O'Really?

April 10, 2008

Would you like to share my toothbrush?

Filed under: informatics — Duncan Hull @ 4:30 pm
Tags: , , , , , , ,

Toothbrush Lovers by Evan RomineMichael 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

  1. Helen Pearson (2001) Biology’s Name Game Nature 411, 631 – 632 (2001) doi:10.1038/35079694, pubmed.gov/11395736.
  2. 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
  3. 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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