View source for 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===
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{|   id="G4e4e87bf879db"  class=" tableEdit Phenotype_Table_2"  
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!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status
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a single strain under different conditions
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*Taxon: Escherichia coli
*Strain: K-12
*Substrain: MG1655
*NCBI Taxon ID: 511145
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*Genotype of Reference Strain:
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*Reference Condition: culture in exponential phase
*Experimental Condition: culture in stationary phase
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OMP:0000001
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decreased antibiotic resistance
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ECO:0000001
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plating dilutions
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Example 4
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complete 
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a mutation or genetic difference within a strain
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*Taxon: Escherichia coli
*Strain: K-12
*Substrain: MG1655
*NCBI Taxon ID: 511145
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*Genotype of Reference Strain: del-minB
*Genotype of Experimental Strain : del-minB slmA
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*Reference Condition:
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OMP: 0000002
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lethality
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ECO:000000
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inability to construct this strain
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Example 3- we need to capture the "synthetic lethal"
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complete 
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a mutation or genetic difference within a strain
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*Taxon: Escherichia coli
*Strain: K-12
*Substrain: MG1655
*NCBI Taxon ID: 511145
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*Genotype of Reference Strain: parE10 (ts)
*Genotype of Experimental Strain : parE(ts), dnaX expressed at high copy
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*Reference Condition: at restrictive temperature
*Experimental Condition: at restrictive temperature
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OMP:000000
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partial suppression of phenotype
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ECO:000000
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high copy suppressor screen
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Example 2- need a place for "temperature-sensitive" and another box will drop so user can fill in the phenotype description in OMP terms.
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complete 
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a distinct species or taxonomic entity
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*Taxon: Escherichia coli
*Strain: K-12
*Substrain: MG1655
*NCBI Taxon ID: 511145
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*Genotype of Reference Strain:
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*Reference Condition: exponential phase culture in rich medium
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OMP: 0000004
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bacillus cell shape
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ECO:0000004
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microscopy
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complete 
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a single strain under different conditions
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*Taxon: Escherichia coli
*Strain: K-12
*Substrain: MG1655
*NCBI Taxon ID: 511145
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*Genotype of Reference Strain:
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*Reference Condition: exponential phase culture in rich medium
*Experimental Condition: stationary phase culture in rich medium
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OMP: 000000
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shortening of cell length
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ECO:0000004
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microscopy
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trying to get at the rod to round transition ''E.coli'' makes when going from exponential to stationary phase.
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complete 
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a mutation or genetic difference within a strain
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*Taxon: Escherichia coli
*Strain: K-12
*Substrain: MG1655
*NCBI Taxon ID: 511145
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*Genotype of Reference Strain: wt
*Genotype of Experimental Strain : parE10
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*Reference Condition: at restrictive temperature
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OMP: 000000
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filamentation
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ECO:0000004
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microscopy
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Example 1- temperature-sensitive
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complete 
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a single strain under different conditions
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*Taxon: Escherichia coli
*Strain: K-12
*Substrain: MG1655
*NCBI Taxon ID: 511145
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*Genotype of Reference Strain: mdtEF
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*Reference Condition: in anaerobically grown cells
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OMP: 000000
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increased efflux activity
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ECO:000000
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transport assay
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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." 
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complete 
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a single strain under different conditions
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*Taxon: Escherichia coli
*Strain: K-12
*Substrain: MG1655
*NCBI Taxon ID: 511145
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*Genotype of Reference Strain: dskA
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*Reference Condition: upon amino acid starvation
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OMP: 000000
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fast stop DNA replication defect
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ECO:000000
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thymidine incorporation
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Example 5 (Phage # 29)- "In the absence of DskA, replication is rapidly arrested upon amino acid starvation."
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complete 

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|<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> || || || || || || || || ||
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===Example 2===
{{AnnotationTableHelp}}
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*   ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. ** 
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{|   id="H4dfa55081758a"  class=" tableEdit PMID_Relative_Phenotype_table"  
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!|OMP Accession!!Taxon Information!!Genotype Information (if known)!!OMP ID!!OMP Term Name!!Phenotype Details!!Related Rows!!ECO ID!!ECO Term Name!!Notes!!Status
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2
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*Taxon: Escherichia coli
*Strain: K-12
*Substrain: MG1655
*NCBI Taxon ID: 511145
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*Genotype of Parent: Lam- rph- F-
*Genetic Difference of Mutant : lacZ-
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OMP: 0000002
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loss of utilization of carbon source
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chemical:lactose
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derivative of parent:OMP 1
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ECO:0000001
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plating on indicator medium
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Figure 1
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complete 
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3
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*Taxon: Escherichia coli
*Strain: K-12
*Substrain: MG1655
*NCBI Taxon ID: 511145
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*Genotype of Parent: Lam-rph- F-
*Genetic Difference of Mutant : parC-
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OMP: 0000003
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filamented cells
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temperature sensitive:37C
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complex phenotype:3
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ECO:0000002
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Microscopy
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Figure 1
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complete 
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1
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*Taxon: Escherichia coli
*Strain: K-12
*Substrain: MG1655
*NCBI Taxon ID: 511145
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*Genotype of Parent: Lam-rph- F-
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OMP: 0000001
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utilization of carbon source
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chemical:lactose
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parent:
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ECO:0000001
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plating on indicator medium
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Figure 1
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complete 
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4
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*Taxon: Escherichia coli
*Strain: K-12
*Substrain: MG1655
*NCBI Taxon ID: 511145
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*Genotype of Parent: Lam-rph- F-
*Genetic Difference of Mutant : parC-
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OMP: 0000004
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centered nucleoid
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temperature sensitive:37C
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complex phenotype:3
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ECO:0000002
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Microscopy
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Figure 1
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complete 

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|<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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