for researching the literature of biology -- e.g., what other work has been done that’s relevant to my research project? (or my patient, my grant, my business) Biological Abstracts/BIOSIS: principal life sciences index, especially for ecology, plant biology, other non-”biomedical” topics Biological Abstracts/BIOSIS: principal life sciences index, especially for ecology, plant biology, other non-”biomedical” topics MEDLINE/PubMed: principal index for health sciences and biomedical research. PubMed is FREE -- learn now, you still have access after graduation. MEDLINE/PubMed: principal index for health sciences and biomedical research. PubMed is FREE -- learn now, you still have access after graduation. Science Citation Index/Web of Science: covers journals across the sciences, links older articles to new ones through citation tracking Science Citation Index/Web of Science: covers journals across the sciences, links older articles to new ones through citation tracking

Biological Abstracts, BIOSIS Covers ~6000 journals in life sciences, from molecular biology/biochemistry through ecosystem ecology Covers ~6000 journals in life sciences, from molecular biology/biochemistry through ecosystem ecology “BIOSIS” includes book chapters, meeting abstracts, other literature beyond journals “BIOSIS” includes book chapters, meeting abstracts, other literature beyond journals Very good database for searching for info on an organism or taxonomic group Very good database for searching for info on an organism or taxonomic group First look at a sample record -- what exactly are we searching through in these indexes? First look at a sample record -- what exactly are we searching through in these indexes? Look over record for a paper titled “Considerations for measuring genetic variation…” Look over record for a paper titled “Considerations for measuring genetic variation…”

Note truncation

Search history, combining sets with Boolean operators

- What additional synonyms for DNA fingerprinting might you also search on?

Searching Taxa I told you to use the term amphibia*. This captures the words amphibia, amphibian, amphibians. I told you to use the term amphibia*. This captures the words amphibia, amphibian, amphibians. When you search for organisms, you should search for both common and scientific names When you search for organisms, you should search for both common and scientific names Example – chimpanzee Example – chimpanzee Where to find scientific names? Entrez Taxonomy; U Mich Animal Diversity Web, Wikipedia/Wikispecies Where to find scientific names? Entrez Taxonomy; U Mich Animal Diversity Web, Wikipedia/Wikispecies

Entrez Taxonomy Access from -> Resources by Subject -> Biology -> Web Sites -> Bioinformatics

PubMed Premier lit database for health sciences and “biomedical” research, including molecular biology, biochemistry, physiology, genetics Premier lit database for health sciences and “biomedical” research, including molecular biology, biochemistry, physiology, genetics Includes 16 million citations, currently going back to 1950’s Includes 16 million citations, currently going back to 1950’s FREE -- Federal tax dollars at work -- learn now, take with you to your next job FREE -- Federal tax dollars at work -- learn now, take with you to your next job You may find PubMed records in Google searches You may find PubMed records in Google searches Links to about 30 other informational databases like OMIM, Entrez Gene, GenBank Links to about 30 other informational databases like OMIM, Entrez Gene, GenBank

Entrez Journal Browser

Field-specific Searching in PubMed Most databases allow you to search not just for text anywhere, but also in specific database “fields” like author, journal title, address, etc. Most databases allow you to search not just for text anywhere, but also in specific database “fields” like author, journal title, address, etc. What if you want to find an article by someone named Silver, in the journal Cell? What if you want to find an article by someone named Silver, in the journal Cell? Use Advanced Search, or “tagging.” Use Advanced Search, or “tagging.”

Science Citation Index/Web of Science For any given article, tracks both what other papers it cited, and what papers have cited it For any given article, tracks both what other papers it cited, and what papers have cited it Provides quick and powerful way to find a body of related literature Provides quick and powerful way to find a body of related literature Covers 3500 major journals across scientific/technical fields Covers 3500 major journals across scientific/technical fields Useful in cross-disciplinary fields (like cognition or biomedical engineering) Useful in cross-disciplinary fields (like cognition or biomedical engineering)

You can now search BIOSIS, MEDLINE, and Web of Science simultaneously on the “Web of Knowledge” site You can now search BIOSIS, MEDLINE, and Web of Science simultaneously on the “Web of Knowledge” site Be aware that you’re searching different databases, as some appear to be missing things (e.g. MEDLINE doesn’t have‘Times Cited’ data) Be aware that you’re searching different databases, as some appear to be missing things (e.g. MEDLINE doesn’t have‘Times Cited’ data) Author searching is flaky at present because of different conventions Author searching is flaky at present because of different conventions