Lewis blood group biosynthesis (R-HSA-9037629)

[ukemi]

• [ ] Make mouse models
  • [X] Lewis X
  • I'm not certain how transferable all of these pathways are to the mouse. Since they are defined by antibody reactivity, some don't have exactly the same oligosaccharide structure in the mouse even though the antibodies still react (PMID:19089612) Maybe close this and move on?
• [x] Not specific to this, but Rhesus blood group is a protein metabolism, but in the Reactome hierarchy it is under carbohydrate metabolism.

[deustp01]

Details of Rhesus true path violation (protein synthesis events made is_a children of carbohydrate metabolism) and possible fix: David Hill has noticed an inconsistency in our “Blood group systems biosynthesis” pathway (R-HSA-9033658). This pathway has three child pathways, for the synthesis of ABO, Lewis, and Rhesus blood group antigens, and is itself a child of “Metabolism of carbohydrates” (R-HSA-71387). Lewis and ABO blood group antigens are oligosaccharides, so their biosynthesis is indeed a kind of carbohydrate biosynthesis. The Rhesus antigens, however, are highly polymorphic proteins and the only feature of their biosynthesis we annotate is the black-box transcription of the Rhesus genes to yield protein products (R-HSA-9037628), so no carbohydrate metabolism is involved and the Rhesus pathway is out of place. We actually already acknowledge this discrepancy in our annotation: the ABO and Lewis pathways have GO:0009312 “oligosaccharide biosynthetic process” as their GO biological process term, while the Rhesus pathway has GO:0043043 “peptide biosynthetic process”. Where should we put it instead? One possibility would be to create a new grouping pathway, “Translation of individual proteins”, and make this new pathway a child of R-HSA-72766, “Translation”, hence a sibling of the pathways that describe the details of specific steps of translation, tRNA aminoacylation, translation initiation, etc.). The current Rhesus pathway could then be a child of this one.

[deustp01]

Alignment of human Reactome reactions with RHEA counterparts would be appropriate as part of this ticket, but as for #180 defer to future to await expertise in carbohydrate chemistry.