refactor: RNA formation, issue #354 #364
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add RNA in nucleus
add reaction MAR13086, transport of RNA from nucleus to cytoplasm
implement the suggestions of issue SysBioChalmers#354 - add compartmentalised metabolite RNA[n] (MAM02847n) - change reaction MAR07161 (RNA creation) from cytoplasm to nucleus - add transport reaction of RNA from the nucleus to cytoplasm (MAR13086) - move gene rule of reaction MAR08639 to reaction MAR13086, as it represents the nuclear pore complex - swap the direction of reaction MAR07162, as explained in issue SysBioChalmers#354 - remove the reaction of DNA transport between the nucleus and cytoplasm MAR08639, since DNA shouldn't go out of the nucleus and the reaction's gene rule is no longer needed
delete reaction MAR08639 and add reaction MAR13086
JonathanRob
requested changes
Feb 18, 2022
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not sure what is the appropriate reaction score for reaction MAR13086
Eh, good question. I think you can use the same score as was used for MAR08639, which was a 2.
and could not find ids form other databases for this reaction, probably beacause RNA has to be first processed into mature RNA (with polyA-tail and 5'Cap) before moving to cytoplasm...
Yeah, it's a very simplified representation of the process, so if you were not able to find anything from other databases after searching for a bit, then I think it's OK to leave it as is.
add deleted reaction MAR08639 to deprecatedReactions.tsv
score of reaction MAR13086 changed to 2
JonathanRob
approved these changes
Feb 21, 2022
mihai-sysbio
changed the title
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Main improvements in this PR:
implement the suggestions of issue #354
Comments:
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