Difference between revisions of "Curation status"

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| align="center" style="background:#f0f0f0;"|'''Curation status source'''
 
| align="center" style="background:#f0f0f0;"|'''Curation status source'''
 
|-
 
|-
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|'''''C. elegans'''''||'''celegans'''||afp,cfp||none||N/A||
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|'''''C. elegans'''''||'''celegans'''||afp,cfp||none||NA|
 
|-
 
|-
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|'''''C. elegans'' other than Bristol'''|| cnonbristol ||afp,cfp||none||N/A||
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|'''''C. elegans'' other than Bristol'''|| cnonbristol ||afp,cfp||none||NA|
 
|-
 
|-
−
|'''Nematodes other than ''C. elegans'''''||nematode||afp,cfp||none||N/A||
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|'''Nematodes other than ''C. elegans'''''||nematode||afp,cfp||none||NA|
 
|-
 
|-
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|'''Non-nematode species'''||nonnematode||afp,cfp||none||N/A||
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|'''Non-nematode species'''||nonnematode||afp,cfp||none||NA|
 
|-
 
|-
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|'''Genes studied in this paper'''||genestudied||afp, cfp, tfp||geneace|||
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|'''Genes studied in this paper'''||genestudied||afp, cfp, tfp||geneace||
 
|-
 
|-
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|'''Newly cloned gene''' || genesymbol ||afp, cfp, jfp||geneace|||
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|'''Newly cloned gene''' || genesymbol ||afp, cfp, jfp||geneace||
 
|-
 
|-
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|'''Newly created allele'''||extvariation||afp, cfp, tfp, jfp||variation NS||home/acedb/karen/cur_status_sources/vargene_ref.txt||
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|'''Newly created allele'''||extvariation||afp, cfp, tfp, jfp||variation NS||home/acedb/karen/cur_status_sources/vargene_ref.txt|
 
|-
 
|-
 
|'''Genetic mapping data'''||mappingdata||cfp, afp||geneace|||
 
|'''Genetic mapping data'''||mappingdata||cfp, afp||geneace|||
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|'''Phenotype analysis''' || newmutant ||cfp, afp, svm ||postgres||postgres|
 
|'''Phenotype analysis''' || newmutant ||cfp, afp, svm ||postgres||postgres|
 
|-
 
|-
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|'''Small-scale RNAi''' (less than 100 experiments reported)|| rnai||afp, cfp, tfp, svm||citace||postgres via paper checkout|
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|'''Small-scale RNAi'''||rnai||afp, cfp, tfp, svm||citace||postgres|
 
|-
 
|-
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|'''Large-scale RNAi''' (more than 100 experiments reported)|| lsrnai||afp, cfp, tfp, svm||citace||postgres via paper checkout|
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|'''Large-scale RNAi'''||lsrnai||afp, cfp, tfp, svm||citace||postgres|
 
|-
 
|-
 
|'''Overexpression phenotype'''||overexpr||afp, cfp, svm||postgres||postgres via transgene-phenotype|
 
|'''Overexpression phenotype'''||overexpr||afp, cfp, svm||postgres||postgres via transgene-phenotype|
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|'''Genetic interactions''' ||geneint||tfp, afp, cfp||postgres||postgres|
 
|'''Genetic interactions''' ||geneint||tfp, afp, cfp||postgres||postgres|
 
|-
 
|-
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|'''Functional complementation'''||funccomp||afp, cfp||?||N/A||
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|'''Functional complementation'''||funccomp||afp, cfp||?||NA|
 
|-
 
|-
 
|'''Gene product interactions''' ||geneprod||afp, cfp||?|||
 
|'''Gene product interactions''' ||geneprod||afp, cfp||?|||
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|'''New expression pattern for a gene'''|| otherexpr ||afp, cfp,SVM ||postgres||postgres|
 
|'''New expression pattern for a gene'''|| otherexpr ||afp, cfp,SVM ||postgres||postgres|
 
|-
 
|-
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|'''Alterations in gene expression by genetic or other treatment'''|| genereg ||afp, cfp||postgres||/home/acedb/karen/cur_status_sources/regulation_ref.txt||
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|'''Alterations in gene expression by genetic or other treatment'''|| genereg ||afp, cfp||postgres||home/acedb/karen/cur_status_sources/regulation_ref.txt|
 
|-
 
|-
 
|'''Regulatory sequence features'''||seqfeat ||afp, cfp||?|||
 
|'''Regulatory sequence features'''||seqfeat ||afp, cfp||?|||
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|PFM, PWM|| matrices||afp, cfp||? |||
 
|PFM, PWM|| matrices||afp, cfp||? |||
 
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|-
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|'''Microarray'''|| microarray ||afp, cfp||citace?||/karen/cur_status_sources/microarray_ref.txt||
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|'''Microarray'''|| microarray ||afp, cfp||citace?||/karen/cur_status_sources/microarray_ref.txt|
 
|-
 
|-
 
|in vitro ''Protein analysis''|| invitro|| SVM?||?|||
 
|in vitro ''Protein analysis''|| invitro|| SVM?||?|||
 
|-
 
|-
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|'''Domain analysis''' || domanal (populated with information previously in "structureinformation")||||?||N/A|
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|'''Domain analysis''' || domanal (populated with information previously in "structureinformation")||||?||NA|
 
