Substance searching in Reaxys - Webinar - 24 March 2015

WEBINAR:SEARCHING FOR

SUBSTANCES IN REAXYS

24 MARCH, 2015

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Damon Ridley

Overview of searching for substances in Reaxys

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1. Search

by

Substance-identifying

terms (in substance

records)

2. Search

by

Words (in bibliographic

records)

DATABASE PRODUCER:

ADDED VALUE

A RECORD IN REAXYS

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AUTHORS

Searched and displayed in

Substance Records

Searched and displayed in

Bibliographic Records

Classes of Substances

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CLASSIC ORGANICS

CLASSIC INORGANICS NUCLEIC ACIDS & PROTEINS

POLYMERS

ORGANOMETALLICS

COORDINATION COMPOUNDS

Found in KEYWORDS in REAXYS BIBLIOGRAPHIC RECORDS

CERAMICS

ALLOYS & METALS

Found in REAXYS SUBSTANCE RECORDS … and …

Search Substances Search Literature

However, for more complex substances

• systematic names can get very complicated

• different indexers use different index terms

In simple cases, systematic names and indexing are easy to follow and easy to use

• 4-chloro-2-butanol

• p-nitroaniline

A personal opinion about naming and indexing of substances

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For > 100 years chemical

scientists and indexers have sought ways to systematically

name and index substances

By structure and by simple name (morphine)

How do scientists refer to, and like to search for, morphine?

That is, most polymers are very difficult to describe in systematic terms (name, structure, formula, shape, molecular weight)

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However, for many substances “indexing” requires a number of “rules”

• which in turn may be very complex &

• which may not tell the “whole story”


INDEXING OF POLYMERS AS “SUBSTANCES”

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• “Issues” arise from inter alia:

• The “shape” of the polymer

• The organisation of monomers in the polymer backbone

• Post-treated polymers (i.e., polymers to which additional groups are later added)

• Polymer blends (how are blends/mixtures of polymers indexed?)

• The conditions under which polymers are formed (e.g., different monomer ratios, different reaction conditions such as temperatures or catalysts, give different “substances”)

The shape of the polymer backboneThe organisation of monomers in the polymer backbone

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• Very few scientists know how complex polymers are indexed

• For example, ask any polymer scientist (or polymer indexer) how the product from

the following reaction would be (systematically) indexed!

Index this product!


We need different systems to “index” different classes of substances

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Easy to describe by structure and/or formula? Yes No

Easy to describe by common chemical name? Yes (if: morphine) No

Easy to index as a substance?

=> registry number

Yes (the structure defines

the substance)No

Easy to describe in text terms (excluding common name)? No Yes

We need different ways to search for polymers, and the same applies to ceramics, ceramers, and indeed to the many classes of substances of most interest to scientists in the materials sciences, in biochemistry, in molecular biology …

There is an enormous amount of information on such “substances” in Reaxys(we just search in a different way)

Reaxys has Index Keywords to help us

search for these “substances”

Polymers, ceramics, materials and proteins/nucleic acids may be most effectively searched by WORDS

Indexing of “SUBSTANCES” in Reaxys: WORDS

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CLASSIC ORGANICS


POLYMERS

ORGANOMETALLICS



CERAMICS

ALLOYS & METALS


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Searching for Substances in Substance Records

(commonly used fields)

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Click Substances to search in the Substance Database

Note the Search Context

Ask Reaxys when you have a simple name for the

substance

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Search by Structure when a clearly defined structure (or

part-structure) is the best way to find substances that meet

your needs

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Try ligand search fields for coordination compounds

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Search for formulas or part-formulas

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Search for chemical names or part-names

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Search for alloys, ceramics and related substances

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Search Querylets

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Search Querylets

Enter term(s)

But how do we know what to enter?

Numeric Field

Text Field

Auto-truncation

Just start typing or

click

Lookup

Auto-suggest

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Ask Reaxys when you have a simple name for the substance1

Ask Reaxys searches both options for us

WORDS in Bibliographic Records

Substance Records

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SUBSTANCE RECORD

BIBLIOGRAPHIC RECORD

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Ask Reaxys

Enter

“Simple Names”

Substances

• Usually “specific” substance searched will be at the top of the list

• Will retrieve other substances (stereoisomers, salts, and some substances related by name)

Show Query => Ask Reaxys – Analysis

References

• Name of substance is searched in Title, Abstract or Keyword Fields

Exact Structure

Part-Structure

Similarity

Include:• Tautomers• Markush

Exclude:• Salts• Mixtures• Isotopes• Charges• Radicals

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Structure and Sub-structure Search2

Structure Query Editor

used to:

• Lock atoms/rings

• Specify isotopes, charges, radicals

• Repeat groups

• Block substitution

and so forth

Keep Queries Simple

For further information: [email protected]

mailto:[email protected]

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Ligand Search Fields for Coordination Compounds3

• The variety and complexity of the structures of coordination compounds present many challenges for the author, the database developer, and for the searcher

• Even such an important and common ligand such as ethylenediamine tetraacetic acid (EDTA) presents problems in that the 2 nitrogens and 4 oxygens in EDTA may coordinate to a central metal or to two metals, or some of the coordination sites may be replaced by other ligands such as water

• To cover possibilities of interest in a single structure search may be challenging

• Reaxys offers another solution through the ability to search for ligands through formulas

The metal is CoAnother ligand is

attached through N

2

2

Another ligand is attached through C

3

3

The main ligand has 2 N’s and 2 O’s

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1

There are three parts of a ligand formula

• The metal

• The ligands attached to the metal

• Each ligand is enclosed in { }

• The coordinating atoms, grouped in codes, e.g.

