Chem 3000
From SubjectGuides
[edit] Week 1: Search Basics / the Library Catalog
- January 12, 2010
Handouts
Web links
- Boolean Searching on the Internet
- A nice overview of Boolean logic with an emphasis on how it applies to Internet search engines.
- Boolean Search Tutorial
- A short and cutsey tutorial on Boolean searching.
- Chemical Information Retrieval -- ACS Guidelines for Bachelor's Degrees
Assignment
- Search Basics and the Library Catalog
[edit] Week 2: Journal Articles: Types; Reading; & Locating
- January 19, 2010
Chem 3000 Web Site
- Chem 3000 -- Journal Articles gives an overview on the types of articles, reading articles, and locating articles.
Web links
- CAS Source Index Search Tool
- Useful for "unravelling" journal title abbreviations (and vice versa)
Handouts
- Akdag, A.; Kocer, H. B.; Worley, S. D.; Broughton, R. M.; Webb, T. R.; Bray, T. H. J. Phys. Chem. B 2007, 111, 5581-5586. DOI: 10.1021/jp070586c
- Korchev, A. S.; Bozack, M. J.; Slaten, B. L.; Mills, G. J. Am. Chem. Soc. 2004, 126, 10-11. DOI: 10.1021/ja037933q
- Finding Journal Articles –- Best Protocol and Examples
- Guide on how to do this week's homework.
Assignment
- Finding Journal Articles
[edit] Week 3: Indexes & Abstracts, Chemical Abstracts
- January 26, 2010
Handouts
- CAS Indexing of Worley's paper "Why Does Kevlar Decompose, while Nomex Does Not, When Treated with Aqueous Chlorine Solutions?" Here is a more compact view of CAS' indexing of this paper.
- CAS Indexing of Mills' paper "Polymer-Initiated Photogeneration of Silver Nanoparticles in SPEEK/PVA Films: Direct Metal Photopatterning"
- Database comparison compares the content of three of the largest index and abstract databases.
- OSA Journals shows coverage of OSA journals in different indexing databases.
[edit] Week 4: SciFinder Scholar: Explore by Research Topic (keyword searching)
- February 2, 2010
Chem 3000 Web Site
- Chem 3000 Keyword Searching in SciFinder Scholar -- An overview of keyword searching.
Handouts & Web Sites
- SciFinder Scholar describes how to access SciFinder Scholar from on-campus and off-campus locations. SciFinder Scholar is available on all computers in OIT labs, including the library. It can also be installed on your computer.
- Under the Hood: SciFinder Scholar gives a visual way of how the SciFinder Scholar works.
- Analyze, Refine, & Categorize shows what options these three SciFinder Scholar features offer.
- The PowerPoint SciFinder Scholar 2007 gives a short overview.
Assignment
- SciFinder Scholar -- Keyword Searching is due February 9, 2010
[edit] Week 5: SciFinder Scholar -- Substances and Reactions
- Feburary 9, 2010
Web sites
- CAS Registry Number and Substance Count shows how many substances are in the CAS Registry File.
Handouts
- Anatomy of a SciFinder Scholar Substance Record shows the CAS Registry record for cyclohexanol, which is a typical substance record. Key elements are the CAS Registry Number, CAS Index Name, chemical structure, synonyms, and links to predicted and experimental property data.
- The Substances handout summarizes how SciFinder Scholar classifies substances.
- Substances & Reactions -- Practice Examples illustrates how to search for substances and reactions in SciFinder Scholar.
Assignment
- SciFinder Scholar -- Substances is due February 16, 2010
[edit] Week 6: Cited Reference Searching
- Feburary 16, 2010
Handouts
- Cited Reference Searching is a two page summary on cited reference searching in Science Citation Index and SciFinder Scholar.
- Cited Reference Searching or ... making the most of a key reference looks more closely at the results of a single cited reference search in Science Citation Index and SciFinder Scholar.
Assignment
- SciFinder Scholar -- Reactions is due February 23, 2010.
[edit] Week 7: Physical Data Compilations: Beilstein & Gmelin
- February 23, 2010
Websites
- Beilstein Subject Guide describes how to access Beilstein and Gmelin via MDL CrossFire Commander.
- At 62 pages, the MDL CrossFire Commander V 7.1 Quick User Guide is a bit of a misnomer, but it can answer many questions about how to used the MDL CrossFire interface to search Beilstein and Gmelin.
