“ good annotation practice ” for chemical data: chebi experience kirill degtyarenko european...
TRANSCRIPT
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““Good annotation Good annotation practicepractice”” for chemical for chemical
data: data: ChEBI experienceChEBI experience
Kirill DegtyarenkoKirill DegtyarenkoEuropean Patent OfficeEuropean Patent Office
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good Naming practice how to give most appropriate names
good Ontology practice how to link the entity of interest by
defined logical relationships to other entities
good Drawing practice
• how to draw unambiguous 2-D diagrams
Good anNODation practice
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or
How to Give Most Appropriate Names
Good Naming Practice
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2-{[3-(trifluoromethyl)phenyl]amino}benzoic acid
NH
O
OH
F
F
F
Systematic Name (IUPAC)
1
23
4
5
6
1
2
34
5
6
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• flufenamic acid (INN English)• acide flufénamique (INN French)• ácido flufenámico (INN Spanish)• acidum flufenamicum (INN Latin)• Flufenaminsäure (German)
NH
O
OH
F
F
F
Common Name
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The Unpronounceables
CHEBI:48935
(E)-roxithromycin
IUPAC name:
(3R,4S,5S,6R,7R,9R,10E,11S,12R,13S,14R)-4-(2,6-dideoxy-3-C-methyl-3-O-methyl-α-L-ribo-hexopyranosyloxy)-14-ethyl-7,12,13-trihydroxy-10-{[(2-methoxyethoxy)methoxy]imino}-6-[3,4,6-trideoxy-3-(dimethylamino)-β-D-xylo-hexopyranosyloxy]-3,5,7,9,11,13-hexamethyloxacyclotetradecan-2-one
O O
O
O
OH
N
O
O
N
OH
OH
O OO
O
OH OH
CH3
CH3
CH3
CH3
CH3CH3
CH3 CH3
CH3
CH3
CH3
CH3
CH3CH3
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O O
O
O
OH
N
O
O
N
OH
OHO
OH OH
CH3
CH3
CH3CH3CH3
CH3 CH3
CH3
CH3
CH3
CH3
CH3CH3
OOO
CH3
CHEBI:32109(Z)-roxithromycin
What is the common name of roxithromycin?
CHEBI:48935(E)-roxithromycinINN: roxithromycin
O O
O
O
OH
N
O
O
N
OH
OH
O OO
O
OH OH
CH3
CH3
CH3
CH3
CH3CH3
CH3 CH3
CH3
CH3
CH3
CH3
CH3CH3
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O O
O
O
OH
N
O
O
N
OH
OH
O OO
O
OH OH
CH3
CH3
CH3
CH3
CH3CH3
CH3 CH3
CH3
CH3
CH3
CH3
CH3CH3
O O
O
O
OH
N
O
O
N
OH
OHO
OH OH
CH3
CH3
CH3CH3CH3
CH3 CH3
CH3
CH3
CH3
CH3
CH3CH3
OOO
CH3
CHEBI:48844 roxithromycin
(E)-roxithromycin
O O
O
O
OH
N
O
O
N
OH
OH
O OO
O
OH OH
CH3
CH3
CH3
CH3
CH3CH3
CH3 CH3
CH3
CH3
CH3
CH3
CH3CH3
(Z)-roxithromycin
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What is thiamine?CHEBI:18385thiamine(1+)aka thiamine
N
N
NH2
CH3 S
CH3
OH
N+
CHEBI:33283thiamine(1+) chlorideINN: thiamine
N
N
NH2
CH3 S
CH3
OH
N+
Cl-
CHEBI:49105 thiamine(2+) dichlorideaka thiamine chloride hydrochloride aka thiamine hydrochloride
N
NH3+
NCH3 S
CH3
OH
N+
Cl-
Cl-
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Problem is not unique to ChEBI
Cf. phenol vs phenols phenol metabolism vs phenols
metabolism
Bad solution: article use a phenol metabolism?