Numbers are assigned when >1

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Ligand Search Fields for Coordination Compounds3

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326 substances

3

170 substances

2

518 substances

4

259 substances

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Search for Formulas or Part-Formulas4

• We may enter the formula in the Molecular Formula Querylet …

• The Formula Builder allows us to build:

• Full or part formulas

• Formulas with groups (e.g., Transition Metals)

• Formulas with variable numbers of elements or groups

• Formulas that may include other elements

• The Formula Builder is particularly useful for finding:

• Substances that are related by formula rather than by structure or name

• Inorganics and organometallics

• Substances with non-standard formulas, e.g., radicals, carbocations and other intermediates

• Groups of substances with variable formulas

Example 1: Find calcium hydrides

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Example 2: Find transition metal halides with 2-4 transition metals

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Example 3: Find dilithio hydrocarbons

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Search for Names or Part-Names5

Example: Find nitrogen-containing organic radicals

Search for radicals by Part-Name

Search for radicals by Part-Formula

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5 Search for Names or Part-Names5

Provide search functions and scientists will use them creatively

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Search for Alloys, Ceramics and Related Substances6

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Search for Alloys, Ceramics and Related Substances6

Searching for substances in Substance Records

(commonly used fields)

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Click Substances to search in the Substance Database

Note the Search Context


substance

1



your needs

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3


4


5


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substance

1



your needs

2


3


4


5


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Ask Reaxys: morphine

Subs + Text answers

Ask Reaxys: cis-platin (Google)

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Numerous Search Functions

8 Different Structure Search Editors

[email protected]

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Search for substances with specific ligands

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Calcium hydrides

(Trm)2-4

halides

Di lithio hydrocarbons

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C, N – containing radicals

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Ti V alloys

Aluminium/Titanium Oxides

Ask Reaxys: titanium vanadium alloys

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mailto:[email protected]

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CLASSIC ORGANICS


POLYMERS

ORGANOMETALLICS



CERAMICS

ALLOYS

S

e

a

r

c

h

S

u

b

s

t

a

n

c

e

s


1 2


Searching for Substances in Bibliographic Records

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Search Querylets

Text Field

Auto-truncation

Enter term(s)

But how do we know what to enter?

Just start typing or

click

Lookup

Auto-suggest

in Substance Records

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HIMBACINE

Searching for Substances

Searching for Substances in Bibliographic Records:

Ask Reaxys

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Key points about Ask Reaxys

• Still being developed

• Enter a few (and simple) terms – nothing too complex

• No truncation or proximity allowed

• Singulars plurals not searched automatically


Citation Basic Index Querylet

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Citation Basic Index Querylet

Found in REAXYS SUBSTANCE RECORDS … and … Found in KEYWORDS in REAXYS BIBLIOGRAPHIC RECORDS

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Polymers: Ask Reaxys

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Polymers: Citation Basic Index Querylet

Start typing here

Highlight term(s) of interest

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Polymers: Citation Basic Index Querylet

Precision vs Comprehension

Different Fields

More/Fewer Terms

Truncation/No truncation

Filter by: Analysis View

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Enzymes: Citation Basic Index Querylet

APOBEC (apolipoprotein B mRNA editing enzyme)

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Difficult “Substances”: Citation Basic Index Querylet

STRANGE IONS – CH5+ STRANGE PARTICLES

ALUMINA ZIRCONIA CERAMICS GAMMA-AMINOBUTYRIC ACID RECEPTORS

Summary: Searching for “substances” that are “not simple”

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• Reaxys provides extensive and flexible keyword search functions which greatly assist

retrieve information on these classes of substances through:

• Ask Reaxys

• Citation Basic Index Querylet, e.g.:

• Auto-suggest text for single terms and phrases

• Automatic or user-driven truncation

• Proximity operators

• In general, Reaxys does not index a number of classes of substances by “Registry Number”

• (That is, they do not appear as separate substances in Reaxys Substance Records)

• The classes involved include:

• Instead, Reaxys “indexes” these classes of substances through Index Keywords in

Bibliographic Records

POLYMERSCERAMICS(Some) ALLOYS CERAMERS PROTEINSNUCLEIC ACIDS

Searching for Information on Substances

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STRUCTURES & PART-

STRUCTURESNAMES &

PART-NAMES

FORMULAS & PART-FORMULAS

LIGANDS

WORDS IN TITLES & ABSTRACTS

INDEX KEYWORDS

Provide search functions and

scientists will use them creatively

ORGANOMETALLICSCLASSIC INORGANICS

POLYMERS

ALLOYS

CERAMICS

NUCLEIC ACIDS


CLASSIC ORGANICS

PROTEINS

AUTO-TRUNCATION

AUTO-SUGGEST

POST-PROCESSING

Some Functions

Some Substance Classes

Some Search Types

Know your options …

… and TRY THEM!

Send email to: [email protected]

Further Information

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Substance searching in Reaxys - Webinar - 24 March 2015

Education

Transcript of Substance searching in Reaxys - Webinar - 24 March 2015