Duplicate inchis for enantiomers

[cmungall]

As noted in #456 there are many cases of 2 chebis having the same inchi

One way to tackle this is to break down into cases where we can use the structure of the inchi. For example, these are cases where we have an enantiomer and its parent form sharing an inchi. In these cases it's clear the enantiomer and its parent should differ predictably via appending the inchi stereochemistry layer

class	name	parent	parent_name	config	inchi	parent_inchi
http://purl.obolibrary.org/obo/CHEBI_38349	(7R)-7-[(2,4-diamino-6-methylpyrimidin-5-yl)methyl]-7,8-dicarba-nido-undecaborane(11)	http://purl.obolibrary.org/obo/CHEBI_38348	7-[(2,4-diamino-6-methylpyrimidin-5-yl)methyl]-7,8-dicarba-nido-undecaborane(11)	(7R)	InChI=1S/C8H19B9N4/c1-3-4(5(18)21-6(19)20-3)2-8-7-9-11-10(8)14(8)12(7,8)13(7,9)15(9,11)16(10,11,14)17(12,13,14)15/h7,9-17H,2H2,1H3,(H4,18,19,20,21)	InChI=1S/C8H19B9N4/c1-3-4(5(18)21-6(19)20-3)2-8-7-9-11-10(8)14(8)12(7,8)13(7,9)15(9,11)16(10,11,14)17(12,13,14)15/h7,9-17H,2H2,1H3,(H4,18,19,20,21)
http://purl.obolibrary.org/obo/CHEBI_38350	(7S)-7-[(2,4-diamino-6-methylpyrimidin-5-yl)methyl]-7,8-dicarba-nido-undecaborane(11)	http://purl.obolibrary.org/obo/CHEBI_38348	7-[(2,4-diamino-6-methylpyrimidin-5-yl)methyl]-7,8-dicarba-nido-undecaborane(11)	(7S)	InChI=1S/C8H19B9N4/c1-3-4(5(18)21-6(19)20-3)2-8-7-9-11-10(8)14(8)12(7,8)13(7,9)15(9,11)16(10,11,14)17(12,13,14)15/h7,9-17H,2H2,1H3,(H4,18,19,20,21)	InChI=1S/C8H19B9N4/c1-3-4(5(18)21-6(19)20-3)2-8-7-9-11-10(8)14(8)12(7,8)13(7,9)15(9,11)16(10,11,14)17(12,13,14)15/h7,9-17H,2H2,1H3,(H4,18,19,20,21)
http://purl.obolibrary.org/obo/CHEBI_48930	(2R,3S)-3-carboxy-2,3-dihydroxypropanoate	http://purl.obolibrary.org/obo/CHEBI_35400	meso-tartrate(1-)	(2R,3S)	InChI=1S/C4H6O6/c5-1(3(7)8)2(6)4(9)10/h1-2,5-6H,(H,7,8)(H,9,10)/p-1/t1-,2+	InChI=1S/C4H6O6/c5-1(3(7)8)2(6)4(9)10/h1-2,5-6H,(H,7,8)(H,9,10)/p-1/t1-,2+
http://purl.obolibrary.org/obo/CHEBI_48931	(2S,3R)-3-carboxy-2,3-dihydroxypropanoate	http://purl.obolibrary.org/obo/CHEBI_35400	meso-tartrate(1-)	(2S,3R)	InChI=1S/C4H6O6/c5-1(3(7)8)2(6)4(9)10/h1-2,5-6H,(H,7,8)(H,9,10)/p-1/t1-,2+	InChI=1S/C4H6O6/c5-1(3(7)8)2(6)4(9)10/h1-2,5-6H,(H,7,8)(H,9,10)/p-1/t1-,2+
http://purl.obolibrary.org/obo/CHEBI_60088	3-[(5R,6S)-5,6-dihydroxycyclohexa-1,3-dienyl]propanoate	http://purl.obolibrary.org/obo/CHEBI_60087	3-(cis-5,6-dihydroxycyclohexa-1,3-dienyl)propanoate	3	InChI=1S/C9H12O4/c10-7-3-1-2-6(9(7)13)4-5-8(11)12/h1-3,7,9-10,13H,4-5H2,(H,11,12)/p-1/t7-,9+/m1/s1	InChI=1S/C9H12O4/c10-7-3-1-2-6(9(7)13)4-5-8(11)12/h1-3,7,9-10,13H,4-5H2,(H,11,12)/p-1/t7-,9+/m1/s1
http://purl.obolibrary.org/obo/CHEBI_138262	(9S,10R)-epoxyoctadecanoic acid	http://purl.obolibrary.org/obo/CHEBI_82464	cis-9,10-epoxyoctadecanoic acid	(9S,10R)	InChI=1S/C18H34O3/c1-2-3-4-5-7-10-13-16-17(21-16)14-11-8-6-9-12-15-18(19)20/h16-17H,2-15H2,1H3,(H,19,20)/t16-,17+/m1/s1	InChI=1S/C18H34O3/c1-2-3-4-5-7-10-13-16-17(21-16)14-11-8-6-9-12-15-18(19)20/h16-17H,2-15H2,1H3,(H,19,20)/t16-,17+/m1/s1
http://purl.obolibrary.org/obo/CHEBI_31018	(+)-gallocatechin	http://purl.obolibrary.org/obo/CHEBI_68330	gallocatechin	(+)	InChI=1S/C15H14O7/c16-7-3-9(17)8-5-12(20)15(22-13(8)4-7)6-1-10(18)14(21)11(19)2-6/h1-4,12,15-21H,5H2/t12-,15+/m0/s1	InChI=1S/C15H14O7/c16-7-3-9(17)8-5-12(20)15(22-13(8)4-7)6-1-10(18)14(21)11(19)2-6/h1-4,12,15-21H,5H2/t12-,15+/m0/s1
http://purl.obolibrary.org/obo/CHEBI_36410	Delta-tris(1,10-phenanthroline)ruthenium(2+)	http://purl.obolibrary.org/obo/CHEBI_36409	tris(1,10-phenanthroline)ruthenium(2+)	Delta	InChI=1S/3C12H8N2.Ru/c31-3-9-5-6-10-4-2-8-14-12(10)11(9)13-7-1;/h31-8H;/q;;;+2	InChI=1S/3C12H8N2.Ru/c31-3-9-5-6-10-4-2-8-14-12(10)11(9)13-7-1;/h31-8H;/q;;;+2
http://purl.obolibrary.org/obo/CHEBI_36411	Lambda-tris(1,10-phenanthroline)ruthenium(2+)	http://purl.obolibrary.org/obo/CHEBI_36409	tris(1,10-phenanthroline)ruthenium(2+)	Lambda	InChI=1S/3C12H8N2.Ru/c31-3-9-5-6-10-4-2-8-14-12(10)11(9)13-7-1;/h31-8H;/q;;;+2	InChI=1S/3C12H8N2.Ru/c31-3-9-5-6-10-4-2-8-14-12(10)11(9)13-7-1;/h31-8H;/q;;;+2
http://purl.obolibrary.org/obo/CHEBI_83816	(10R,11R)-dihydroxy-10,11-dihydrocarbamazepine	http://purl.obolibrary.org/obo/CHEBI_83532	10,11-trans-dihydroxy-10,11-dihydrocarbamazepine	(10R,11R)	InChI=1S/C15H14N2O3/c16-15(20)17-11-7-3-1-5-9(11)13(18)14(19)10-6-2-4-8-12(10)17/h1-8,13-14,18-19H,(H2,16,20)/t13-,14-/m1/s1	InChI=1S/C15H14N2O3/c16-15(20)17-11-7-3-1-5-9(11)13(18)14(19)10-6-2-4-8-12(10)17/h1-8,13-14,18-19H,(H2,16,20)/t13-,14-/m1/s1

