Fix: GPR curation for Glycosphingolipid metabolism

[JHL-452b]

Main improvements in this PR:

As proposed in #893 #894 #895 :

• Remove ENSG00000174684 from MAR00889;
• Remove ENSG00000102595, ENSG00000134910, ENSG00000163527, ENSG00000119227, ENSG00000177191, ENSG00000069943, ENSG00000175711, ENSG00000139044, ENSG00000156966, ENSG00000060642, ENSG00000162885, ENSG00000172461, ENSG00000176383, ENSG00000147162, ENSG00000136731, ENSG00000180549, ENSG00000085998, ENSG00000143315, ENSG00000198488, ENSG00000170340, ENSG00000109586, ENSG00000179913, ENSG00000172728, ENSG00000176597, ENSG00000196371, ENSG00000182272 from MAR00924;
• Remove ENSG00000134910, ENSG00000069943, ENSG00000162885, ENSG00000176383, ENSG00000136731, ENSG00000180549, ENSG00000167889, ENSG00000175711, ENSG00000172461, ENSG00000177191, ENSG00000170340, ENSG00000139044, ENSG00000060642, ENSG00000179913, ENSG00000187676, ENSG00000147162, ENSG00000176597, ENSG00000143315, ENSG00000198488, ENSG00000102595 from MAR00925;
• Remove ENSG00000102595, ENSG00000134910, ENSG00000163527, ENSG00000119227, ENSG00000109586, ENSG00000139044, ENSG00000156966, ENSG00000060642, ENSG00000187676, ENSG00000162885, ENSG00000176383, ENSG00000136731, ENSG00000172728, ENSG00000180549, ENSG00000085998, ENSG00000198488, ENSG00000167889, ENSG00000170340, ENSG00000175711, ENSG00000143315, ENSG00000069943, ENSG00000147162, ENSG00000176597, ENSG00000177191 from MAR00926;
• Remove ENSG00000138641 from MAR08379;
• Remove ENSG00000138641 from MAR07185;
• Remove ENSG00000156413 from MAR00873.

I hereby confirm that I have:

• Tested my code on my own computer for running the model
• Selected develop as a target branch
• Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists

[github-actions]

This PR has been automatically tested with GH Actions. Here is the output of the MACAW test:

Starting dead-end test...
 - Found 1523 dead-end metabolites.
 - Found 1328 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
 - Found 1975 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends.
Starting duplicate test...
 - Skipping redox duplicates because no redox_pairs and/or proton_ids were provided.
 - Found 447 reactions that were some type of duplicate:
   - 0 were completely identical to at least one other reaction.
   - 13 involve the same metabolites but go in the opposite direction or have the opposite reversibility as at least one other reaction.
   - 447 involve the same metabolites but with different coefficients as at least one other reaction.

This and a more detailed output from MACAW are also committed to data/macawResults/.

Note: In the case of multiple test runs, this post will be edited.

[hhl-24]

LGTM!

[github-actions]

This PR has been automatically tested with GH Actions. Here is the output of the gene essentiality test:

     cellLine     TP     TN     FP     FN     accuracy    sensitivity    specificity       F1         MCC   
    __________    __    ____    ___    ___    ________    ___________    ___________    ________    ________

    {'DLD1'  }    50    2141     84    270     0.8609       0.15625        0.96225       0.22026     0.17591
    {'GBM'   }    57    2132     77    278    0.86046       0.17015        0.96514       0.24307      0.2048
    {'HCT116'}    71    2173     69    287    0.86308       0.19832        0.96922       0.28514     0.25578
    {'HELA'  }    35    2213    105    249    0.86395       0.12324         0.9547       0.16509     0.10772
    {'RPE1'  }    21    2156    113    254    0.85574      0.076364         0.9502       0.10269    0.036922
    {'all'   }     8    2350    132    112    0.90623      0.066667        0.94682      0.061538    0.012534

Note: In the case of multiple test runs, this post will be edited.