PMID Table Mock-up

Background

It was discussed at the June meeting that the phenotype annotation table on the literature page needs to be reformatted. The user would select whether the phenotype entered was for a taxonomic entity (state phenotype) or a genetic difference (relative). Once this selection has been made, the nature of the table headings would change to reflect this selection. Below are the mock-ups for the different tables. Additional changes are listed.

• add “Relative to” column so people can input the reference (e.g. with respect to WT, single mutant, etc).
• information regarding the species, taxon ID, and "genetic difference" (to replace "gene name") would be displayed in one box instead of multiple boxes across the table
• linking multiple single annotations together for the purpose of capturing more complex single phenotypes. The idea of setting IDs for the individual annotations (rows) and linking them together

Issues to be Discussed

• 1 vs. 2 tables
• How would we parse the "Taxon Information"?
• How would we link rows together to capture complex phenotypes?
• How would we capture the "wild type" or "parent" phenotypes in a paper and will these be marked within the table?

Debby's suggestions

• Change "Genus and species" to "Organism"
• For E. coli, at least, need to add substrain
• Come up with more user-friendly names for tables

Relative Phenotype Annotations

See Help:AnnotationTable for details on how to edit this table.

Taxon Information	Relative To	OMP ID	OMP Term Name	With/From	ECO ID	ECO Term Name	Notes
Genus and Species: Escherichia coli Strain: K-12 substrain: MG1655 NCBI Taxon ID: 511145 Genetic Difference (if known): lacZ- (describe a single mutation)	lacZ+	OMP:0000001	Automatic Fill-in	This will appear when certain terms are selected	ECO:0000001	Automatic Fill-in	Table 1
Genus and Species: Escherichia coli Strain: K-12 substrain: MG1655 NCBI Taxon ID: 511145 Genetic Difference (if known): ftsK- (describe a double mutant?)	ftsK+ ftsZ-	OMP:0000001	Automatic Fill-in	It may not be called "with/from," but you get the idea	ECO:0000001	Automatic Fill-in	Figure 2
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State Phenotype Annotations

This table is meant to describe the phenotype for a taxonomic entity.

See Help:AnnotationTable for details on how to edit this table.

Taxon Information	OMP ID	Term Name	With/From	ECO ID	ECO Term Name	Notes
Genus and Species: Escherichia coli Strain: MG1655 NCBI Taxon ID: 511145	OMP:xxxxxxx	Automatic Fill-in	This will appear when certain terms are selected.	ECO:xxxxxxx	Microscopy	Figure 1
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