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Proposed library instruction for chemical biology and
synthetic chemistry
by Jeffery Loo, jeff@jeffloo.com
1 – Components of a library program for chemical
biology and synthetic chemistry
Characteristic of chemical biology
Competency area
Integrates traditional disciplines
Core chemical information literacy skills
Interdisciplinary
Interdisciplinary learning and
knowledge
Data intensive
Data transformation
 Data retrieval
 Data analysis
Computationally intensive
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Diversity oriented
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Structurally and visually oriented
Digital research and scholarship
 eScience management
 Computer assisted techniques
for design, screening and
experimentation
 Visualization
New research and dissemination
models
Scholarship and research support
 Scholarly communications
 Funding
 Research collaborations
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2 – Core competencies and skill sets
2.1 – Core chemical information literacy skills
Understanding scientific information and using the chemistry library
 Understand the nature of scientific communication: types of resources and
their purpose, evaluation of research quality, peer review process
 Use primary, secondary, and tertiary resources, including databases,
protocols, reference sources, background sources (e.g., dictionaries,
encyclopedia, textbooks)
 Use library resources and reference services
Search for physical and chemical properties
 Use resources such as:
o NIST Chemistry WebBook
o CRC Handbook of Chemistry and Physics
o Beilstein and Gmelin
o SciFinder Scholar / Chemical abstracts
Search for spectra
 Use resources such as:
o Sadtler spectra collections
o Aldrich Library of spectra
o NIST Chemistry WebBook
Search for safety information
 Use resources such as:
o Material Safety Data Sheets (MSDS)
o CRC Handbook Of Laboratory Safety
Search for chemical literature
 Search the chemical literature – particularly by subject, name, chemical
classification systems (e.g., CAS – RN, chemical nomenclature) – using
resources such as:
o SciFinder Scholar / Chemical Abstracts
o Web of Science / Science Citation Index
 Find background sources, such as:
o Chemical Reviews [American Chemical Society journal]
o Annual Reviews in Biochemistry
o Encyclopedias
 Search patents
 Search with Boolean operators and controlled vocabularies
Search for crystallography and structural data
 Use resources such as CCDC’s Cambridge Structural Database
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Based on: Craig, Cory; Maddux, Linda, Eds. Information Competencies for
Chemistry Undergraduates: the elements of information literacy, January 2007.
Special Libraries Association, Chemistry Division, Ad Hoc Committee on
Information Literacy. [http://units.sla.org/division/dche/il/cheminfolit.pdf]
2.2 – Interdisciplinary learning and knowledge
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Identify key reference sources in biology, chemistry, chemical engineering,
molecular biology, bioinformatics, cheminformatics, computational science,
software and automation engineering
o Sample resources: NCBI Entrez, PubMed, BIOSIS
Aggregate, manipulate and mashup content from around the web: web
feeds, web pages, RSS, newsgroups, discussion lists, blogs, pipes
Use wikis and blogs to share knowledge with diverse team members
Identify interdisciplinary resources such as:
o PubChem
o ChemBank
Select appropriate chemical and life science information resources and
databases to search
Select resources for self-directed learning: textbooks, review articles,
guides
Use current awareness alerting services, such as:
o Current Contents Connect
o Faculty of 1000
o Database email function for latest content
Use tools to organize and identify trends in diverse fields, such as:
o Mendeley
o NCBI Entrez
2.3 – Data transformation
2.3.1 – Data retrieval
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Generate search queries in a variety of chemical structure representations:
InCHi, MOL file, SMILES, nomenclature, CAS RN
Search by drawn structure
Conduct structural and activity similarity searching
Search for molecular probes, bioactivity and protocols
Download datasets in a number of different formats, such as XML, MOL
file, etc.
