1 Supporting Information Chemical Information Literacy at a Liberal Arts

Supporting Information Chemical Information Literacy at a Liberal Arts College George Greco Department of Chemistry Goucher College 1021 Dulaney Valley Road Baltimore, MD 21204 1 Table of Contents Course Syllabus 3-6 Handout 1: The Chemical Literature 7-8 Handout 2: Types of Papers 9 Handout 3: Citations 10-11 Handout 4: Secondary Sources 12-15 Handout 5: SciFinder 16-18 Handout 6: Free Public Databases 19-22 Handout 7: InChI and SMILES 23-25 Handout 8: Reaxys, Beilstein and Gmelin 26-27 Handout 9: Patents 28-32 Handout 10: Reading papers for current events 33 Handout 11: The publication process 34-37 Handout 12: Structure and sequence databases 38-41 Handout 13: Databases of Spectral and Thermodynamic Properties 42-43 HW #1: The Chemical Literature 44 SciFinder Assignment 45-46 HW #4: PubMed and PubChem 47 HW #5: SMILES and InChI 48 Current Events Assignment 49-50 Note about final exam 51 2 Chemistry 245 – Spring 2015 Chemical Information Literacy Instructor : Dr. George Greco Office : Hoffberger 220 Phone : 410-337-6313 Email : [email protected] Class Meetings : Tuesdays 11:45– 12:35 Hoffberger 223 Office hours: Monday 11:00-12:30, Wednesday 1:30-3:00 or by appointment (e-mail me) Optional Text : Chemical Information for Chemists: A Primer edited by Judith N. Currano and Dana L. Roth. Published by RSC Publishing. ISBN 978-1-84973-551-3 Disclaimer: This is the first time we are offering this course. It is my first time teaching a course like this. I don’t expect everything to go 100% smoothly. Please be patient with me. Even if it is not perfect, you will learn something. GoucherLearn : Please check Goucher Learn site for any assignments or information that I may need to post. Grading Grades for this course will be computed as follows: Class Participation and classwork: 20% Homework Assignments: 25% Major Project (Annotated Bibliography): 25% Final Exam: 30% Laptop Please bring a laptop to each class if you have one. If you do not have a laptop, consult the instructor. A tablet should be fine for most of what we will do in class, but I would recommend something larger than a phone. Attendance and Promptness: Attendance is highly encouraged. Since this is a one credit course and many assignments and activities will be explained during class time, it is important to attend each class meeting. Also, part of your grade is based on classwork. In addition, it is expected you will be ready for class at the scheduled time and we will start class on time. This policy avoids the problem of having people wander in late and not being able to pick up the discussion. Homework Assignments: There will be homework assignments given most weeks. Homework may be handed out, announced in class, or posted on Goucher Learn. Major Project: Annotated Bibliography The final project will be to create an annotated bibliography covering either -The work of a particular chemist working in academia -A specific research topic 3 -A specific molecule, or class of molecules (including drugs) You may choose a topic from any area of chemistry – one of the purposes of this course is to be sub-discipline independent. My goal is for you to find out what is going on in the field in an area of chemistry that interests you. If you choose an area of chemistry that I am not familiar with, I may solicit the advice of faculty members in that area when evaluating your assignment. Specifically, an annotated bibliography is a list of references (with full citation information), and a summary (in your own words – not the published abstract) of what that paper is about. This would be the first step towards writing a review article about a particular topic. I would like your bibliography to contain a minimum of 20 references from the primary or secondary literature. If you come across a paper that you would like to look over, but we do not subscribe to that journal, let me know – in many cases I can get access through Johns Hopkins. At least four of your references should come from the past three years, and at least 12 of your 20 references should be from the primary literature. This project will be due on Tuesday April 14 (I think we are all better off if it is not too close to the end of the semester). Learning Objectives By the end of this course, you should 1. Understand the structure of the scientific literature in order to interpret and evaluate published results, and follow a logical path of inquiry. a. Describe the structure of the chemical literature in order to understand how the results in a particular paper fit into the published scientific record b. Compare qualities of primary/secondary/tertiary resources in order to distinguish the type and purpose of research/information found in each resource. c. Describe reasons