Solution: prepositional phrases metabolism of phenols
Plurals and singulars
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or
How to Draw Unambiguous 2-D Diagrams
Good Drawing Practice
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Linear forms of monosaccharides
CHO
CH2OH
H OH
OH H
OH H
H OH
OH
O
H OH
OH H
OH H
H OH
H H
OH
OH
OH
OH
OH
O
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Pyranose forms of monosaccharides
O
OHH
HOH
HOH
H OH
H
CH2OH
O
CH2OH
OH
OH
OH
OH
OH
OH
OH
OH
OOH
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Fused systems
(R)-camphor
ambiguous unambiguous
CH3
OCH3
CH3
O
CH3CH3
CH3
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Square planar geometry
InChI=1/2ClH.2H3N.Pt/h2*1H;2*1H3;/q;;;;+2/p-2
Pt
N Cl
ClN
HH
H
H
HH
Pt
NCl
N Cl
H H
H
H
HH
cisplatin transplatin
SMILES: [H][N]([H])([H])[Pt](Cl)(Cl)[N]([H])([H])[H]
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Compositional uncertainty
Positional uncertainty
Configurational uncertainty
Conformational uncertainty
Uncertainty and ambiguity in chemistry
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Examples
an alkali metal cation
vanadate(V) anion
[2H]ethanol
Compositional uncertainty
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Examples
L-bromohistidine residue
pteroic acid (several tautomers)
Positional uncertainty
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Examples
androstane
rel-(2R,3R)-2-amino-3-methylpentanoic acid
tetradec-11-enoic acid
Configurational uncertainty
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Examples
cyclohexane: chair, boat, twist
protein secondary structure: , , …
Conformational uncertainty
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or
How to Link the Entity of Interest by Defined
Logical Relationships to Other Entities
Good Ontology Practice
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• Molecular structure ontology• Subatomic particle ontology• Biological role ontology • Application ontology
ChEBI ontology
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Relationships in ChEBI ∆ Is A generic
⋄ Is Part Of generic
♯ Is Conjugate Acid Of specific
♭ Is Conjugate Base Of specific
Is Enantiomer Of specific
Is Tautomer Of specific
ℛ Is Substituent Group From
specific
ℋ Has Parent Hydride specific
ℱ Has Functional Parent specific
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Is A relationship
NH2
O
OHSH
NH2
O
OHSH∆
L-cysteine
cysteineis a
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NH3+
O
OHSH
NH3+
O
OHSH
L-cysteinium
Is Part Of
⋄
L-cysteine hydrochloride
is part of
Cl-
has part
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NH2
O
OHSH
Is Enantiomer Of
NH2
O
OHSH
L-cysteine
NH2
O
OHSH
∆ ∆
D-cysteine
is enantiomer of
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Is Tautomer Of
3H-pyrrole
NH
N N
2H-pyrrole
1H-pyrrole
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NH2
O
O-
S-
NH3+
O
OHSH
NH2
O
O-
SH
Is Conjugate Acid Of
NH2
O
OHSH♯
L-cysteine
L-cysteinate(1–)is conjugate acid of
L-cysteinium
L-cysteinate(2–)
♯♯
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NH2
O
O-
SH
Is Conjugate Base Of
NH2
O
OHSH
♭
L-cysteine
L-cysteinate(1–)
NH2
O
O-
S-
NH3+
O
OHSH
L-cysteinium
L-cysteinate(2–)
♭ ♭
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NH2
O
O-
SH
Acid/base relationships
NH2
O
OHSH
♭L-
cysteineL-cysteinate(1–)
NH2
O
O-
S-
NH3+
O
OHSH
L-cysteinium
L-cysteinate(2–)
♭
♯
♭♯♯
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NH2
O
SH
L-cysteinyl
NH
O
SH
NH
O
OHSH
Is Substituent Group From
NH2
O
OHSHL-cysteine
L-cysteine residue
L-cysteino
ℛ
ℛ
ℛ
*
*
*
*
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salutaridinol
Has Parent Hydride
has parent hydride
is parent hydride of
ℋ NHH
morphinan
OH
N
O
O
CH3
OH
CH3
CH3
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7-O-acetylsalutaridinol
Has Functional Parent
has functional parent
is functional parent of
ℱ
salutaridinol
OH
N
O
O
CH3
CH3
CH3
OCH3
O
OH
N
O
O
CH3
OH
CH3
CH3
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Live annotation demo
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Going to SourceForge…
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Reading a request…
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Going to curator tool…
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Search result…
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Adding new entry…
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Editing new entry…
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Success!
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Let’s draw
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Success again!
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Using ACD/Name (1)
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Using ACD/Name (2)
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Adding IUPAC name (1)
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Adding IUPAC name (2)
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Classifying (1)
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Classifying (2)
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Classifying (3)
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Classifying (4)
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The last touch (1)
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The last touch (2)
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Responding request…
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A job well done…
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The team
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