MetaboLights MTBLS19 → GO bridge coverage
Input: MetaboLights MTBLS19
Generated by coverage_probe.py — all numbers
computed live from OLS4 (ChEBI), the Rhea REST API, and the GO rhea2go mapping.
Why this probe exists
Reported metabolite ChEBI ids rarely match Rhea participants directly,
for two reasons we test as successive normalization tiers:
- Protonation — Rhea writes participants in their major protonation
state at pH 7.3 (citrate(3-),ATP(4-)); repositories report neutral
forms. We expand over ChEBIis_protonated_form_of/
is_deprotonated_form_of(the protonation family). - Structure / skeleton — a study reports a generic, non-stereospecific
compound (isoleucine) while Rhea uses the stereospecific zwitterion
(L-isoleucine zwitterion). We expand over the broader structural
relations (+ tautomer/enantiomer + generic→specificchildren), bounded
to the seed's InChIKey skeleton. This tier is stereo/charge-blind, so
it is reported separately as the more permissive fallback.
Headline
- Metabolites probed: 34 (resolved to ChEBI: 34)
- In a Rhea reaction — exact: 5/34 → +protonation: 12/34 → +structure: 20/34
- Reaching a GO MF term (rhea2go) — exact: 4 → +protonation: 11 → +structure: 17 (of 34)
- Recovered by protonation: 7; additionally by structure/skeleton: 8
Per-metabolite
Tier reached: exact < proton (protonation) < struct (skeleton) < — (miss).
| Metabolite | Seed ChEBI | q | Tier | GO MF (exact→proton→struct) | Rhea-matched form |
|---|---|---|---|---|---|
| oleamide | CHEBI:116314 | 0 | exact | 1→1→1 | oleamide (CHEBI:116314, q=0) |
| N(2)-(2-carboxyethyl)-L-arginine | CHEBI:15427 | 0 | struct | 0→0→2 | N(2)-(2-carboxyethyl)-L-arginine dizwitterion (CHEBI:57304, q=0) |
| 3-guanidinopropanoic acid | CHEBI:15968 | 0 | struct | 0→0→1 | 3-guanidinopropanoic acid zwitterion (CHEBI:57593, q=0) |
| taurochenodeoxycholic acid | CHEBI:16525 | 0 | proton | 0→8→8 | taurochenodeoxycholate (CHEBI:9407, q=-1) |
| 15,16-dihydrobiliverdin | CHEBI:16790 | 0 | proton | 0→9→9 | 15,16-dihydrobiliverdin(2-) (CHEBI:57899, q=-2) |
| glycocholic acid | CHEBI:17687 | 0 | proton | 0→24→24 | glycocholate (CHEBI:29746, q=-1) |
| O-octanoyl-L-carnitine | CHEBI:18102 | 0 | exact | 1→1→1 | O-octanoyl-L-carnitine (CHEBI:18102, q=0) |
| octadecadienoic acid | CHEBI:25627 | 0 | struct | 0→0→13 | linoleate (CHEBI:30245, q=-1) |
| glycodeoxycholic acid | CHEBI:27471 | 0 | proton | 0→4→4 | glycodeoxycholate (CHEBI:82982, q=-1) |
| O-decanoyl-L-carnitine | CHEBI:28717 | 0 | exact | 0→0→0 | O-decanoyl-L-carnitine (CHEBI:28717, q=0) |
| glycochenodeoxycholic acid | CHEBI:36274 | 0 | proton | 0→9→9 | glycochenodeoxycholate (CHEBI:36252, q=-1) |
| p-Ts-L-Lys-Me | CHEBI:45847 | 0 | — | 0→0→0 | — |
| phenylacetone | CHEBI:52052 | 0 | exact | 1→1→1 | phenylacetone (CHEBI:52052, q=0) |
| 3-hydroxyicosanoic acid | CHEBI:52347 | 0 | proton | 0→4→4 | icosanoate (CHEBI:32360, q=-1) |
| lysophosphatidylcholine O-16:0/0:0 | CHEBI:64496 | 0 | exact | 4→4→4 | lysophosphatidylcholine O-16:0/0:0 (CHEBI:64496, q=0) |
