Difference between revisions of "PMID Table Mock-up"

From OMPwiki
(Table edited by Azweifel via TableEdit)
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==Phenotype Annotations==
 
==Phenotype Annotations==
{{AnnotationTableHelp}}
+
===Example 1===
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*  
 
*  
 
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{|  id="H4dfa55081758a"  class=" tableEdit PMID_Relative_Phenotype_table"   
+
{|  id="G4e4e87bf879db"  class=" tableEdit Phenotype_Table_2"   
 
|-
 
|-
!|OMP Accession!!Taxon Information!!Genotype Information (if known)!!OMP ID!!OMP Term Name!!Phenotype Details!!Related Rows!!ECO ID!!ECO Term Name!!Notes!!Status
+
!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status
 
|-  
 
|-  
 
|
 
|
2
+
a single strain under different conditions
 
|
 
|
 
*Taxon: Escherichia coli
 
*Taxon: Escherichia coli
Line 33: Line 33:
 
*NCBI Taxon ID: 511145
 
*NCBI Taxon ID: 511145
 
|
 
|
*Genotype of Parent: Lam- rph- F-
+
*Genotype of Reference Strain:
*Genetic Difference of Mutant : lacZ-
 
 
|
 
|
OMP: 0000002
+
*Reference Condition: culture in exponential phase
 +
*Experimental Condition: culture in stationary phase
 
|
 
|
loss of utilization of carbon source
+
OMP: 0000001
 
|
 
|
chemical:lactose
+
decreased antibiotic resistance
|
 
derivative of parent:OMP 1
 
 
|
 
|
 
ECO:0000001
 
ECO:0000001
 
|
 
|
plating on indicator medium
+
plating dilutions
 
|
 
|
Figure 1
+
 
 
|
 
|
 
complete  
 
complete  
 
|-  
 
|-  
 
|
 
|
3
+
a mutation or genetic difference within a strain
 
|
 
|
 
*Taxon: Escherichia coli
 
*Taxon: Escherichia coli
Line 60: Line 58:
 
*NCBI Taxon ID: 511145
 
*NCBI Taxon ID: 511145
 
|
 
|
*Genotype of Parent: Lam-rph- F-
+
*Genotype of Reference Strain: del-minB
*Genetic Difference of Mutant : parC-
+
*Genotype of Experimental Strain : del-minB slmA
 
|
 
|
OMP: 0000003
+
*Reference Condition:
 
|
 
|
filamented cells
+
OMP: 0000002
 
|
 
|
temperature sensitive:37C
+
lethality
 
|
 
|
complex phenotype:3
+
ECO:0000001
 
|
 
|
ECO:0000002
+
inability to construct this strain
 
|
 
|
Microscopy
+
 
|
 
Figure 1
 
 
|
 
|
 
complete  
 
complete  
 
|-  
 
|-  
 
|
 
|
1
+
a mutation or genetic difference within a strain
 
|
 
|
 
*Taxon: Escherichia coli
 
*Taxon: Escherichia coli
Line 87: Line 83:
 
*NCBI Taxon ID: 511145
 
*NCBI Taxon ID: 511145
 
|
 
|
*Genotype of Parent: Lam-rph- F-
+
*Genotype of Reference Strain: parE (ts)
 +
*Genotype of Experimental Strain : parE(ts) dnaX expressed at high copy
 
|
 
|
OMP: 0000001
+
*Reference Condition:
 
|
 
|
utilization of carbon source
+
OMP: 0000003
 
|
 
|
chemical:lactose
+
suppression of phenotype
 
|
 
|
parent:
+
ECO:0000003
 
|
 
|
ECO:0000001
+
high copy suppressor screen
 
|
 
|
plating on indicator medium
+
 
|
 
Figure 1
 
 
|
 
|
 
complete  
 
complete  
 +
 +
|- class="tableEdit_footer"
 +
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=2ccfb3c7bf1208312f02a69e64bfd9e0.2146.G4e4e87bf879db&page=2146&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</span> || || || || || || || || ||
 +
|}
 +
<!--box uid=2ccfb3c7bf1208312f02a69e64bfd9e0.2146.G4e4e87bf879db--></protect>
 +
 +
 +
===Example 2===
 +
{{AnnotationTableHelp}}
 +
<protect><!--box uid=2ccfb3c7bf1208312f02a69e64bfd9e0.2146.H4dfa55081758a-->
 +
<!--
 +
******************************************************************************************
 +
*
 +
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
 +
*
 +
****************************************************************************************** -->
 +
{|  id="H4dfa55081758a"  class=" tableEdit PMID_Relative_Phenotype_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
 
|-  
 
|-  
 
|
 
|
4
+
2
 
|
 
|
 
*Taxon: Escherichia coli
 
*Taxon: Escherichia coli
Line 113: Line 127:
 