|-
 
|-
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|'''Covalent modification'''|| covalent||||?||N/A||
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|'''Covalent modification'''|| covalent||||?||NA||
 
|-
 
|-
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|'''Structural information'''|| structinfo||||?||N/A||
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|'''Structural information'''|| structinfo||||?||NA||
 
|-
 
|-
 
|'''Mass spectrometry'''|| massspec||afp, cfp||Hinxton|||
 
|'''Mass spectrometry'''|| massspec||afp, cfp||Hinxton|||
 
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|-
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|'''''C. elegans'' antibodies'''|| antibody ||tfp||postgres?||/karen/cur_status_sources/antibody_ref.txt||
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|'''''C. elegans'' antibodies'''|| antibody ||tfp||postgres?||/karen/cur_status_sources/antibody_ref.txt|
 
|-
 
|-
 
|'''Integrated transgenes'''||transgene||tfp, jfp ||postgres||postgres|
 
|'''Integrated transgenes'''||transgene||tfp, jfp ||postgres||postgres|
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|'''Transgenes used as tissue markers'''|| marker||afp, cfp||postgres||postgres|
 
|'''Transgenes used as tissue markers'''|| marker||afp, cfp||postgres||postgres|
 
|-
 
|-
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|'''Gene structure correction''' || structcorr (this use to be two different fields)|||||||
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|'''Gene structure correction''' || structcorr (this use to be two different fields)||?||||
 
|-
 
|-
 
|'''Sequencing mutant alleles''' ||seqchange |||||||
 
|'''Sequencing mutant alleles''' ||seqchange |||||||

Revision as of 19:28, 8 June 2011

A number of pages have been set up to keep track of the papers that have been flagged and curated for respective datatypes; unfortunately not all datatypes are easily tracked and so the information in regards to whether or not a paper has been curated for that datatype may not be up to date. Eventually this page should point to a table that is a comprehensive display of the curation status of a given paper as well as a table that can show how far we've come along in curating the nematode published corpus in our database.

Current status forms

Datatypes, curation storage and source for generating curation status

Data type afp PGdb name Flagging method(s) Pre-build db storage of curated data Curation status source
C. elegans celegans afp,cfp none
C. elegans other than Bristol cnonbristol afp,cfp none
Nematodes other than C. elegans nematode afp,cfp none
Non-nematode species nonnematode afp,cfp none
Genes studied in this paper genestudied afp, cfp, tfp geneace
Newly cloned gene genesymbol afp, cfp, jfp geneace
Newly created allele extvariation afp, cfp, tfp, jfp variation NS
Genetic mapping data mappingdata cfp, afp geneace
Phenotype analysis newmutant cfp, afp, svm postgres
Small-scale RNAi rnai afp, cfp, tfp, svm citace
Large-scale RNAi lsrnai afp, cfp, tfp, svm citace
Overexpression phenotype overexpr afp, cfp, svm postgres
Chemicals chemicals (molecule?) afp, cfp postgres
Mosaic analysis mosaic afp, cfp ?
Tissue or cell site of action siteaction afp, cfp ?
Time of action timeaction afp, cfp ?
Molecular function of a gene product genefunc afp, cfp ?
Homolog of a human disease-associated gene. humdis afp, cfp ?
Genetic interactions geneint tfp, afp, cfp postgres
Functional complementation funccomp afp, cfp ?
Gene product interactions geneprod afp, cfp ?
New expression pattern for a gene otherexpr afp, cfp,SVM postgres
Alterations in gene expression by genetic or other treatment genereg afp, cfp postgres
Regulatory sequence features seqfeat afp, cfp ?
PFM, PWM matrices afp, cfp ?
Microarray microarray afp, cfp citace?
in vitro Protein analysis invitro SVM? ?
Domain analysis domanal (populated with information previously in "structureinformation") ?
Covalent modification covalent ? NA
Structural information structinfo ? NA
Mass spectrometry massspec afp, cfp Hinxton
C. elegans antibodies antibody tfp postgres?
Integrated transgenes transgene tfp, jfp postgres
Transgenes used as tissue markers marker afp, cfp postgres
Gene structure correction structcorr (this use to be two different fields) ?
Sequencing mutant alleles seqchange
New SNPs newsnp
Ablation data ablationdata
Cell function cellfunc
Phylogenetic data phylogenetic N/A
Other bioinformatics analysis othersilico N/A
Supplemental materials supplemental
Comment nocuratable
Feedback comment
Strain ? jfp, afp?? textpresso, postgres??
Rearrangements ? jfp, afp? textpresso, postgres?
Cell/anatomy terms and synonyms ? jfp, afp?? textpresso, postgres? /karen/cur_status_sources

/anatomy_ref.txt|

New phenotype ? jfp, afp?? textpresso, postgres

afp = Author first pass

cfp = Curator first pass

tfp = Textpresso first pass

jpf = Journal first pass

SVM = Support Vector Machine

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