| lysophosphatidylcholine 20:4 | CHEBI:64568 | 0 | struct | 0→0→2 | 2-arachidonoyl-sn-glycero-3-phosphocholine (CHEBI:76079, q=0) |
| lysophosphatidylcholine 20:1 | CHEBI:67057 | 0 | — | 0→0→0 | — |
| O-oleoylcarnitine | CHEBI:72689 | 0 | — | 0→0→0 | — |
| 10-hydroxy-(2E,8E)-decadien-4-ynoic acid | CHEBI:72691 | 0 | — | 0→0→0 | — |
| octadecadienal | CHEBI:72693 | ? | — | 0→0→0 | — |
| tetracosahexaenoic acid | CHEBI:72714 | ? | — | 0→0→0 | — |
| O-linoelaidylcarnitine | CHEBI:72715 | 0 | — | 0→0→0 | — |
| N-dodecanoylsphingosine 1-phosphate | CHEBI:72718 | 0 | proton | 0→18→18 | N-dodecanoylsphingosine 1-phosphate(2-) (CHEBI:72960, q=-2) |
| 4E,15Z-bilirubin IXa | CHEBI:72719 | 0 | — | 0→0→0 | — |
| phosphatidylethanolamine 20:4/18:1 | CHEBI:72721 | 0 | — | 0→0→0 | — |
| Phe-Phe | CHEBI:72723 | 0 | struct | 0→0→0 | Phe-Phe zwitterion (CHEBI:191205, q=0) |
| 3beta,6beta-dihydroxy-5beta-cholan-24-oic acid | CHEBI:72724 | 0 | — | 0→0→0 | — |
| hydroxypalmitic acid | CHEBI:72726 | 0 | struct | 0→0→0 | 10-hydroxypalmitate (CHEBI:194446, q=-1) |
| 3alpha,7beta-dihydroxy-5beta-cholest-24-en-26-oic acid | CHEBI:72727 | 0 | — | 0→0→0 | — |
| tert-butylglycine | CHEBI:72770 | 0 | — | 0→0→0 | — |
| beta-leucine | CHEBI:72772 | 0 | struct | 0→0→1 | (3R)-beta-leucine zwitterion (CHEBI:57428, q=0) |
| O-palmitoylcarnitine | CHEBI:73067 | 0 | struct | 0→0→1 | O-palmitoyl-L-carnitine (CHEBI:17490, q=0) |
| sodium glycochenodeoxycholate | CHEBI:87818 | 0 | — | 0→0→0 | — |
| sodium glycodeoxycholate | CHEBI:87819 | 0 | — | 0→0→0 | — |
Recovered by structure (skeleton) normalization
Generic / stereochemistry mismatches the protonation tier could not fix,
recovered by InChIKey-skeleton expansion:
- N(2)-(2-carboxyethyl)-L-arginine (CHEBI:15427) → N(2)-(2-carboxyethyl)-L-arginine dizwitterion (CHEBI:57304, q=0)
- 3-guanidinopropanoic acid (CHEBI:15968) → 3-guanidinopropanoic acid zwitterion (CHEBI:57593, q=0)
- octadecadienoic acid (CHEBI:25627) → linoleate (CHEBI:30245, q=-1)
- lysophosphatidylcholine 20:4 (CHEBI:64568) → 2-arachidonoyl-sn-glycero-3-phosphocholine (CHEBI:76079, q=0)
- Phe-Phe (CHEBI:72723) → Phe-Phe zwitterion (CHEBI:191205, q=0)
- hydroxypalmitic acid (CHEBI:72726) → 10-hydroxypalmitate (CHEBI:194446, q=-1)
- beta-leucine (CHEBI:72772) → (3R)-beta-leucine zwitterion (CHEBI:57428, q=0)
- O-palmitoylcarnitine (CHEBI:73067) → O-palmitoyl-L-carnitine (CHEBI:17490, q=0)
Example GO molecular functions reached
- N(2)-(2-carboxyethyl)-L-arginine (CHEBI:15427) → GO:0033848 N2-(2-carboxyethyl)arginine synthase activity; GO:0034027 (carboxyethyl)arginine beta-lactam-synthase activity
- 3-guanidinopropanoic acid (CHEBI:15968) → GO:0047972 guanidinopropionase activity
- taurochenodeoxycholic acid (CHEBI:16525) → GO:0004090 carbonyl reductase (NADPH) activity; GO:0008397 sterol 12-alpha-hydroxylase activity; GO:0015020 glucuronosyltransferase activity
