Michael Ashburner at the University of Cambridge once famously quipped that “Biologists would rather share their toothbrush than share a gene name” [1]. And so we have many different colourful and imaginative names for genes. The same mis-naming rule applies the reactants and products (input and output) of metabolism. Here are some example names, would you like to share my toothbrush chemical name? There are so many different toothbrushes names to choose from…
For example, consider these reactants and products named in Mark Poolman’s version of the Calvin Cycle shown in the table below. The left hand column shows the name used in the curated biomodel. The right hand column shows the alternate forms (case sensitive) looked up with a program written by Neil Swainston for doing term disambiguation. If you’re interested in using it, and you ask him nicely, he might send you the source code. [update: Since writing this, Neil has told me he’s planning on writing a two-page application note on how it all works, and making the code freely available.]
| Name | Synonyms, looked up using KEGG, ChEBI and PubChem. |
|---|---|
| x_CO2 | CARBON DIOXIDE, CO(2), [CO2], CO2, Carbon dioxide, carbon dioxide |
| RuBP_ch | D-Ribulose 1,5-bisphosphate, D-ribulose 1,5-bisphosphate |
| PGA_ch | 3-Phospho-D-glycerate, D-Glycerate 3-phosphate, 3-phospho-D-glycerate, 3-phospho-D-glyceric acid, D-glycerate 3-phosphate, 3-Phospho-(R)-glycerate |
| ATP_ch | ADENOSINE-5′-TRIPHOSPHATE, Adenosine 5′-triphosphate, Adenosine triphosphate, H4atp, ATP |
| BPGA_ch | 3-phospho-D-glyceroyl phosphate, (R)-2-Hydroxy-3-(phosphonooxy)-1-monoanhydride with phosphoric, propanoic acid, 3-phospho-D-glyceroyl dihydrogen phosphate, 1,3-Bisphospho-D-glycerate, 3-Phospho-D-glyceroyl phosphate, (R)-2-Hydroxy-3-(phosphonooxy)-1-monoanhydride with phosphoric propanoic acid |
| x_NADPH_ch | NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, dihydronicotinamide-adenine dinucleotide phosphate, NADPH, reduced nicotinamide-adenine dinucleotide phosphate, TPNH, NADPH2 |
| GAP_ch | D-Glyceraldehyde 3-phosphate, glyceraldehyde 3-phosphate, Glyceraldehyde 3-phosphate, Glyzerinaldehyd-3-phosphat, 3-phosphoglyceraldehyde, 2-hydroxy-3-(phosphonooxy)propanal, Glycerinaldehyd-3-phosphat, gliceraldehido-3-fosfato,(2R)-2-Hydroxy-3-(phosphonooxy)-propanal, glyceraldehyde-3-phosphate, D-glyceraldehyde 3-phosphate, glyceraldehyde 3-(dihydrogen phosphate), DL-Glyceraldehyde 3-phosphate |
| Pi_ch | PHOSPHATE ION, Phosphate, Orthophosphate, phosphate(3-), phosphate, Phosphoric acid, Orthophosphoric acid, PO4(3-), [PO4](3-) |
| DHAP_ch | Dihydroxyacetone phosphate, 1-Hydroxy-3-(phosphonooxy)acetone, Glycerone phosphate, DHAP, 2-Propanone, 1-hydroxy-3-(phosphonooxy)-, glycerone phosphate, 1,3-Dihydroxy-2-propanone monodihydrogen phosphate |
| FBP_ch | D-Fructose 1,6-bisphosphate, beta-D-fructofuranose 1,6-bisphosphate, BETA FRUCTOSE 1,6-DIPHOSPHATE, beta-D-Fructose 1,6-bisphosphate, D-fructose 1,6-bisphosphate, 1,6-di-O-phosphono-beta-D-fructofuranose, 1,6-di-O-phosphono-D-fructose |
| F6P_ch | D-fructose 6-phosphate, D-Fructose 6-phosphoric acid, beta-D-fructofuranose 6-phosphate, Fructose-6-phosphate, D-Fructose 6-phosphate, D-fructose 6-phosphates, Neuberg ester, FRUCTOSE-6-PHOSPHATE, beta-D-fructose 6-phosphate, beta-D-Fructose 6-phosphate, 6-O-phosphono-beta-D-fructofuranose |
| E4P_ch | ERYTHOSE-4-PHOSPHATE, 4-O-phosphono-D-erythrose, D-erythrose 4-phosphate, D-Erythrose 4-phosphate |