[amalik01]

Hi Chris,

We are aware of this issue. The duplicate InChI arises as a result of structures that are relative configurations where there are potentially two possible configurations of the structure. Since we are unable to show both structures on the same ChEBI entry, we therefore tend to show one of them for depiction purposes but the IUPAC name will have the word 'rel' in front of it so that the user knows that it is the relative configuration of the structure (which means that its either the structure shown or its opposite configuration which is not shown). In an ideal world, it be good to show both structures on a single ChEBI entry and show the InChi of the relative configuration but it's the best we can do at the moment based on the technology we have, otherwise we would have to delete all of the structures of all the relative configurations in ChEBI.

[K-r-ll]

The particular problem of both Λ-tris(1,10-phenanthroline)ruthenium(2+) (CHEBI:36411) and its enantiomer Δ-tris(1,10-phenanthroline)ruthenium(2+) (CHEBI:36410) having the same InChI is due to the fact that InChI algorithm yet does not differentiate between non-tetrahedral (in this case, octahedral) stereoisomers. Hopefully this will be eventually sorted out if/when the InChI “coordination layer” is implemented. See e.g. https://cheminf20.org/2020/10/18/coordination-inchi-for-inorganics-now-with-stereochemistry/

[rwst]

See also https://chemistry.stackexchange.com/questions/151072/can-cis-trans-isomers-have-same-inchi

[cmungall]

It looks like this was "closed as completed" but the problem still remains?

[amalik01]

At present, this issue cannot be resolved since our curator tool is only able to generate standard InChI's. We will need to include stereo options in the curator tool to generate InChI's for absolute, relative, undefined and racemic stereocenters.

[cmungall]

Some solutions:

• include a mapping predicate that states the relationship between the CHEBI term and the INCHI (exact, broad, narrow, related)
• simply exclude non-exact INCHI mappings, instead make sure there is an equivalent term, allowing the user to infer the precise relationship from any CHEBI term

On Wed, Aug 31, 2022 at 6:26 AM amalik01 @.***> wrote:

At present, this issue cannot be resolved since our curator tool is only able to generate standard InChI's. We will need to include options in the curator tool to generate InChI's for absolute, relative, undefined and relative stereocenters.

— Reply to this email directly, view it on GitHub https://github.com/ebi-chebi/ChEBI/issues/4080#issuecomment-1232937573, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOIL3CFPR4JENU7WB43V35MRTANCNFSM43VJEIHQ . You are receiving this because you authored the thread.Message ID: @.***>

[cmungall]

If none of these are possible and you don't want the issue clogging things up, I suggest you "close as not planned" rather than "close as completed"

On Wed, Aug 31, 2022 at 7:24 AM Chris Mungall @.***> wrote:

Some solutions:

• include a mapping predicate that states the relationship between the CHEBI term and the INCHI (exact, broad, narrow, related)
• simply exclude non-exact INCHI mappings, instead make sure there is an equivalent term, allowing the user to infer the precise relationship from any CHEBI term

On Wed, Aug 31, 2022 at 6:26 AM amalik01 @.***> wrote:

At present, this issue cannot be resolved since our curator tool is only able to generate standard InChI's. We will need to include options in the curator tool to generate InChI's for absolute, relative, undefined and relative stereocenters.

— Reply to this email directly, view it on GitHub https://github.com/ebi-chebi/ChEBI/issues/4080#issuecomment-1232937573, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOIL3CFPR4JENU7WB43V35MRTANCNFSM43VJEIHQ . You are receiving this because you authored the thread.Message ID: @.***>