Judith Currano and Professor Damon Ridley debated key chemistry information retrieval related topics, such as :
• What you need to teach, should there be dedicated courses or course integrated instruction for example?
• Is chemical information retrieval something that can be self-taught?
• How much time is needed to teach general search strategies?
• Should teaching be more problem based?
2. Why I became interested in chemical information retrieval
2
1983
1. Electronic storage of chemical
information was the future of
the “chemistry library”
2. There were exciting challenges
to understand
• Indexing of documents
• Indexing of substances
By 1985 …
There is only so much chemistry you
can teach in lectures
3. “If I cannot teach ‘all of
chemistry’, then I’d better
include in my courses something
about how to search the
literature”
3. 3
1990s: The Greatest Breakthrough for Chemistry in the last 20 years
Primary
Literature
Secondary
Literature
4. 4
Teaching Chemical Information Retrieval
The first thing …
“ the chemical literature has a specific
organization and specialized entry points, and
that, although it is possible to find some
information without learning to use them, one is
much more efficient and effective if one spends a
little bit of time learning ‘the rules.’ ”
Reproduced with permission from Currano, Judith N. “Teaching chemical information for the
future: The more things change, the more they stay the same.” The Future of the History of
Chemical Information, McEwen, L. R.; Buntrock, R. E. Eds. ACS Symposium Series v. 1167.
Washington, DC: American Chemical Society, 2014. Copyright 2014 American Chemical Society.
5. We invited you to indicate topics to discuss …
5
1. Does chemical information retrieval need to be taught?
=> Engaging staff and students.
2. Who should teach what course? Faculty or Library staff?
=> Dedicated/Integrated courses?
3. Teaching about databases?
4. Teaching search skills or teaching solutions?
5. Teaching substructure (and related) searching?
6. 1. Does chemical information need to be taught?
=> Engaging Staff and Students
6
7. 1. Engaging Staff and Students
7
1a. The retrieval of chemical information is more complex than the
retrieval of information in any other subject
COMMON TO ALL SUBJECTS
• Searching bibliographic information (authors, institutions, journal titles …)
• Searching citations
• Searching topics
• Issues include:
• Synonyms, truncation (L- and R-), proximity, Boolean, index terms and
index hierarchies, single terms, phrases
• Auto-truncation, implied proximity
• Intellectually/Algorithmically controlled searches
• Understanding the search engine and its defaults
• Plain text and special text
• Greek characters, superscripts, subscripts
GABAA => GABAA or GABA A?
UNIQUE TO CHEMISTRY – and all its allied fields
• Searching substances, reactions, properties
• Numerous issues with database building and searching
OTHER FIELDS
• Technical/engineering drawings
• Circuit diagrams
• Mathematical equations
8. 8
1b. Arguably the chemical literature is the largest and most
commercialised literature of all
1. Engaging Staff and Students
• The chemical literature provides a lot of value to its customers
• To the companies who use it
• To the students who rely on information for their research degrees …
…who will become the future chemists in industry and in academia
• It costs a lot of money to:
• Produce high quality articles/journals (open-access or subscription-
based)
• Produce databases, especially for substances, reactions, and
properties
• Provide services to customers (24/7 access, data usage figures,
training materials, repositories)
10. 10
1d. The Full Text Misconception
Ask the question: “If this was a particularly relevant article to our work, how would we find it?”
1. Engaging Staff and Students
The two major commercial products that extract
the most information from primary articles are:
Reaxys and SciFinder
11. There is a big difference between what you read and what you search
11
The Primary Literature is READ
The Secondary Literature is SEARCHED
1d. The Full Text Misconception
• We read:
• A single document
It does not matter what terms the authors used.
We have the document!
• We search:
• Millions of documents
We do not know what terms the authors used
We have to add a lot of terms to cover
all the options, then more synonyms => more records
We have a problem!
12. 2. Who should teach what course? Faculty or Library staff?