| X5P_ch | D-Xylulose 5-phosphate, D-xylulose 5-phosphate, 5-O-phosphono-D-threo-pentos-2-ulose, D-Xylulose-5-phosphate, 5-O-phosphono-D-xylulose |
| SBP_ch | D-altro-Heptulose 1,7-biphosphate, Sedoheptulose 1,7-bisphosphate, D-Sedoheptulose 1,7-bisphosphate, sedoheptulose 1,7-bisphosphate, altro-Heptulose 1,7-biphosphate |
| S7P_ch | sedoheptulose 7-phosphate, altro-Heptulose 7-phosphate, D-altro-Heptulose 7-phosphate, D-Sedoheptulose 7-phosphate, Sedoheptulose 7-phosphate |
| R5P_ch | D-Ribose 5-phosphate, 5-O-phosphono-D-ribose, D-ribose 5-phosphate, Ribose 5-phosphate |
| Ru5P_ch | D-ribulose 5-phosphate, D-Ribulose 5-phosphate |
| x_Pi_cyt | PHOSPHATE ION, Phosphate, Orthophosphate, phosphate(3-), phosphate, Phosphoric acid, Orthophosphoric acid, PO4(3-), [PO4](3-) |
| x_GAP_cyt | Glycerinaldehyd-3-phosphat, gliceraldehido-3-fosfato, Glyceraldehyde 3-phosphate, glyceraldehyde 3-phosphate, glyceraldehyde-3-phosphate, Glyzerinaldehyd-3-phosphat, 3-phosphoglyceraldehyde, glyceraldehyde 3-(dihydrogen phosphate), 2-hydroxy-3-(phosphonooxy)propanal, DL-Glyceraldehyde 3-phosphate |
| G6P_ch | alpha-D-Glucose 6-phosphate, alpha-D-glucose 6-phosphate, D-glucose 6-phosphate, ALPHA-D-GLUCOSE-6-PHOSPHATE, 6-O-phosphono-alpha-D-glucopyranose |
| x_NADP_ch | NADP+, NADP(+), TPN, oxidized nicotinamide-adenine dinucleotide phosphate, beta-nicotinamide adenine dinucleotide phosphate, beta-Nicotinamide adenine dinucleotide phosphate, Nicotinamide adenine dinucleotide phosphate, Triphosphopyridine nucleotide, NADP |
| x_PGA_cyt | 3-Phospho-D-glycerate, D-Glycerate 3-phosphate, 3-phospho-D-glycerate, 3-phospho-D-glyceric acid, D-glycerate 3-phosphate, 3-Phospho-(R)-glycerate |
| ADP_ch | 5′-adenylphosphoric acid, ADP, H3adp, Adenosine 5′-diphosphate, ADENOSINE-5′-DIPHOSPHATE |
| x_DHAP_cyt | Dihydroxyacetone phosphate, 1-Hydroxy-3-(phosphonooxy)acetone, Glycerone phosphate, DHAP, 2-Propanone, 1-hydroxy-3-(phosphonooxy)-, glycerone phosphate, 1,3-Dihydroxy-2-propanone monodihydrogen phosphate |
| x_Proton_ch | proton, (1)1H(+), (1)H(+), p(+), H(+), p, hydron, H+ |
| G1P_ch | beta-D-glucose 1-phosphate, 1-O-phosphono-beta-D-glucopyranose, alpha-D-Glucose 1-phosphate, D-glucose 1-phosphate, beta-D-Glucose 1-phosphate, 1-O-phosphono-alpha-D-glucopyranose, D-Glucose 1-phosphate, Cori ester, 1-phospho-beta-D-glucopyranose, alpha-D-glucose 1-phosphate, 1-O-phosphono-D-glucopyranose, Phospho-beta-D-glucoside, D-Glucose alpha-1-phosphate |
| x_Starch_ch | amylum, Staerke, Starch, amidon, starch |
So ♫ You say “tom-ay-to”, I say “tom-ah-to”. You say “Glucose-6-phosphate (G6P)“, I say “α-D-glucose 6-phosphate (CHEBI:17665)” ♫
Thanks to ChEBI, KEGG and PubChem we don’t have to call the whole thing off. Without these tools it would be near impossible to do any comparison of different models and Science would be going rapidly backwards rather than slowly forwards.
References
- Helen Pearson (2001) Biology’s Name Game Nature 411, 631 – 632 (2001) doi:10.1038/35079694, pubmed.gov/11395736.
- Kirill Degtyarenko et al [2008] ChEBI: a database and ontology for chemical entities of biological interest Nucleic Acids Research January; 36(Database issue): D344-D350 doi:10.1093/nar/gkm791 pubmed.gov/17932057
- Hiroyuki Ogata et al (1999) KEGG: Kyoto Encyclopedia of Genes and Genomes Nucleic Acids Research 27(1): 29–34. pubmed.gov/9847135
[Toothbrush Lovers picture credit by Evan Romine]
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