From chemical
name to structure:
finding a noodle
in the haystack
Presented at
The CAS/IUPAC Conference on Chemical
Identifiers and XML for Chemistry,
July 1, 2002
“Haystacks - End of Summer”
Jonathan Brecher
Director, Software Development
CambridgeSoft Corporation
1890-91
Claude Monet
Names: The most common identifiers
“What is aspirin?”
O
O
H
O
Chemist says:
l
Non-chemist says:
– Headache medicine
– Bayer makes it
– Good for the heart
O
l
Both are right!
H
H
O
H
O
H
O
O
H
H
O
H
O
O
H
O
H
O
H
H
H
HO
O
H
O
O
H H
H
H
H
O
H
O
O
H
O
H
C
H
2
O
H
H
H
O
H
O
H
O
H
H
O
H
H
H
H
H H
O
O
H
H
O
O
HO
H
H
O
H
H
O
O
H
O
O
H
O
H
H
H
O
H
C
H
O
O
H
Names are substance identifiers,
not structure identifiers
“50 mg of glucose”
Don’t read too much into a name
l
Two true statements:
– Copper sulfate is a blue crystalline solid
– The CAS RN for copper sulfate is 7758-98-7
l
...combine to make one false one:
– CAS RN 7758-98-7 is a blue crystalline solid
l
TRUE
TRUE
FALSE!
Only the hydrated form is blue
(copper sulfate, pentahydrate
= CAS RN 7758-99-8)
http://www.chss.montclair.edu/~pererat/0000d.jpg
So why do we care?
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Sometimes names are the only identifier available
– Lots of existing data available in no other form
– “Better” identifiers available only from trained chemists
l
People like names!
The challenge:
When you have to interpret a name, how to best
extract as much information as possible from it?
Names aren’t always meaningful
Catalog Num
...
84289
...
12345
23456
34567
45678
56789
Product Name
Price
1-Eicosene
$50/25g
Enzyme
Enzyme
Enzyme
Enzyme
Enzyme
$100/g
$5/mg
$32/g
$70/g
$100/mg
Names aren’t always sensical
Catalog Num
...
84289
84289
...
12345
Product Name
Price
5-Aminosalicylic acid
-Aminosuberic acid
$100/100g
$150/50mg
5-Amino-2-sulfonic acid
$15/25g
Names aren’t always reasonable
O
2
HN
H
6
HN
HH
2 5S
O H
S
[(anilinocarbothioyl)amino](dioxo)phenyl-lambda6-sulfane
N-phenyl-N'-(phenylsulfonyl)thiourea
Names aren’t always reasonable, 2
N-butyl-N'-nitroguanidine
-
O2 +
NN H O
H+ 2 +
H
2
HN
HN
N
H
2-[(butylamino)(imino)methyl]-1-oxohydrazinium-1-olate
“Why can’t I find any information?”
“I've been trying to look for the structure (and CAS number) of
o,s diethyl methyl phosphonothlolate
I've looked on the free online databases as well as the CAS
substance index, but I could'nt find anything.”
-- posted to the CCL mailing list May 21, 2002
archaic (and redundant)
capitalization
o,s diethyl methyl phosphonothlolate
missing hyphen,
added space
missing locant
typo
Best approach for dealing with chemical names
l
Assume the name was intended to be accurate
– Recognize standard nomenclature systems
(IUPAC, CAS)
– Be flexible about minor typographical variations
(spaces, capitals)
– Don’t second-guess!
(benzyne and benzine aren’t necessarily typos for benzene)
l
If the name can’t be interpreted as provided,
then be a little more flexible
– But only if the original name couldn’t be interpreted!