=> Dedicated/Integrted Courses
12
Other difficult question!
• My feeling is that teaching is best done by the specialists in the subject
• The collection and dissemination of Chemical Information is the responsibility of
the library and of the teaching faculties
• Areas for which the library is primarily responsible include:
• Researching the different resources
• Advising Faculty of alternatives, and of developments
• Managing acquisition budgets
• Negotiating with suppliers (either through the institution or through consortia
arrangements)
• Teaching dedicated courses or classes to develop skills to a basic level…
…from which more advanced, specialized and research-related instruction may easily be
developed by Faculty
• Understanding required information competencies for chemistry graduates, and ensuring that
the library provides the resources required
• Updating information on library websites
• e.g., new releases of, and developments in, information retrieval resources
13. 13
• Areas for which Faculty is primarily responsible include:
• Ensuring that courses include training in information retrieval to
meet professional standards or mandates
• Providing their graduates with the levels of information literacy
required to meet their immediate postgraduate research needs
and their future professional needs
2. Who should teach what course? Faculty? Library staff?
The roles of Faculty and the Library?
• Teaching specialized skills in chemical information retrieval that
relate to knowledge of chemical topics and fields such as the
retrieval of substance, reaction, property and health & safety
information
• In most cases teaching these specialized skills is best done through integration
of instruction on chemical information issues into relevant parts of lecture,
tutorial or laboratory coursework
14. 3. Teaching Databases (Library)
3a. Judith’s Principles
14
Principle 1:
If it is not there, you cannot find it. If it is there, you need to
know what to call it.
Principle 2:
Information systems take you literally …
Except when they don’t … And even then,
they do!
Principle 3:
If you want to use a source effectively, you need to understand its
scope and organization.
Principle 5:
To choose a source effectively, you need
to understand the information
landscape.
Principle 4:
All information sources are not created equal.
Different:
• Keywords
• Substances
• Reactions
• Properties
Currano, Judith N. “Teaching chemical information for the future: The more things change, the more they stay the same.” The Future of the History of Chemical Information, McEwen, L.
R.; Buntrock, R. E. Eds. ACS Symposium Series v. 1167. Washington, DC: American Chemical Society, 2014. Copyright 2014 American Chemical Society.
15. 3. Teaching Databases (Library)
3b. Buying and teaching databases are intimately linked
15
When Buying
Databases we should:
When Teaching
Databases we should:
subscribe to a
database only if it
adds clear value to
our primary collection
teach the limitations
of searching the
primary literature
Buying and Teaching Databases are Intimately Linked
understand the unique
features and functions
of the database
teach the unique
features and functions
of the database
16. 16
3c. Buying/Teaching Databases
i. The Value that Databases may Add
Databases add value through
grouping together all
primary documents in the
discipline
The breadth and depth of the
grouping (journal articles,
patents) is of importance
(“the numbers game”) …
… but far more
important is …
… what is extracted
from these articles
… what additional
content is added
… how it is searched
… what (answer)
analysis tools does it
have
17. What content is added
17
3c. Buying/Teaching Databases
ii. New content added in records
Controlled Vocabulary
Index Headings/Index Keywords
• May help with search
precision/comprehension, but how can we
use them?
18. 18
IntellectuallyAlgorithmically
3c. Buying/Teaching Databases
iii. How it is searched
• Synonyms, truncation (L- and R-),
proximity, Boolean, index terms and index
hierarchies, single terms, phrases
• Auto-truncation
• Auto-suggest
• Understanding the
search engine and its defaults
• Plain text and special text
• Greek characters, superscripts,
subscripts –
GABAA => GABAA or GABA A?
Ask Reaxys
“Google”?
