PMID Table Mock-up

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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
[[Category:OMP:0000001_!_motility_phenotype|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

ECO:000000

inability to construct this strain

Example 3- we need to capture the "synthetic lethal"

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: parE10 (ts)
  • Genotype of Experimental Strain : parE(ts), dnaX expressed at high copy
  • Reference Condition: at restrictive temperature
  • Experimental Condition: at restrictive temperature
OMP:000000

partial suppression of phenotype

ECO:000000

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

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

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 restrictive temperature

OMP: 000000

filamentation

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


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