Search cheminformatics and bioinformatics tools, such as:
o PubChem
o Chembank
o NCBI Entrez
Awareness of database suppliers such as: Daylight, ACD Labs, CCDC,
Bielstein
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2.3.2 – Data analysis
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Transform data into different file formats for computer processing
Conduct clustering and similarity analyses of small molecule structures
and their activity in biological assays with applications such as:
o http://www.cellprofiler.org/
Identify trends and patterns in a personal collection of research papers
with software such as:
o Zotero
o Mendeley
Identify software to conduct data analyses
Use data mining tools that identify linkages and patterns between data
2.4 – Digital research and scholarship
2.4.1 – eScience management
Understand and complete tasks related to the following data governance issues:
 Long term storage in appropriate data formats with metadata
 Transformation of data sets
 Data storage in repositories
 Data preservation
 Data publishing
Develop cyberinfrastructure for collaborative, data rich, and computing intensive
research and discovery
 Use informatics tools for workflow management, data integration and
collaboration, such as wikis, blogs, repositories, lab informatics systems
 Understand data sharing policies, such as NIH and NSF data sharing
policy
 Understand how grid computing works
2.4.2 – Computer assisted techniques for design, screening and
experimentation
Overview: Use tools for small molecule discovery, synthesis design, synthesis
protocols and techniques, and optimization across the disciplines of medicinal
chemistry, combinatorial chemistry, organic synthesis, and chemical and
automation engineering
Conduct synthesis design
 Search for syntheses and reactions by reactant, product, synthetic
pathways
 Identify reactants for purchase
 Screen datasets for potential drugs, ligands and probes
 Design diversity-oriented synthesis pathways
 Search for structurally related compounds
 Use synthesis design resources such as:
http://bit.ly/berk21
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Beilstein
Gmelin
SciFinder Scholar / Chemical Abstracts
Organic Syntheses
Bioactives Cookbook (Synthetic Protocols)
MOS (Methods in Organic Synthesis) Online
Organic Syntheses Online
Science of Synthesis
Design combinatorial libraries
 Identify resources for combinatorial techniques and protocols
 Develop virtual libraries
 Design combinatorial libraries through pharmacophore identification and
finding small molecules that are similar in terms of structure and bioactivity
Conduct virtual screening and docking experiments
 Use computer-assisted services for design of bioactive compounds
 Screen compounds for match to pharmacophores
 Use analytic tools for identifying structure-activity relationships
2.4.3 – Visualization
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Identify and use molecular visualization, simulation and modeling tools
such as:
o Cn3D
o PC3D viewer of small molecules
2.5 – Scholarship and research support
Practice methods of scholarly communication
 Identify publications for manuscript submission
 Write scientific papers and technical reports
 Prepare presentation papers and posters
 Use citation management tools
 Use digital publishing tools: blogs, wiki, online publishing systems
 Understand the principles of open access and open data
 Using style guides, such as ACS Style guide
Identify grant funding and research support resources
Understand research ethics practices
 Understand ethical principles, such as:
o ACS Ethical Guidelines
 Understand plagiarism and how to prevent it
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2.6 – Core chemical biology information literacy skills
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Search and download chemical, bioactivity, bioassay, and biological data
for analysis in different applications.
Visualize the data through heatmaps and clustering by structure and
bioactivity in order to facilitate structure-activity analysis
For a particular small molecule X, find similar structures in order to predict
X’s bioactivity
Quickly visualize bioassay test results for multiple molecules with tools
such as heatmaps
For screening and follow-up chemistry, retrieve molecules tested in a
particular bioassay
After retrieving small molecules tested in a bioassay, query and filter
compounds according to activity levels or physical and chemical
properties
Determine the activity of small molecules to influence biological pathways
and processes
For a small molecule, identify the different bioactivity response patterns
For a known biological function, find structurally related small molecules
that may perturb it
(based on ChemBank functionalities, http://chembank.broadinstitute.org)
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3 – Instructional methods
Factors to address in instruction
Audience
Graduate
class
Setting
Motivation
Classroom
Educational Research
Main campus
Individual
student
Department
Off main
campusLBNL
Educational Lecture
Problem
solving
Curiosity
Laboratory
Video
Chemical
biology library
guide
Gain
knowledge
and
awareness
Workshop
Curriculumintegrated
instruction
Self-directed
Instructional
Time-strapped wiki and web
pages
Library
adverse
Searchable
learning
objects with
case
scenarios and
solutions
One-on-one
consultation
Self-directed
tutorials
Departmental
and library
orientation
Blog - tip of
the week
http://bit.ly/berk21
Goal
Develop skill
Virtual
In-person /
reference
desk
Instructional
method and
technology
Solve a
problem
Acquire
information,
resource or
data
Find answer
to question
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Instructional scenarios
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Curriculum-integrated program for classroom instruction
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Remote, self-directed and visual instruction that is problem-based
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Embedded librarian and reference services as instructional opportunities
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Collaborative training
Targets
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Needs assessment
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Instructional methods
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Content
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Evaluation
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