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

• 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?
• Can we sort the table by columns or rows?
• Can we show/hide columns
• Auto-suggest a term, then be able to walk up or down the tree for the most appropriate term

Phenotype Annotations

Example 1

Phenotype of	Taxon Information	Genotype Information (if known)	Condition Information	OMP ID	OMP Term Name	ECO ID	ECO Term Name	Notes	Status
a single strain under different conditions	Taxon: Escherichia coli Strain: K-12 Substrain: MG1655 NCBI Taxon ID: 511145	Genotype of Reference Strain:	Reference Condition: culture in exponential phase Experimental Condition: culture in stationary phase	OMP:0000001	decreased antibiotic resistance	[[:Category:ECO:0000001_!_inference_from_background_scientific_knowledge|ECO:0000001]]	plating dilutions	Example 4	complete
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: MG1655 NCBI Taxon ID: 511145	Genotype of Reference Strain: del-minB Genotype of Experimental Strain : del-minB slmA	Reference Condition:	OMP: 0000002	lethality	[[:Category:ECO:0000001_!_inference_from_background_scientific_knowledge|ECO:0000001]]	inability to construct this strain	Example 3	complete
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: MG1655 NCBI Taxon ID: 511145	Genotype of Reference Strain: parE (ts) Genotype of Experimental Strain : parE(ts), dnaX expressed at high copy	Reference Condition: at permissive temperature Experimental Condition: at restrictive temperature	OMP:0000003	partial suppression of phenotype	[[:Category:ECO:0000003_!_reconstitution_assay_evidence|ECO:0000003]]	high copy suppressor screen	Example 2- need a place for "temperature-sensitive" and another box will drop so user can fill in the phenotype description in OMP terms.	complete
a distinct species or taxonomic entity	Taxon: Escherichia coli Strain: K-12 Substrain: MG1655 NCBI Taxon ID: 511145	Genotype of Reference Strain:	Reference Condition: exponential phase culture in rich medium	OMP: 0000004	bacillus cell shape	[[:Category:ECO:0000004_!_cell_fractionation_evidence|ECO:0000004]]	microscopy		complete
a single strain under different conditions	Taxon: Escherichia coli Strain: K-12 Substrain: MG1655 NCBI Taxon ID: 511145	Genotype of Reference Strain:	Reference Condition: exponential phase culture in rich medium Experimental Condition: stationary phase culture in rich medium	OMP: 000000	shortening of cell length	[[:Category:ECO:0000004_!_cell_fractionation_evidence|ECO:0000004]]	microscopy	trying to get at the rod to round transition E.coli makes when going from exponential to stationary phase.	complete
a mutation or genetic difference within a strain	Taxon: Escherichia coli Strain: K-12 Substrain: MG1655 NCBI Taxon ID: 511145	Genotype of Reference Strain: wt Genotype of Experimental Strain : parE10	Reference Condition: at permissive temperature Experimental Condition: at restrictive temperature	OMP: 000000	filamentation	[[:Category:ECO:0000004_!_cell_fractionation_evidence|ECO:0000004]]	microscopy	Example 1- temperature-sensitive	complete
a single strain under different conditions	Taxon: Escherichia coli Strain: K-12 Substrain: MG1655 NCBI Taxon ID: 511145	Genotype of Reference Strain: mdtEF	Reference Condition: in anaerobically grown cells	OMP: 000000	increased efflux activity	ECO:000000	transport assay	Example 6 (Phage # 81)- "Expression of mdtEF is up-regulated more than 20-fold by the anaerobic global regulator ArcA, resulting in increased efflux activity and enhanced drug tolerance in anaerobically grown "'E.coli cells."	complete
a single strain under different conditions	Taxon: Escherichia coli Strain: K-12 Substrain: MG1655 NCBI Taxon ID: 511145	Genotype of Reference Strain: dskA	Reference Condition: upon amino acid starvation	OMP: 000000	fast stop DNA replication defect	ECO:000000	thymidine incorporation	Example 5 (Phage # 29)- "In the absence of DskA, replication is rapidly arrested upon amino acid starvation."	complete
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Example 2

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

OMP Accession	Taxon Information	Genotype Information (if known)	OMP ID	OMP Term Name	Phenotype Details	Related Rows	ECO ID	ECO Term Name	Notes	Status
2	Taxon: Escherichia coli Strain: K-12 Substrain: MG1655 NCBI Taxon ID: 511145	Genotype of Parent: Lam- rph- F- Genetic Difference of Mutant : lacZ-	OMP: 0000002	loss of utilization of carbon source	chemical:lactose	derivative of parent:OMP 1	ECO:0000001	plating on indicator medium	Figure 1	complete
3	Taxon: Escherichia coli Strain: K-12 Substrain: MG1655 NCBI Taxon ID: 511145	Genotype of Parent: Lam-rph- F- Genetic Difference of Mutant : parC-	OMP: 0000003	filamented cells	temperature sensitive:37C	complex phenotype:3	ECO:0000002	Microscopy	Figure 1	complete
1	Taxon: Escherichia coli Strain: K-12 Substrain: MG1655 NCBI Taxon ID: 511145	Genotype of Parent: Lam-rph- F-	OMP: 0000001	utilization of carbon source	chemical:lactose	parent:	ECO:0000001	plating on indicator medium	Figure 1	complete
4	Taxon: Escherichia coli Strain: K-12 Substrain: MG1655 NCBI Taxon ID: 511145	Genotype of Parent: Lam-rph- F- Genetic Difference of Mutant : parC-	OMP: 0000004	centered nucleoid	temperature sensitive:37C	complex phenotype:3	ECO:0000002	Microscopy	Figure 1	complete
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