1. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu Researcher’s Toolkit: Bioresearch Tools Christopher Stave, MLS Liaison & Instructional Services Coordinator cstave@stanford.edu Yannick Pouliot, PhD Bioresearch Informationist lanebioresearch@stanford.edu © 2007 Lane Medical Library & Knowledge Management Center 12/6/2007

2. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 2 We’re Trying Something New Here… A small step in trying to foster translational research:  Clinical  basic research  Basic research  clinical

3. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 3 The Bioresearch Informationist: At Your Service Yannick Pouliot, PhD, Lane Medical Library & Knowledge Management Center Bioresearch Informationist ≈ computational biologist in residence Lane Library service Closely coordinated with CMGMCMGM Role: Support laboratory researchers regarding biocomputational resources and their use …especially postdocs Contact: lanebioresearch@stanford.edulanebioresearch@stanford.edu

4. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 4 Clinical Information Services Librarian Christopher Stave, MLS, Lane Medical Library & Knowledge Management Center Christopher Stave Medical Librarian Literature searches (including more extensive searches for meta-analyses and systematic reviews) General medical reference Role: Support Medical Center students, staff and faculty in biomedical information retrieval and management Contact: cstave@stanford.educstave@stanford.edu

5. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 5 So Why Are We Here? Need to find needle in a haystack…  Information is probably out there  “Traditional” databases not enough “New” sources:  Full-text DBs  Protocols DBs  Patent DBs  Specialty DBs  Biotools  Funding  Stanford internal Searching can lead to this…

6. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 6 Contents How to use Lane’s Bioresearch Metasearch as the first step for finding difficult/non-traditional information  Focus on actual use cases (all basic research, unfortunately)

7. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 7 Introducing Bioresearch Metasearch

8. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 8 Example Applications of Bioresearch Metasearch All examples derived from questions posted to SUPD postdoc mailing list

9. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 9 Translational Research Examples ABCB1: gene which when mutated confers multi-drug resistance to antineoplastic drugs  Clinical trials  Drugs  Genetic variants conferring drug resistance Iressa  Tyrosine kinase inhibitor for treatment of non- small cell lung cancer Who is working on X at Stanford?

10. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 10 Example 1: Finding Campus Expertise Problem: “I was wondering whether anybody has experience with/or is doing EBV transformation of B-cells. Any help is greatly appreciated.” Solution Use Bioresearch Metasearch with search key = “stanford university" EBV transformation b-cells Results Highly relevant profile found in All SOM: http://www.stanford.edu/group/TIL/)http://www.stanford.edu/group/TIL/ Highly relevant paper found in Scirus: http://www.cedars-sinai.edu/pdf/Dorigo- O_Development-of-a-novel-2004-10659.pdfhttp://www.cedars-sinai.edu/pdf/Dorigo- O_Development-of-a-novel-2004-10659.pdf

11. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 11 Results for EBV transformation of B-cells at Stanford

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13. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 13 Not To Be Ignored: COS Expertise @ Stanford

14. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 14 Example 2: Finding (Physical) Resources on Campus Problem: “Anyone ever heard of a free flow electrophoresis system somewhere on campus? “ Solution: PubMed Central yielded answer…

15. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 15 Results: Resources on Campus

16. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 16 Example 3: Finding (Physical) Resources on Campus - 2 Problem: “Is there a core microarray facility on campus?” Solution: Results under Core Facilities

17. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 17 Results for Core Facilities on Campus

18. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 18 Example – 4: Finding Published Applications of a Lab Kit Problem: You want to find papers that use the BLOCK- iT miR RNAi expression vector from InVitrogen Corp.BLOCK- iT Solution: 1. Search Bioresearch metasearch with "BLOCK-iT" Invitrogen 2. Analyze results in 1. HighWire/Scirus – Journals (full-text databases) 2. Protocols

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20. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 20 Results: HighWire

21. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 21 Results: Protocols

22. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 22 Search problems… Solution: re-run search using Advanced Search Preferences  Use “All of the words” option

23. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 23 Tips Metasearch best for broad queries, followed by refining the query within specific search engines directly Full-text literature search engines are optimal for very specific queries where results likely to be in body of text  … rather than in abstract/title/indexing keywords When number of hits too high, re-run search in individual search engine using better parameters

24. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 24 Yannick Pouliot, PhD lanebioresearch@stanford.edu

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