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#785 New term request: Cell Reprogramming
editor preferred term: Cell Reprogramming
alternative terms: Reprogramming, Cellular reprogramming
textual definition: Is a planned process with an objective of transforming one adult somatic cell type into an induced pluripotent stem cell.
definition source for the textual definition: https://www.stemgent.com/knowledge/cellular_reprogramming
logical definition (or parent term): Processed material -> Cell culture
term editor: Sagar Jain
Shall we specify:
cell reprogramming
has_specified_input some 'somatic cell' http://purl.obolibrary.org/obo/CL_0002371
has_specified_output some 'induced pluripotent stem cell' http://www.ebi.ac.uk/efo/EFO_0004905
Notes: 'induced pluripotent stem cell' is a subClassOf 'pluripotent stem cell' http://purl.obolibrary.org/obo/CL_0002248
However, the cell terms defined in CL are native cell or in vivo cell. The cells used in the reprogramming are cells in vitro. How to deal with this?
Great point, we can specify this by:
http://purl.obolibrary.org/obo/CL_0001034
has_specified_input some 'cell in vitro'
definition: A cell that is maintained or propagated in a controlled artificial environment for use in an investigation.
Revised definition: Is a planned process with an objective of transforming an input of some cell in vitro, with some somatic cell type, to an output of some induced pluripotent stem cell.
Call 11/9:
Change planned process --> material transformation.
Revised label: 'reprogramming cells to induced pluripotent stem cells'
Revised textual definition:
Is a material transformation with an objective of transforming somatic cells in vitro into induced pluripotent stem cells.
has_specified_input some 'cell in vitro' and ('derived from' some 'somatic cell')
has_specified_output some 'induced pluripotent stem cell' http://www.ebi.ac.uk/efo/EFO_0004905
In general, we need to have a clear design pattern that specifies exactly how an in vitro cell is linked to the originalting cell in vivo. 'Derived from' is not ideal. Maybe transformed from is better, but this is a general issue. Linked to: https://sourceforge.net/p/obi/obi-terms/765/
editor preferred term: reprogramming cells to induced pluripotent stem cells
alternative terms: stem cell reprogramming, iPSC reprogramming
textual definition: Is a material transformation with an objective of transforming somatic cells in vitro into induced pluripotent stem cells.
definition source for the textual definition: https://www.stemgent.com/knowledge/cellular_reprogramming
logical definition (or parent term): Processed material -> Cell culture
has_specified_input some 'cell in vitro' and ('derived from' some 'somatic cell')
has_specified_output some 'induced pluripotent stem cell'
term editor: Sagar Jain
Still have issues with logical axioms as discussed on Nov. 16 call. EFO's iPSC is not defined as an in vitro cell which is the output of this process.
has_specified_input some 'somatic cell' because most people care about where the cell came from.
This touches on the issue of simplifying the axioms to what people need and are interested in. This aproach should be our general pattern for these axioms.
Last edit: Chris Stoeckert 2015-11-16
send iPSC term request to CLO: https://github.com/CLO-ontology/CLO/issues/24