*NCBI Taxon ID: 511145
 
*NCBI Taxon ID: 511145
 
|
 
|
*Genotype of Parent: Lam-rph- F-
+
*Genotype of Parent: Lam- rph- F-
*Genetic Difference of Mutant : parC-
+
*Genetic Difference of Mutant : lacZ-
 
|
 
|
OMP: 0000004
+
OMP: 0000002
 
|
 
|
centered nucleoid
+
loss of utilization of carbon source
 
|
 
|
temperature sensitive:37C
+
chemical:lactose
 
|
 
|
complex phenotype:3
+
derivative of parent:OMP 1
 
|
 
|
ECO:0000002
+
ECO:0000001
 
|
 
|
Microscopy
+
plating on indicator medium
 
|
 
|
 
Figure 1
 
Figure 1
 
|
 
|
 
complete  
 
complete  
 
|- class="tableEdit_footer"
 
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=2ccfb3c7bf1208312f02a69e64bfd9e0.2146.H4dfa55081758a&page=2146&pagename={{FULLPAGENAMEE}}&type=0&template=PMID_Relative_Phenotype_table edit table]</span> || || || || || || || || || ||
 
|}
 
<!--box uid=2ccfb3c7bf1208312f02a69e64bfd9e0.2146.H4dfa55081758a--></protect>
 
 
 
<protect><!--box uid=2ccfb3c7bf1208312f02a69e64bfd9e0.2146.G4e4e87bf879db-->
 
<!--
 
******************************************************************************************
 
*
 
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
 
*
 
****************************************************************************************** -->
 
{|  id="G4e4e87bf879db"  class=" tableEdit Phenotype_Table_2" 
 
|-
 
!|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
+
3
 
|
 
|
 
*Taxon: Escherichia coli
 
*Taxon: Escherichia coli
Line 157: Line 154:
 
*NCBI Taxon ID: 511145
 
*NCBI Taxon ID: 511145
 
|
 
|
*Genotype of Reference Strain:
+
*Genotype of Parent: Lam-rph- F-
 +
*Genetic Difference of Mutant : parC-
 +
|
 +
OMP: 0000003
 
|
 
|
*Reference Condition: culture in exponential phase
+
filamented cells
*Experimental Condition: culture in stationary phase
 
 
|
 
|
OMP: 0000001
+
temperature sensitive:37C
 
|
 
|
decreased antibiotic resistance
+
complex phenotype:3
 
|
 
|
ECO:0000001
+
ECO:0000002
 
|
 
|
plating dilutions
+
Microscopy
 
|
 
|
 
+
Figure 1
 
|
 
|
 
complete  
 
complete  
 
|-  
 
|-  
 
|
 
|
a mutation or genetic difference within a strain
+
1
 
|
 
|
 
*Taxon: Escherichia coli
 
*Taxon: Escherichia coli
Line 182: Line 181:
 
*NCBI Taxon ID: 511145
 
*NCBI Taxon ID: 511145
 
|
 
|
*Genotype of Reference Strain: del-minB
+
*Genotype of Parent: Lam-rph- F-
*Genotype of Experimental Strain : del-minB slmA
+
|
 +
OMP: 0000001
 
|
 
|
*Reference Condition:
+
utilization of carbon source
 
|
 
|
OMP: 0000002
+
chemical:lactose
 
|
 
|
lethality
+
parent:
 
|
 
|
 
ECO:0000001
 
ECO:0000001
 
|
 
|
inability to construct this strain
+
plating on indicator medium
 
|
 
|
 
+
Figure 1
 
|
 
|
 
complete  
 
complete  
 
|-  
 
|-  
 
|
 
|
a mutation or genetic difference within a strain
+
4
 
|
 
|
 
*Taxon: Escherichia coli
 
*Taxon: Escherichia coli
Line 207: Line 207:
 
*NCBI Taxon ID: 511145
 
*NCBI Taxon ID: 511145
 
|
 
|
*Genotype of Reference Strain: parE (ts)
+
*Genotype of Parent: Lam-rph- F-
*Genotype of Experimental Strain : parE(ts) dnaX expressed at high copy
+
*Genetic Difference of Mutant : parC-
 +
|
 +
OMP: 0000004
 
|
 
|
*Reference Condition:
+
centered nucleoid
 
|
 
|
OMP: 0000003
+
temperature sensitive:37C
 
|
 
|
suppression of phenotype
+
complex phenotype:3
 
|
 
|
ECO:0000003
+
ECO:0000002
 
|
 
|
high copy suppressor screen
+
Microscopy
 
|
 
|
 
+
Figure 1
 
|
 
|
 
complete  
 
complete  
  
 
|- class="tableEdit_footer"  
 
|- class="tableEdit_footer"  
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=2ccfb3c7bf1208312f02a69e64bfd9e0.2146.G4e4e87bf879db&page=2146&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table]</span> || || || || || || || || ||
+
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=2ccfb3c7bf1208312f02a69e64bfd9e0.2146.H4dfa55081758a&page=2146&pagename={{FULLPAGENAMEE}}&type=0&template=PMID_Relative_Phenotype_table edit table]</span> || || || || || || || || || ||
 
|}
 
|}
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+
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Revision as of 14:27, 19 August 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

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

ECO:0000001

plating dilutions

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:0000001

inability to construct this strain

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:

OMP: 0000003

suppression of phenotype

ECO:0000003

high copy suppressor screen

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