SciFinder: Explore
by Research Topic
20. 20
Judith:
“Teach Relevant,
Transferrable Skills, and
Use Resources to
Demonstrate Those
Skills”
4. Teaching search skills or teaching solutions? (Library)
Reproduced with permission from Currano, Judith N. “Teaching chemical information for the future: The more things change, the more they stay the
same.” The Future of the History of Chemical Information, McEwen, L. R.; Buntrock, R. E. Eds. ACS Symposium Series v. 1167. Washington, DC:
American Chemical Society, 2014. Copyright 2014 American Chemical Society.
21. 21
5. Specialised Searches (Library/Faculty)
5a. Substance Searches
Reproduced with permission from Currano, Judith N. “Teaching chemical information for the future: The more things change, the more they stay the
same.” The Future of the History of Chemical Information, McEwen, L. R.; Buntrock, R. E. Eds. ACS Symposium Series v. 1167. Washington, DC:
American Chemical Society, 2014. Copyright 2014 American Chemical Society.
22. 22
MAYBE …
…but in many cases MAYBE NOT
5. Specialised Searches (Library/Faculty)
5a. Substance Searches
• CAS Registry Numbers are the systematic indexing entries for substances in CAS databases...
…but other databases have different ways to systematically index substances
• Some databases also list CAS Registry Numbers…
… but usually the CAS RNs they list will be quite different from the CAS RNs listed in records from
the same original document
23. 23
5. Specialised Searches (Library/Faculty)
5a. Substance Searches
CAS Registry Numbers are relatively:
• Easy to find when substances have specific structure, formula, or
a simple name
• Difficult to find (and you may have to use a number of them) in
“more complex substances” such as substances:
• that do not have specific structures or formulas
• that, in the literature, may be variously described …
… such as topaz
24. 24
Search Google: CAS Registry Number for topaz
5. Specialised Searches (Library/Faculty)
5a. Substance Searches
25. 25
5. Specialised Searches (Library/Faculty)
5b. Substructure Searches
Teaching Students to Think… Like a Database!
Preconception: This is acetone!
In a substructure search hydrogen
atoms are not assumed. Think of it
as a template drawn on a piece of
glass and superimposed over
substances in the database.
OK, this result makes sense
The template overlaps this
substance in an expected way.
I have no idea why I retrieved
this substance.
The template actually does overlap
this substance, but the topology
may not be what you wanted!
Questions to encourage your students to ask
1. Questions about atoms
A. Can a site be substituted?
B. If so, how
2. Questions about bonds
A. Does stereochemistry matter?
B. Must the bond orders be as drawn?
C. Are there restrictions on topology?
These questions should be asked for everything
drawn, as well as those things not drawn!
26. 26
Think about how the database will treat your query
1. Choose the database that contains the content that you want to find
2. Construct the query using the tools available in that database
What are the defaults for free sites/substitution?
What are the defaults for topology?
What kinds of predefined variables and groups are available?
Will the system allow you to build your own R-group (if needed)
How will the system allow you to control substituents that are
not drawn?
3. Build and run your query
4. Review your results to see if they are relevant
5. Refine your query or construct a new query and combine hit sets
with the original query for greater precision
5. Specialised Searches (Library/Faculty)
5b. Substructure Searches
27. 27
5. Specialised Searches (Library/Faculty)
5b. Substructure Searches
Undergraduate students
•When to teach: Upper-level lecture and laboratory classes
•What to teach
•Substructure theory
•Basics: free sites vs unsubstituted sites, bond order/topology variability
•When to use substructure searching
Graduate students, MS scientists, and PhD scientists
•When to teach
•Organic synthesis classes
•Information courses and library orientation sessions
•Database-specific and general information skills workshops
•What to teach
•Substructure theory and basics
•Setting bond order, and topology
•R-groups and advanced skills (ex. repeating units, variable points of attachment)
•Applications to reaction searching
When should substructure searching be taught, and which skills are
important at each level?
28. 28
Teaching the searching of:
• Reactions
• Properties
When you log off this session you will be
asked if you would like further information
• Please check the boxes of interest
If you would like further information …
29. For further questions or
comments -
Send email to:
bdtraining@elsevier.com
Contact Us
29