- 15,16-dihydrobiliverdin (CHEBI:16790) → GO:0004392 heme oxygenase (decyclizing) activity; GO:0047705 bilirubin oxidase activity; GO:0050617 15,16-dihydrobiliverdin:ferredoxin oxidoreductase activity
- glycocholic acid (CHEBI:17687) → GO:0003954 NADH dehydrogenase activity; GO:0004090 carbonyl reductase (NADPH) activity; GO:0008397 sterol 12-alpha-hydroxylase activity
- octadecadienoic acid (CHEBI:25627) → GO:0004467 long-chain fatty acid-CoA ligase activity; GO:0004623 A2-type glycerophospholipase activity; GO:0004806 triacylglycerol lipase activity
- glycodeoxycholic acid (CHEBI:27471) → GO:0004090 carbonyl reductase (NADPH) activity; GO:0015020 glucuronosyltransferase activity; GO:0033881 bile-acid-CoA transferase activity
- glycochenodeoxycholic acid (CHEBI:36274) → GO:0004090 carbonyl reductase (NADPH) activity; GO:0008397 sterol 12-alpha-hydroxylase activity; GO:0015020 glucuronosyltransferase activity
- 3-hydroxyicosanoic acid (CHEBI:52347) → GO:0004467 long-chain fatty acid-CoA ligase activity; GO:0017040 N-acylsphingosine amidohydrolase activity; GO:0047372 monoacylglycerol lipase activity
- lysophosphatidylcholine 20:4 (CHEBI:64568) → GO:0008970 glycerophospholipid phospholipase A1 activity; GO:0047190 2-acylglycerophosphocholine O-acyltransferase activity
- N-dodecanoylsphingosine 1-phosphate (CHEBI:72718) → GO:0004031 aldehyde oxidase activity; GO:0008481 sphingosine kinase activity; GO:0016297 fatty acyl-[ACP] hydrolase activity
- beta-leucine (CHEBI:72772) → GO:0050047 L-leucine 2,3-aminomutase activity
- O-palmitoylcarnitine (CHEBI:73067) → GO:0004095 carnitine O-palmitoyltransferase activity
Residual misses (after both normalization tiers)
Resolved to ChEBI but matched no Rhea reaction even after protonation and
skeleton normalization — typically derivatives Rhea represents only in a
conjugated/acylated form, or compounds genuinely absent from Rhea.
- p-Ts-L-Lys-Me (CHEBI:45847, family size 1)
- lysophosphatidylcholine 20:1 (CHEBI:67057, family size 1)
- O-oleoylcarnitine (CHEBI:72689, family size 1)
- 10-hydroxy-(2E,8E)-decadien-4-ynoic acid (CHEBI:72691, family size 1)
- octadecadienal (CHEBI:72693, family size 1)
- tetracosahexaenoic acid (CHEBI:72714, family size 2)
- O-linoelaidylcarnitine (CHEBI:72715, family size 1)
- 4E,15Z-bilirubin IXa (CHEBI:72719, family size 1)
- phosphatidylethanolamine 20:4/18:1 (CHEBI:72721, family size 1)
- 3beta,6beta-dihydroxy-5beta-cholan-24-oic acid (CHEBI:72724, family size 1)
- 3alpha,7beta-dihydroxy-5beta-cholest-24-en-26-oic acid (CHEBI:72727, family size 1)
- tert-butylglycine (CHEBI:72770, family size 1)
- sodium glycochenodeoxycholate (CHEBI:87818, family size 1)
- sodium glycodeoxycholate (CHEBI:87819, family size 1)
Method / reproducibility
- ChEBI access + protonation traversal:
chebi.py(OLS4). - Rhea network + rhea2go:
rhea.py(Rhea REST, GO external2go). - Caches under
.cache/(gitignored); delete to force a fresh pull. - This is a coverage probe (does the bridge connect?), not yet a
statistical enrichment; GO-BP lift + ORA are the next step (see the
project page).