– (Assumes a very accurate interpreter for names)
l
Don’t expect perfection
Many naming conventions
cupric
copper
copper(II)
copper(2+)
CuSO4
sulfate
sulphate
Other complications
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Capitalization
– copper sulfate, Copper sulfate, Copper Sulfate, COPPER SULFATE
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Spacing
– copper sulfate, coppersulfate
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Punctuation
– copper sulfate, “copper, sulfate”
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Parentheses
– copper(II) sulfate, copper[II] sulfate
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“Commentary”
– Copper sulfate, 99%
Copper sulfate searches on ChemFinder.com
Normalized names
Exact
70
12
11
8
8
7
7
7
7
6
5
5
4
4
4
4
4
4
3
3
3
3
3
3
2
2
2
2
2
2
2
2
2
copper sulfate
cupper sulfate
cupric sulfate
Cooper Sulfate
copper sulphate
copper (ii) sulfate
copper 2 sulfate
copper 2 sulphate
cuppersulfate
Kupfersulfat
Cooper Sulphate
copper(2) sulfate
*copper sulfate*
coper sulfate
copper sufate
copper sulfate*
coppersufate
cuprum sulfate
Copper (2) sulfate
copper(2)sulphate
coppersulphate
cuperic sulfate
cupric sulfate crystals
kopersulfaat
*coppersulfate*
cooper (ii) sulfate
cooper sulfat
copper sulate
copper sulphate crystals
copper suphate
copper(11) sulphate
Copper(2)Sulfate
copper(ii) sulfate
2
2
2
2
2
2
2
2
2
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
Structures from typos
Structures from names
Copper2Sulfate
coppersulfate
cuppersulfat
Cupric (II) sulfate
cupric sulphate
curpic sulfate
Kupfer(II)-Sulfat
sulfate copper
sulfate cupric
*copper(ii)sulphate*
*coppersulphate*
blue copper sulfate
capric sulphate
cobber*sulfat
cobbersulfat
cobbersulfate
Cooper (II) sulfate anhydrous
cooper+sulfate
coopper sulfate
coper(II) sulfate
copper sulfate
Copper (11) Sulfate
copper (11) sulphate
copper (2) sulphate
copper (2)sulfate
Copper (II) sulpate
copper (ii) sulphate
copper (ii)sulpahate
copper 11 sulfate
copper and sulfate
copper ll sulfate
COPPER SELFATE
Copper Silphate
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
copper siulphate
copper slate
copper slfate
copper solfate
copper suflate
copper sulfate crystal
copper sulfate crystals
copper sulfate II
Copper Sulfate Powder
copper sulfate structure
copper sulfate(4)
copper sulfate\
copper sulfated
copper sulfates
copper sulfatr
copper sulfaye
copper sulffate
copper sulfiate
copper sulfste
copper sulpahte
copper sulpate
copper sulphare
Copper sulphate 0.1M
copper sulphate II
Copper sulphate physical data
copper sulphate supplier
copper sulphate(VI)
copper sulphate*
copper sulphte
copper(2) sulphate
copper(20sulphate
copper(ii) sulphate
copper(II) sulphate(VI)
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
copper(ii)sulfate
copper(II)sulfste
copper+ sulphuric acid
copper+sulfate
copper+sulfuric acid
copper+sulphate
copper-2-sulphate
copper-sulphate crystals
copper2 sulfate
copper2sulphate
coppre sulfate
COPPSULPHATE
coprum sulfuricum
COPSULPHATE
cu2+sulfate
cubber(II)sulfate
cubbersulfate
cubric sulfate
cuperic sulphate
cupfersulphate
cupic sufate
cupic sulfate
cuppe sulphate
cupper (II) sulfate
cupper sulfure
cupper sulphate
cupperic sulfate
cuppersulphat
cuppersulphate
Cupric ( copper )Sulfate
Cupric su;fate
cupric sulfare
cupric sulfathe
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
cupric sulfhate
cupric(I)sulfate
cupric+sulfate
cupris sulfate
cuprisulfat
cuprit sulfate
cuprite sulfate
cuprium sulphate
cupro sulfate
curite sulfate
curpic sulphate
curpric sulfate
Dicopper sulfate
distilling Cuperous sulfate
EPA Registered Copper Sulfate
granular copper sulphate
hazards of copper sulphate
kobber(II)-sulfat
kopparsulfat
Kupfer(II)sulfat
kupric sulfate
sulfate coperate
sulfate cupic
sulfato cobre
sulfato cuprico
sulfato de cobre
sulfato de cobre 2
sulfuric coperate
Copper sulfate, hydrated
40
19
16
9
8
8
8
5
5
4
3
3
3
3
3
3
3
2
2
2
2
2
2
2
2
2
2
hydrated copper sulfate
copper sulfate hydrate
hydrated cupric sulfate
hydrated copper sulphate
copper 2 sulfate pentahydrate
copper sulfate pentahydrate
Copper(II) sulfate hydrate
copper sulfate solution
hydrous copper sulfate
cupric sulfate hydrate
copper (II) Sulfate hydrate
copper ii sulfate pentahydrate
copper sulfate dihydrate
copper sulfate heptahydrate
copper(2) sulfate pentahydrate
cupric sulfate penta hydrate
hydrated copper(II) sulfate
