“ Good annotation practice ” for chemical data: ChEBI experience Kirill Degtyarenko European Patent Office

§good N aming practice l how to give most appropriate names §good O ntology practice l how to link the entity of interest by defined logical relationships to other entities  good D rawing practice how to draw unambiguous 2-D diagrams Good anNODation practice

or How to Give Most Appropriate Names Good Naming Practice

2-{[3-(trifluoromethyl)phenyl]amino}benzoic acid Systematic Name (IUPAC)

flufenamic acid (INN English) acide flufénamique (INN French) ácido flufenámico (INN Spanish) acidum flufenamicum (INN Latin) Flufenaminsäure (German) Common Name

The Unpronounceables CHEBI:48935 ( E )-roxithromycin IUPAC name: (3 R,4 S,5 S,6 R,7 R,9 R,10 E,11 S,12 R,13 S,14 R )-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

CHEBI:32109 ( Z )-roxithromycin What is the common name of roxithromycin? CHEBI:48935 ( E )-roxithromycin INN: roxithromycin

Roxithromycin (2) CHEBI:48844CHEBI:48844 roxithromycin ( E )-roxithromycin( Z )-roxithromycin

What is thiamine? CHEBI:18385 thiamine(1+) aka thiamine CHEBI:33283 thiamine(1+) chloride INN: thiamine CHEBI:49105CHEBI:49105 thiamine(2+) dichloride aka thiamine chloride hydrochloride aka thiamine hydrochloride

 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

or How to Draw Unambiguous 2-D Diagrams Good Drawing Practice

Linear forms of monosaccharides

Pyranose forms of monosaccharides

Fused systems ( R )-camphor ambiguousunambiguous

Square planar geometry InChI=1/2ClH.2H3N.Pt/h2*1H;2*1H3;/q;;;;+2/p-2 cisplatintransplatin SMILES: [H][N]([H])([H])[Pt](Cl)(Cl)[N]([H])([H])[H]

 Compositional uncertainty  Positional uncertainty  Configurational uncertainty  Conformational uncertainty Uncertainty and ambiguity in chemistry

Examples  an alkali metal cation  vanadate( V ) anion  [ 2 H]ethanol Compositional uncertainty

Examples  L -bromohistidine residue  pteroic acid (several tautomers)pteroic acid Positional uncertainty

Examples  androstane  rel -(2 R,3 R )-2-amino-3-methylpentanoic acid  tetradec-11-enoic acid Configurational uncertainty

Examples  cyclohexane: chair, boat, twist  protein secondary structure: , ,  … Conformational uncertainty

or How to Link the Entity of Interest by Defined Logical Relationships to Other Entities Good Ontology Practice

Molecular structure ontology Subatomic particle ontology Biological role ontology Application ontology ChEBI ontology

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

Is A relationship ∆ L -cysteinecysteine is a

L -cysteinium Is Part Of ⋄ L -cysteine hydrochloride is part of has part

Is Enantiomer Of  L -cysteine ∆∆ D -cysteine is enantiomer of

Is Tautomer Of 3 H -pyrrole2 H -pyrrole  1 H -pyrrole 

Is Conjugate Acid Of ♯ L -cysteine L -cysteinate(1–) is conjugate acid of L -cysteinium L -cysteinate(2–) ♯♯

Is Conjugate Base Of ♭ L -cysteine L -cysteinate(1–) L -cysteinium L -cysteinate(2–) ♭♭

Acid/base relationships ♭ L -cysteine L -cysteinate(1–) L -cysteinium L -cysteinate(2–) ♭ ♯ ♭♯ ♯

L -cysteinyl Is Substituent Group From L -cysteine L -cysteine residue L -cysteino ℛ ℛ ℛ * * * *

salutaridinol Has Parent Hydride has parent hydride is parent hydride of ℋ morphinan

7- O -acetylsalutaridinol Has Functional Parent has functional parent is functional parent of ℱ salutaridinol

Live annotation demo

Going to SourceForge…

Reading a request…

Going to curator tool…

Search result…

Adding new entry…

Editing new entry…

Success!

Let’s draw

Approving structure

Success again!

Using ACD/Name (1)

Using ACD/Name (2)

Adding IUPAC name (1)

Adding IUPAC name (2)

Classifying (1)

Classifying (2)

Classifying (3)

Classifying (4)

The last touch (1)

The last touch (2)

Responding request…

A job well done…

Rafael Alcántara Michael Ashburner Volker Ast * Michael Darsow * Paula de Matos Marcus Ennis Janna Hastings Alan McNaught * Chris Steinbeck Martin Zbinden * The team

Kristian Axelsen Hélène Courrier Anne Morgat Ian Unwin Our faithful Users EU: funding Thanks