clarifications sought for: genetic modification

[obi-bot]

http://purl.obolibrary.org/obo/OBI_0001151

Definition: A material entity, organism or cell, that is the output of a genetic transformation process

material entity subsumes organism or cell so why not just say material entity?

The equivalence axiom is odd:

      genetically modified organism or ((cell
      and (is_specified_output_of
      some 
      genetic transformation)))

it seems to preclude other material entities.

based on the definition of http://purl.obolibrary.org/obo/OBI_0000312 is specified output of, which is a subprop of participation, something ceases to be GM material after it stops participating in the GM process, and the property would not be inherited across generations. This may not align with intuitive expectatiions

The process http://purl.obolibrary.org/obo/OBI_0600043 genetic transformation

Definition: The introduction, alteration or integration of genetic material into a cell or organism

Seems quite odd and would encompass traditional breeding, as well as natural UV radiation etc

More broadly: is this even a biologically useful grouping? genetic modification (in the stricter sense of directed modification using modern recombinant techniques) encompasses a range of techniques (many missing from OBI, .e.g. CRISPR-Cas9) it's not clear which of these this is intended to group.

The term 'genetic modification' has a regulatory meaning as well, but this may be relative to different states or transnational organizations

Reported by: cmungall

Original Ticket: obi/obi-terms/797

[obi-bot]

Discussed on March 14, 2016 call.
Three issues:

1. Material entity or just organism and cell. We think just organism and cell if to be inherited. Question of a person injected in liver with viruses for gene therapy - are they now genetically modified?
2. Genetic transformation definition. Agree that it should reflect modern recombinant techniques and not breeding or UV irradiation.
3. specified output. the fact of participation does not change at the end of a planned process therefore we think specified outputs continue to be participants. Point about passing on to offspring is a good one that we agree with the intuition is that the offspring are also genetically modified. Should look at other RO options. Need to add to additional relation to capture.

Follow ups are to identify and add an appropriate relation for capturing inheritance of the modification. Clarification of definitions as noted.

Original comment by: cstoeckert

[obi-bot]

• assigned_to: Chris Stoeckert

Original comment by: cstoeckert

[obi-bot]

How about adding 'derives from' to the definition? as in:
'genetically modified organism' or (cell and (is_specified_output_of some genetic transformation)) or derives_from some 'genetically modified organism' or derives_from (cell and (is_specified_output_of some genetic transformation))
Given that we are viewing genetically modified material as only organisms or cells, how about just making a genetically modified cell to simplify things. We can still keep 'genetically modified material' if needed and define as 'genetically modified organism' or 'genetically modified cell'

Original comment by: cstoeckert

[obi-bot]

I think that's better

My personal preference is to avoid long complicated definitions with unions, and to instead break things down into named classes.

• an insertion event
• a progenitor genome
• organisms with genomes derived from that progenitor

Each could have its own named class. This might be useful anyway, to allow people to better describe a sequence of events. The complexity of the class definition could be spread across these.

But onto the broader point, maybe we're thinking at the wrong level. A formal biological description for a grouping class that IMHO is not so useful for biologists. As a grouping class it may be more useful in plant/food regulatory contexts, but this may be out of scope for OBI.

Original comment by: cmungall