copper sulfate aqueous
copper sulfate pentahydride
copper sulfate penthydrate
Copper Sulfate Tetrahydrate
copper sulfate trihydrate
copper sulfate water
copper sulphate hydrate
copper sulphate penta hydrate
copper2 sulfate pentahydrate
cupric sulfate heptahydrate
2
2
2
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
cupric sulfate pentahydrate
hydrated copper (II) sulfate
hydrous cupric sulfate
"copper sulfate hydrate"
aqeous copper sulfate
aqueous copper(II)sulfate
cooper sulfate pentahyd
coper (2) sulfate pentahydrate
copper sulfate penahydrate
copper (2) sulfate hydrate
copper (II) sulfate dihydrate
copper (II) sulphate (hydrate)
copper 1 sulfate pentahydrate
copper I sulphate pentahydrate
copper II sulfate penahydrate
copper II sulfate petahydrate
copper II sulphate hydrate
copper pentasulfate
copper sufate pentahydrate
Copper Sulfate + 5 Water
copper sulfate 6hydrate
Copper Sulfate decahydrate
Copper Sulfate Di-hydrate
copper sulfate five hydride
copper sulfate hydrated
copper sulfate hydrous
Copper Sulfate nonahydrate
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
Copper Sulfate octahydrate
copper sulfate p*
copper sulfate penta hydrate
copper sulfate penta-hydrate
Copper Sulfate penta-water
Copper Sulfate Pentahidrate
copper sulfate pentahydattte
copper sulfate pentahydiate
copper sulfate pentahydrae
copper sulfate pentahydrous
copper sulfate pentahydryate
copper sulfate pentanhydride
Copper Sulfate Penthaidrate
Copper Sulfate Penthaidrate§
copper sulfate petahydrate
Copper Sulfate Tetra Hydrate
Copper Sulfate(aq)
copper sulfate(hydrous)
copper sulphare monohydrate
copper sulphate hdrate
copper sulphate heptahydrate
copper sulphate penta hydrated
copper sulphate penta hydrous
copper sulphate penta-hydrated
Copper sulphate pentahidrat
Copper Sulphate Pentahidrate
copper sulphate pentahydtrate
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
copper sulphate pentahyhdrate
copper sulphate pentra hyrdate
copper sulphate pentrahydrate
copper sulphate pentrahyrdate
copper sulphate septahydrate
copper sulphate solution
copper(2)sulfate pentahydrate
copper(I) sulfate pentahydrate
copper(II) sulfate dihydrate
copper(II) sulphate hydrate
Copper(II)Sulfate Decahydrate
copper(II)sulfate Monohydrate
copper2 sulphate pentahydrate
copperas heptahydrate
copperII sulfate penahydrate
copperIIsulfatepentahydrate
coppersulfate heptahydrate
coppersulfate+5H2O
coppersulfatepentahydrat
coppersulfteperwater
cuppric sulfate monohydrate
cupric pentasulfate
cupric sulfate dihydrate
cupric sulfate hydrated
cupric sulfate monohydrate
cupric sulfate pentahdrate
cupric sulfate pentahydrated
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
cupric sulfate pntahydrate
cupric sulfate quadrahydrate
cupric sulfate-5h20
cupric sulfatte pentahydrate
cupric sulphate pentahydride
cuproc sulfate pentahydrate
cuprous sulfate pentahydrate
hydated copper sulphate
hydrate copper sulfate
hydrate copper sulphide
hydrate copper(II) sulfate
hydrated Copper II Sulfate
hydrated copper(II) Sulphate
hydrated cupric sulphate
hydrated cuprous sulfate
hydratedcoppersulphate
hydrdated copper sulfate
hydrolyzed copper sulfate
Hydrous copper sulphate
Kupfersulfat-Pentahydrat
kupfersulfatepentahydrat
pentahidrate copper sulfate
pentahidrated copper sulfate
pentahidrated sulfate copper
Penthydrous Copper Sulfate
Other copper-and-sulfur searches
copper (I) sulfate
copper bisulfate
20
19
13
6
5
3
3
3
2
1
1
1
1
1
1
1
1
1
1
1
1
3
2
2
2
2
2
1
1
1
1
1
1
1
1
1
1
1
1
Copper (I) sulfate
Cuprous Sulfate
copper(I) sulfate
copper I sulfate
Copper (1) sulfate
copper(1) sulfate
copper(I) sulphate
copper(I)sulfate
cyprous sulfate
copper (1) sulfide
copper (I) and sulfate
copper (I) sulphate
copper 1 sulphate
copper I sulphate
copper l sulphate
COPPER SULFATEI
copper(1) sulphate
copper(I)\ sulphate
cuperous sulfate
Cupprous Sulfate
cupro(I)sulfate
Copper disulfate
COPPER sulfate basic
copper(I) hydrogen sulfite
copper(II) hydrogensulfate
CUPRIC SULFATE BASIC
cuprous bisulfate
copper bisulfate pentahydrate
copper bisulphate
COPPER HYDRAZIDE SULFATE
copper hydrogen sulfite
Copper hydrogensulfite
copper sulfate acidic
copper(I) hydrogen sulfate
COPPERsulfatebasic
cupric bisulfate
hydrogen copper sulphate
tribasic copper sulfate
Tribasic Copper Sulphate
copper sulfide
2
2
2
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
copper(III) sulfide
coppor sulfide