for citing the literature in one's own writing in order to develop conventional research and publication habits. d. Interpret citations to the literature in order to follow the citation back to the original source. e. Create citations to the literature using appropriate formatting and standard abbreviations in order to present citations in a consistent manner. f. Interpret journal abbreviations in order to find the original publication. g. Describe indexing/abstracting concepts (such as controlled vocabulary, unique identifier like CAS #, etc.) in order to understand the content and organization of a database h. Describe the purpose of different types of journal publications in order to understand different venues for reporting or describing research. i. Describe the purpose of different types of journal articles in order to understand different venues for reporting or describing research. j. Describe the purpose and parts of patents in order to relate intellectual property to chemical research. 4 k. Describe the purpose and implications of citation counts in order to illustrate one method of measuring scholarly impact. l. Compare methods of measuring the scholarly impact of publications/research in order to evaluate the potential influence or importance of information. 2. Develop search strategies, including using unique features of the chemical literature, in order to most efficiently obtain needed information related to publications. a. Perform appropriate search strategies within databases (author, topic, numeric, structure, etc.) in order to fulfill a particular information need. b. Perform appropriate search strategies for research articles in order to collect current and/or historical information on a particular topic. c. Perform appropriate search strategies for review articles in order to collect background information on a particular topic. d. Perform appropriate search strategies within handbooks, encyclopedias, treatises, and other reference works in order to collect background information on a particular topic. e. Perform appropriate search strategies for patents in order to identify intellectual property related to a particular topic, person, or organization. f. Use appropriate database tools to perform citation searches in order to gather information on the potential scholarly impact of a publication. g. Use appropriate database tools to analyze and refine literature searches (by topic, author, year, document type, language, etc.) in order to limit to more desired search results. h. Use appropriate database tools to analyze and refine substance/reaction searches (by structure, yield, steps, classification, etc.) in order to limit to more desired search results. 3. Develop search strategies, including using unique features of the chemical literature, in order to most efficiently obtain needed information related to data. a. Locate physical and chemical properties in secondary/tertiary sources in order to identify commonly accepted data on compounds. b. Locate physical and chemical properties in the primary literature in order to identify experimental values for lesser studied compounds. c. Locate syntheses for compounds in order to determine possible outcomes for particular reactants/reagents/catalysts and/or for synthesizing desired compounds. d. Locate spectra and spectral data in the literature in order to identify data for lesser studied compounds. e. Locate crystallographic data in order to identify data for known crystal structures. 4. Understand the scientific publication process (both formal and informal), especially as it relates to issues involving ethics and accountability, in order to be well informed managers, producers and consumers of information. a. Explain the general nature of the peer review process b. Understand what Open Access publication is c. Explain issues related to intellectual property (especially copyright) and publication 5 d. Explain issues related to “author’s rights” and publication e. Use RefWorks to manage citations and documents in order to incorporate the use of bibliographic management software into the research process. Order of Topics: Topic 1: Introduction. Why this course? ; Structure of Chemical Information Topic 2: Primary Literature Overview; Types of Journals ; Types of Articles Topic 3: Citations Why and How? Using RefWorks citation manager Topic 4: Secondary/Tertiary Literature. Review Articles, Compiled Data, Handbooks, Encyclopedias, “Comprehensive” works, Reactions, Syntheses Topic 5: Abstracting and Indexing resources: Chemical Abstracts/SciFinder, PubMed, PubChem Topic 6: Formulating an Effective Search Strategy: Searching by text, structure, and citations Topic 7: Patents Topic 8: Current Events. What kind of papers do we find in a current journal, and how do we go about reading

Load more