Teaching chemical information retrieval 26 May 2015

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WEBINAR:

TEACHING CHEMICAL

INFORMATION RETRIEVAL

26 MAY, 2015

Damon RidleyJudith Currano

Why I became interested in chemical information retrieval

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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”

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1990s: The Greatest Breakthrough for Chemistry in the last 20 years

Primary Literature

Secondary Literature

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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.

We invited you to indicate topics to discuss …

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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?

1. Does chemical information need to be taught? => Engaging Staff and Students

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1. Engaging Staff and Students

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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

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1b. Arguably the chemical literature is the largest and most commercialised literature of all


• 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)

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1c. Course Competencies

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1d. The Full Text MisconceptionAsk the question: “If this was a particularly relevant article to our work, how would we

find it?”


The two major commercial products that extract the most information from primary

articles are:

Reaxys and SciFinder

There is a big difference between what you read and what you search

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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!

2. Who should teach what course? Faculty or Library staff? => Dedicated/Integrted Courses

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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

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• 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

3. Teaching Databases (Library)3a. Judith’s Principles

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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• Substance

s• 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.

3. Teaching Databases (Library)3b. Buying and teaching databases are intimately linked

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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

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3c. Buying/Teaching Databasesi. 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

What content is added

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3c. Buying/Teaching Databasesii. New content added in records

Controlled VocabularyIndex Headings/Index Keywords

• May help with search precision/comprehension, but how can

we use them?

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IntellectuallyAlgorithmically

3c. Buying/Teaching Databasesiii. 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

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SciFinder: Analyze, Refine, Categorize (“Precision Tools”,

SciPlanner)

Reaxys: Filter by: Analysis View (Synthesize, Synthesis

Planner)

Scopus: Analyze Search Results

3c. Buying/Teaching Databasesv. Post-processing tools

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Judith:“Teach Relevant,

Transferrable Skills, and Use Resources to Demonstrate Those

Skills”

4. Teaching search skills or teaching solutions? (Library)


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5. Specialised Searches (Library/Faculty)5a. Substance Searches


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MAYBE … …but in many cases MAYBE NOT


• 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

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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

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Search Google: CAS Registry Number for topaz


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5. Specialised Searches (Library/Faculty)5b. Substructure Searches

Teaching Students to Think… Like a Database!

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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.

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OK, this result makes sense

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The template overlaps this substance in an expected way.

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I have no idea why I retrieved this substance.

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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!

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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 query4. Review your results to see if they are relevant5. Refine your query or construct a new query and combine hit

sets with the original query for greater precision


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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?

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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 …

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Wittig Reaction – Ask Reaxys

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Teaching chemical information retrieval 26 May 2015