Difference between revisions of "PMID Table Mock-up"

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(Table edited by Azweifel via TableEdit)
(Table edited by Azweifel via TableEdit)
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{|  id="H4dfa55081758a"  class=" tableEdit PMID_Relative_Phenotype_table"   
 
{|  id="H4dfa55081758a"  class=" tableEdit PMID_Relative_Phenotype_table"   
 
|-
 
|-
−
!|OMP Accession!!Taxon Information!!Genotype Information (if known)!!OMP ID!!OMP Term Name!!With/From!!ECO ID!!ECO Term Name!!Notes!!Status
+
!|OMP Accession!!Taxon Information!!Genotype Information (if known)!!OMP ID!!OMP Term Name!!With/From!!Accessions!!ECO ID!!ECO Term Name!!Notes!!Status
 
|-  
 
|-  
 
|
 
|
−
 
+
1
 
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*Taxon: Escherichia coli
 
*Taxon: Escherichia coli
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*NCBI Taxon ID: 511145
 
*NCBI Taxon ID: 511145
 
|
 
|
−
*Genotype or OMP Accession of Parent: Lam-rph- F-
+
*Genotype of Parent: Lam-rph- F-
 +
*Genetic Difference of Mutant : lacZ-
 
|
 
|
 
OMP: 0000001
 
OMP: 0000001
 
|
 
|
−
Automatic Fill-in
+
utilization of carbon source
 +
|
 +
lactose
 
|
 
|
  
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ECO:0000001
 
ECO:0000001
 
|
 
|
−
Automatic Fill-in
+
plating on indicator medium
 +
|
 +
Figure 1
 +
|
 +
complete
 +
|-  
 +
|
 +
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
 +
|
 +
absent utilization of carbon source
 +
|
 +
lactose
 +
|
 +
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
 +
|
 +
 
 +
|
 +
 
 +
|
 +
ECO:0000002
 +
|
 +
Microscopy
 +
|
 +
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
 +
|
 +
 
 +
|
 +
3
 +
|
 +
ECO:0000002
 +
|
 +
Microscopy
 
|
 
|
−
Table 2
+
Figure 1
 
|
 
|
−
+
complete
  
 
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Revision as of 15:59, 28 June 2011

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

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

OMP Accession Taxon Information Genotype Information (if known) OMP ID OMP Term Name With/From Accessions ECO ID ECO Term Name Notes Status

1

  • Taxon: Escherichia coli
  • Strain: K-12
  • Substrain: MG1655
  • NCBI Taxon ID: 511145
  • Genotype of Parent: Lam-rph- F-
  • Genetic Difference of Mutant : lacZ-

OMP: 0000001

utilization of carbon source

lactose

ECO:0000001

plating on indicator medium

Figure 1

complete

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

absent utilization of carbon source

lactose

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

ECO:0000002

Microscopy

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

3

ECO:0000002

Microscopy

Figure 1

complete

edit table

</protect>

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