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Porthmeus / MeMoMe

Metabolic Model Merging - a semiautomated way to merge genome scale metabolic models
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Annotate inchi might annotate Inchis with conflicting charges #137

Open Porthmeus opened 2 months ago

Porthmeus commented 2 months ago

As we observed in a test case, it might happen, that Inchi strings get annotated which differ in charge with the charge that is encoded in the SBML model for the metabolite. This could lead to problems during model merging later on - depending on which route we go there. We could improve that, if we choose the inchi, which has smallest difference to the model encoded charge.

Unaimend commented 2 months ago

Could we create a minimal model that demonstrates this case? Then add this as a test case, so the behaviour is documented and tested

Unaimend commented 2 months ago

Output of branch origin/thomas/feature/81. Demonstrates the inchi overwriting python -m unittest tests.test_MeMoModel.Test_annotateBulkRoutines.test_annotationCount

glc__D_e
OLD InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1
NEW InChI=1S/C6H12O6/c7-1-3(9)5(11)6(12)4(10)2-8/h1,3-6,8-12H,2H2/t3-,4+,5+,6+/m0/s1

pi_c
OLD InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-1
NEW InChI=1S/Ca.2H3O4P/c;2*1-5(2,3)4/h;2*(H3,1,2,3,4)/q+2;;/p-4

pi_e
OLD InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-1
NEW InChI=1S/Ca.2H3O4P/c;2*1-5(2,3)4/h;2*(H3,1,2,3,4)/q+2;;/p-4

r5p_c
OLD InChI=1S/C5H11O8P/c6-3-2(1-12-14(9,10)11)13-5(8)4(3)7/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5+/m1/s1
NEW InChI=1S/C5H11O8P/c6-3-2(1-12-14(9,10)11)13-5(8)4(3)7/h2-8H,1H2,(H2,9,10,11)/p-2/t2-,3-,4-,5?/m1/s1

r5p_c
OLD InChI=1S/C5H11O8P/c6-3-2(1-12-14(9,10)11)13-5(8)4(3)7/h2-8H,1H2,(H2,9,10,11)/p-2/t2-,3-,4-,5?/m1/s1
NEW InChI=1S/C5H11O8P/c6-3-2(1-12-14(9,10)11)13-5(8)4(3)7/h2-8H,1H2,(H2,9,10,11)/p-2/t2-,3-,4-,5+/m1/s1

q8_c
OLD InChI=1S/C49H74O4/c1-36(2)20-13-21-37(3)22-14-23-38(4)24-15-25-39(5)26-16-27-40(6)28-17-29-41(7)30-18-31-42(8)32-19-33-43(9)34-35-45-44(10)46(50)48(52-11)49(53-12)47(45)51/h20,22,24,26,28,30,32,34H,13-19,21,23,25,27,29,31,33,35H2,1-12H3/b37-22+,38-24+,39-26+,40-28+,41-30+,42-32+,43-34+
NEW InChI=1S/C49H76O4/c1-36(2)20-13-21-37(3)22-14-23-38(4)24-15-25-39(5)26-16-27-40(6)28-17-29-41(7)30-18-31-42(8)32-19-33-43(9)34-35-45-44(10)46(50)48(52-11)49(53-12)47(45)51/h20,22,24,26,28,30,32,34,50-51H,13-19,21,23,25,27,29,31,33,35H2,1-12H3/b37-22+,38-24+,39-26+,40-28+,41-30+,42-32+,43-34+
Unaimend commented 2 months ago

@SteFlor I could need your help here for minimal model creating, Need a model that only contains the above metabolites

Porthmeus commented 1 month ago

I think I know how to fix the problem, let me try.