Edit: Renamed from upregulated by to upregulated in
Edit2: Renamed from upgregulated in to expressed in
We received new data and found that expressed in is a better descriptor of how the data was experimentally determined in the case of Chlamydia. In PMID 22014092, 426 proteins were found to be expressed in the EB form, while 269 were found to be expressed in the RB form.
Proposed mapping of a chlamydia protein to elementary body
Motivation
Chlamydia is an organism that takes several forms - an infectious form called the Elementary Body and a noninfectious form called the Reticulate Body. The form of Chlamydia determines which proteins are expressed. I propose we create a new property "expressed in" which would describe which proteins are expressed in different forms of an Organism.
biological phase (P4774) maps a biological process with a phase. A protein isn't really a biological process and doesn't really capture the fact that the protein is "enriched" in the elementary and/or reticulate body.Djow2019 (talk) 19:18, 24 July 2018 (UTC)[reply]
The domain of the property can be extended after a discussion. Without the quantitative expression levels, "upregulated" is very subjective, and the nuance of "enriched" is not so useful. I think it is enough to use biological phase (P4774) with a qualifier applies to part (P518)gene expression (Q26972). Apart from that, is this proposed property only used for elementary and reticulate body( of Chlamydia)? Also, are "elementary body" and "reticulate body" phase? or place? What do you think? --Okkn (talk) 15:07, 21 July 2018 (UTC)[reply]
EB and RB refer to the infectious and non infectious forms of Chlamydia, and the Chlamydia proteins are expressed in both forms. However, some proteins are "activated" more in one form, or they could even have the same level in both. Using applies to part (P518)gene expression (Q26972) wouldn't exactly tell us anything about the differential regulation because the proteins already exist in both forms and would always have that same qualifier regardless.Djow2019 (talk) 19:18, 24 July 2018 (UTC)[reply]
How do you deal with proteins equally expressed in both forms? They are not “upregulated”, are they? Also why can you say the protein is upregulated? Some proteins may not be upregulated, but be inversely downregulated in the other form. In addition, it would be better if there are quantitative data of (relative) expression levels. --Okkn (talk) 20:20, 24 July 2018 (UTC)[reply]
You are correct that when proteins appear in both forms, they are no longer "upregulated" in one form over the other. After discussion with domain expert, we found that the best term is actually expressed in and I have updated the post accordingly. Djow2019 (talk) 18:31, 2 August 2018 (UTC)[reply]
With regards to Okkn's comment on reusability and generalizability. This property could be applied to other biological entities which are upregulated during other time periods, biological phases, or specific conditions. For example, you could say what proteins or hormones or compounds are upregulated during stress, or during puberty. In fact I'd think creating both "upregulated in/during" and "downregulated in/during" would be useful for wikidata as a whole. Gstupp (talk) 19:34, 24 July 2018 (UTC)[reply]
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Comment "Elementary body" and "reticulate body" are phases of life cycle, right? We have already had biological phase (P4774), and it may used for this purpose. --Okkn (talk) 05:30, 18 July 2018 (UTC)
Support it. --Okkn (talk) 19:01, 2 August 2018 (UTC)
Done. Please make good use of it. --Okkn (talk) 14:27, 4 August 2018 (UTC)