How to capture the host cell/tissue where a microbial phenotype occurs

[dsiegele]

microbe-host interaction phenotypes

Specific issue: The authors assayed the ability of various Salmonella mutants to invade and replicate inside different macrophage cell lines. Do we capture the macrophage cell line information as an extension to the OMP term? or as part of the environment? or both?

[dsiegele]

You can see an example in the annotations table on this OMP page:

https://microbialphenotypes.org/wiki/index.php?title=OMP_ST:74684_!_Salmonella_enterica_subsp._enterica_serovar_Typhimurium_HA420

[dsiegele]

The issue was discussed in an OMP call on xxxx.

• We agreed that this is a good idea, but not sure how to implement it.
• DAS was tasked with looking for sources of identifiers that could be used.
• The question of where to capture this information in an annotation is still open for discussion.

[dsiegele]

The Cell Line Ontology (CLO) may be a source of identifiers. For example, CLO has accessions for several mouse macrophage cell lines including J774A.1, which was used in the paper referenced in the previous comment.

[dsiegele]

Discussed in OMP call on 7/112/2019. The consensus among the three of us on the call (Michelle, Jim, and Debby) was that information about the cell type or cell line where the experiments were performed would be captured in the evidence.

The Cell Ontology (CO) is another source of stable identifiers for cell types in animal cells.