Handouts
- Beilstein and Gmelin via CrossFire Commander describes how to search for properties and spectra for a specific substance. It also points out the mostly likely reasons why a search failed.
- The Beilstein: Sample Records covers what is in a substance record, a reaction record, and a citation record.
- The Beilstein and SciFinder Scholar Comparison handout summarizes the content of the two major chemistry databases.
Assignment
- Beilstein & Gmelin is due March 9, 2010.
[edit] Week 8: Beilstein & Gmelin -- In-Class work time
- March 2, 2010
- No new material will be covered, except that which emerges while working on the Beilstein & Gmelin homework.
[edit] Week 9: Medline (PubMed) and MeSH
- March 9, 2010
Websites
- Medical Subject Headings (MeSH) is the controlled vocabulary (aka Index Terms)for the Medline database.
- Searching PubMed using MeSH® Field Tags is a short how-to guide for advanced searching in PubMed.
Handouts
- SciFinder Scholar, Medline, and Science Citation Index are three of the largest Index & Abstract science databases (see Database Comparison). This is the same handout from week 3.
[edit] Week 10: Safety & Toxicology / Current Awareness / CRC Handbook of Chemistry & Physics
- March 23, 2010
Websites
- ToxNet is portal to 14 health and toxicological databases. Particularly useful for chemists are ...
- Hazardous Substance Data Bank -- Detailed records for roughly 5,000 substances
- ToxLine -- Index & Abstract database with over 3,000,000 records on the biochemical, pharmacological, physiological, and toxicological effects of drugs and other chemicals
- Vermont SIRI MSDS Collection -- There are many online collections of Material & Safety Data Sheet (MSDS), but this is one of the most dependable. Getting MSDSs for chemical is fairly easy to do online because manufacturers and vendors are required to get MSDSs into the hands of those that use the chemicals they make or sell.
- The Alerts page summarizes how to stay current with the literature.
Handouts
- Chemical Safety and Toxicology points to print and online resources.
Assignment
- CRC Handbook of Chemistry & Physics is due March 30, 2010. If you download the homework, you must also request a "Compound Number" from the instructor by email.
- Use only the CRC Handbook of Chemistry & Physics located at Ref QD 65 .H3 V90 or V89.
- Do not use SciFinder Scholar, Google, or any other database.
- Do not use other people or even your "personal knowledge."
- The point of the assignment is to explore how to use the CRC Handbook of Chemistry & Physics. It is a terrific one-stop reference work.
- Please return the handbook to the Reference area when you are done so the rest of the class can find it.
- Use only the CRC Handbook of Chemistry & Physics located at Ref QD 65 .H3 V90 or V89.
[edit] Week 11: Dictionaries, Handbooks, and Discipline Literature: Analytical, Biochemistry, Inorganic, Organic, Physical
- March 30, 2010
Websites
- The NIST Chemistry WebBook offers roughly 8,700 IR and 13,000 MS spectra.
- The Sigma-Aldrich Catalog has over 20,000 compounds, many with IR and NMR spectra.
- SBDS Structural Database offers roughly 50,000 IR, 23,000 MS, 14,000 1H NMR, and 12,000 13C NMR spectra.
- NMRShiftDB is a growing NMR spectra repository for 41,571 compounds (as of 3/30/10).
Handouts
- Selected Dictionaries in the RBD Library points to the most useful chemical, foreign language, and "names" dictionaries.
- Selected Chemistry Handbooks points to the most useful handbooks in the RBD Library and free web sites that offer chemical data.
- One handout with four parts.
- Analytical and Spectral Data summarizes online and library resources for IR, NMR, and MS spectra and crystal structures.
- The library has Subject Encyclopedias for specific disciplines within chemistry.
- The library has Synthesis and Reaction Chemistry resources for the two main classes of compounds: inorganic and organic.
- For each discipline of chemistry there are resources that review the Chemistry Techniques & Methods that are important for the discipline.
- The Comprehensive Data Sources handout summarizes the major collections of property data and how to locate smaller data collections.
Assignment
- Dictionaries and Handbooks is due April 13, 2010. Here are some guidelines on the kind of information and the level of detail required for this assignment.
[edit] Week 12: No Class
- April 6, 2010
[edit] Week 13: Patents
- April 13, 2010
Websites
- The U.S. Patent and Trademark Office offers many resources for patents, trademarks, and copyright. The USPTO Search page can be tricky to find, but once you find a search page that uses a red, white, and blue color scheme, you have found it.
