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ncatlett avatar ncatlett commented on August 16, 2024

why not endocytosis() instead of intake()?

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johnbachman avatar johnbachman commented on August 16, 2024

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cthoyt avatar cthoyt commented on August 16, 2024

Do you think endocytosis would be more appropriate for extracellular -> cytoplasm, cell surface -> cytoplasm, or both?

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ncatlett avatar ncatlett commented on August 16, 2024

I think both extracellular and cell membrane to cytoplasm (see http://purl.obolibrary.org/obo/GO_0006897), but that could be challenging for BEL purposes since the translocation term should connect A[loc1] to A[loc2].

going with a more generic import() (http://purl.obolibrary.org/obo/GO_0098657) would pose the same challenges, but would include the additional transport processes mentioned by @johnbachman .

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cthoyt avatar cthoyt commented on August 16, 2024

Perhaps this would warrant adding another field to the translocation() function to specify how translocation was done? Otherwise writing a translocation from the outside/surface of a cell to the inside loses the information on how it was done, and make endocytosis, active transport, passive transport, etc. effectively the same

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cthoyt avatar cthoyt commented on August 16, 2024

Without being so specific as to describe the method by which a molecule/protein/etc. moves into a cell, I think this might be the best term

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