Write BEP for uptake function

[cthoyt]

Much like secretion() and cellSurfaceExpression() it would be nice to have an intake() function that's syntactic sugar around the translocation() function that represents the opposite direction of movement from secretion().

This would have some nice examples for viruses pulling themselves into cells, for endocytosis of chemicals like neurotransmitters, and for chemicals activating receptors which then get endocytosis-ed as well

[ncatlett]

why not endocytosis() instead of intake()?

[johnbachman]

Yes, endocytosis would be a better name, unless you also mean to include active and passive transport processes for metabolites, electrolytes, etc.

On Wed, Jun 27, 2018 at 9:18 AM, Natalie Catlett notifications@github.com wrote:

why not endocytosis() instead of intake()?

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[cthoyt]

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

[ncatlett]

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 .

[cthoyt]

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

[cthoyt]

• CTD uses "uptake" as a general term and "import" as a more specific term (see: http://ctdbase.org/help/glossary.jsp)
• GO uses import into cell with synonym "uptake"

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