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The Ontology for Biomedical Investigations
http://obi-ontology.org
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New term request: Cell Reprogramming #768

Open obi-bot opened 9 years ago

obi-bot commented 9 years ago

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

Reported by: sbjain

Original Ticket: obi/obi-terms/785

obi-bot commented 9 years ago

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?

Original comment by: zhengj2007

obi-bot commented 9 years ago

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.

Original comment by: sbjain

obi-bot commented 9 years ago

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/

Original comment by: bpeters42

obi-bot commented 9 years ago

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

Original comment by: sbjain

obi-bot commented 9 years ago

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.

Original comment by: cstoeckert

obi-bot commented 9 years ago

send iPSC term request to CLO: https://github.com/CLO-ontology/CLO/issues/24

Original comment by: zhengj2007