- European Patent Office offers more convenient access to the full-text of U.S. and foreign (European & non-European) patents.
- Being able to keyword search the full-text of pre-1976 U.S. Patents is the main advantage of the still-in-beta Google Patents.
- The ACS has written an excellent overview of patents from a chemist's perspective.
- What Every Chemist Should Know About Patents (3rd Edition, 2002)
Three elements of a Patent
- Utility => A patent must descibe something useful. Do Expressed Sequence Tags (ESTs) meet that criteria? For a summary of Monsanto's effort to patent ESTs see the Harvard Law Review, 2006 119(8) 2604-2611.
- Novelty => A patent must describe something new. Upon a patent challenge from the Indian Council of Scientific and Industrial Research, the U.S. Patent Office rejected US 5,401,504 in which the University of Mississippi Medical Center had patented tumeric for its medicical properties that have long been known on the Indian subcontinent. Related to the idea that patents must be "novel" is that facts cannot be patented. However, in the Supreme Court ruling on LabCorp vs. Metabolite , one may argue that the heart of US 4,949,658 is a fact and not an invention.
- Non-Obviousness => A patent cannot be obvious to those who are "skilled in the art". There must indeed be some sort of invention. Is Pfizer's "besylate" patent on its hypertension drug Amlodipine obvious or not? Is it not obvious for a pharmaceutical company to use one of roughly thirty anions that are considered safe to use in pharmaceutical formulations?
Handouts
- Patent Literature and Chemistry gives an overview of online patent and trademark resources.
- An annotated version of Bayer's patent for Cipro U.S. 4,670,444 highlights the key elements of a U.S. patent.
[edit] Week 14: Publication Cycle and the Chemical Literature
- April 20, 2010
- Primary Literature is the first place that a scientist publishes their results.
- Secondary Literature provides access to the primary literature. Access routes can be subdivided into three types, but there is some overlap.
- Indexes -- SciFinder Scholar, Beilstein, Gmelin, Web of Science, PubMed, etc.
- Compacters -- Reviews, encyclopedias, and books
- Repackagers -- Handbooks such as the CRC Handbook of Chemistry & Physics, Beilstein, Gmelin, etc.
Handouts
- Use this Excel spreadsheet to place research-related activities on a timeline. The sort function allows you to reorder the research-related activities. Note: some activities may share the same place on a timeline or may come slightly before or after other activities -- just lump them together if that makes sense.
- The Publication Cycle handout provides one way of looking at the use of information and the chemical literature.
Websites
- The amount of money spent by U.S. university research libraries for journals and books since 1984 compared to inflation is shown graphically at Monographs and Serial Expenditures in ARL Libraries, 1984-2004.
[edit] Week 15: Exam
- April 27, 2010
Breakdown of the Exam
- 27 points => SciFinder
- 17 points => Journal articles
- 14 points => Dictionaries and handbooks
- 11 points => Beilstein & Gmelin
- 10 points => Indexes & Abstract Databases
- 9 points => Publication Cycle
- 6 points => Cited reference searching
- 4 points => Patents
- 2 points => Health and Safety
Number of Questions
- 7 True or False
- 3 Mulitple Choice
- 12 Short Answer
- 1 "Longer" Short Answer
[edit] Sample Exam Questions
- True or False
- For the most part, print directories have been replaced by online directories. (2 points)
- Mulitple Choice
- Which of the follow sources is most likely to provide thermodynamic data?
- Circle the letter for the best answer. (2 points)
- (a) Merck Index
- (b) NIST Chemistry WebBook
- (c) Dictionary of Organic Compounds
- (d) Inorganic Syntheses
- (e) Sigma-Aldrich Catalog
- Short Answer
- A U.S. utility patent must meet three conditions. What are they? (6 points)
- Give two reasons why a Cited Reference Search in SciFinder Scholar might find fewer citing articles than a Cited Reference Search on the same article in Web of Science. (6 points)
- What is the key difference between the following two Research by Topic searches in SciFinder Scholar? Focus on what each search retrieves. (4 points)
- Search #1 = hydrogen storage with metal hydrides
- Search #2 = hydrogen storage and metal hydrides
- "Longer" Short Answer
- Compare and contrast "footnote chasing" to the use of the Index & Abstract database SciFinder Scholar. What are the limitations and advantages of each method of searching the chemical literature? (12 points)
- Comments or questions? Please contact:
- Bob Buchanan buchara@auburn.edu