WEBINAR:SEARCHING FOR
SUBSTANCES IN REAXYS
24 MARCH, 2015
1
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”
A personal opinion about naming and indexing of substances
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!
A personal opinion about naming and indexing of substances
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
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 …
1 2
Search Substances Search Literature
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
1
Search by Structure when a clearly defined structure (or
part-structure) is the best way to find substances that meet
your needs
2
Try ligand search fields for coordination compounds
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Search for formulas or part-formulas
4
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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Ask Reaxys when you have a simple name for the substance1
SUBSTANCE RECORD
BIBLIOGRAPHIC RECORD
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Ask Reaxys when you have a simple name for the substance1
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]
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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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Search for Formulas or Part-Formulas4
Example 2: Find transition metal halides with 2-4 transition metals
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Search for Formulas or Part-Formulas4
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
Ask Reaxys when you have a simple name for the
substance
1
Search by Structure when a clearly defined structure (or
part-structure) is the best way to find substances that meet
your needs
2
Try ligand search fields for coordination compounds
3
Search for formulas or part-formulas
4
Search for chemical names or part-names
5
Search for alloys, ceramics and related substances
6
Ask Reaxys when you have a simple name for the
substance
1
Search by Structure when a clearly defined structure (or
part-structure) is the best way to find substances that meet
your needs
2
Try ligand search fields for coordination compounds
3
Search for formulas or part-formulas
4
Search for chemical names or part-names
5
Search for alloys, ceramics and related substances
6
Ask Reaxys: morphine
Subs + Text answers
Ask Reaxys: cis-platin (Google)
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Numerous Search Functions
8 Different Structure Search Editors
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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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CLASSIC ORGANICS
CLASSIC INORGANICS NUCLEIC ACIDS & PROTEINS
POLYMERS
ORGANOMETALLICS
COORDINATION COMPOUNDS
Found in KEYWORDS in REAXYS BIBLIOGRAPHIC RECORDS
CERAMICS
ALLOYS
S
e
a
r
c
h
S
u
b
s
t
a
n
c
e
s
Found in REAXYS SUBSTANCE RECORDS … and …
1 2
Search Substances Search Literature
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
Searching for Substances in Bibliographic Records:
Citation Basic Index Querylet
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Searching for Substances in Bibliographic Records:
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
COORDINATION COMPOUNDS
CLASSIC ORGANICS
PROTEINS
AUTO-TRUNCATION
AUTO-SUGGEST
POST-PROCESSING
Some Functions
Some Substance Classes
Some Search Types
Know your options …
… and TRY THEM!