cuprous sulfide
"cupric sulfide"
cooper (II) sulfide
cooper 2 sulfide
cooper disulfide
cooper II sulfide
cooper sulfide
cooper(II)isulfide
cooper(II)sulfide
coopric sulfide
copersulfide
copper (I) sulfider
copper (ii) hydrogensulfide
copper di-sulfide
copper disulfide
copper hydrogensulfide
copper hydrogensulphide
copper hydrosulfide
copper sufide
Copper Sulfde
copper sulfide
Copper Sulfide Ore
copper sulfied
copper tetrasulfide
copper(2)sulfide
copper2 sulfide
copperic sulfide
coppersulfied
copperus sulfide
coppric sulfide
Kupfersulfid
copper sulfite
other
34
7
5
4
4
3
2
2
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
4
3
3
2
1
1
1
1
1
1
1
1
1
1
1
1
copper sulfite
cupric sulfite
copper (I) sulfite
COPPER(I) SULFITE
cuprous sulfite
Copper II sulfite
Copper(II) sulfite
Coppersulfit
Coper (I) sulfite
copper (1) sulfite
copper (II) sulfite
copper 1 sulfite
copper I sulfite
Copper II sufite
Copper II sufite pentahydrate
Copper II sulfite pentahydrate
copper sulphite
Copper(I)Sulfite
Copper(II)sulfite
copper* sulfite
copperI1 sulfite
coppersulfite
curpric sulfite
sulfite cuprous
copper persulfate
copper III sulfate
copper sulfer
copper sulfur
copper (lll) sulfate
copper + sulfur
copper 3 sulfate
COPPER PYROSULFATE
copper sulfate anhydride
copper sulfon
copper sulfonate
Copper(III) Sulfate
cuppersulfur
cupric persulfate
cuprous persulfate
cuprous sulfonate
Second-guessing can be embarrassing
Case study: Google
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If possible, answer the question that was asked
Case study: Google
l
If not possible to answer the direct question, use
some intelligence to try to figure it out
Case study: Google
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Ideally, look for “unusual” terms and try to offer
alternatives – but always answer the question
asked, regardless
-
May be impossible for chemical names in the general case!
Names are often incorrect
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Ideally, look for “unusual” terms and try to offer
alternatives – but always answer the question
asked, regardless
-
May be impossible for chemical names in the general case!
Chemical names are more difficult to
interpret than regular English
l
Lots of very similar “words” used in similar contexts
– -ane / -ene / yne
– -ol / al / yl
– methyl / ethyl / menthyl
l
methylethyl malonate
O
-
O
O
methyl ethylmalonate
-O
O
O
O
O
O
O
O
methyl ethyl malonate
O
O
O
O
Even spaces change the meaning of a name
O
l
methylethylmalonate
Google can use some techniques (Soundex, etc.) that
don’t work with chemical names
Existing systems
l
CambridgeSoft
– ChemDraw Ultra, and batch version
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ACD/Labs
– ACD/Name, and batch version
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[MDL]
– In development, announced in 2001
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[Chemical Abstracts]
– Mentioned in several journal articles, but not publicly available
Benchmarks for Name Structure interpretation
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>> 90% of organic nomenclature rules
– Depends on how you count the rules!
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Can generate structures for 70-90% of most real-life
lists of chemical names
– Remainder are generally not systematic and/or have no structure
that could possibly be generated
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> 99% accurate for the structures that are generated
– Remainder are generally ambiguous names to start with
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Can process > 10,000 names/minute
– Pentium III, 933 MHz
Future growth: Algorithms
l
Not much!
l
Could implement a few more rules
– All remaining ones are obscure
– Would have little practical effect
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Support for some classes currently disabled
– Not a limitation of the name interpretation,
but difficult to generate appealing structures:
metallocenes, fullerenes, etc
Future growth: Intelligence
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Typo recognition
– Often difficult to guess what was intended
– Can be very slow
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Context recognition
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Integration with other types external resources
“Haystack”
1890-91
Claude Monet