Difference between revisions of "Curation status"

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| align="center" style="background:#f0f0f0;"|'''Pre-build db storage of curated data'''
 
| align="center" style="background:#f0f0f0;"|'''Pre-build db storage of curated data'''
 
| align="center" style="background:#f0f0f0;"|'''Curation status source'''
 
| align="center" style="background:#f0f0f0;"|'''Curation status source'''
 +
| align="center" style="background:#f0f0f0;"|'''Notes/actions'''
 
|-
 
|-
−
|'''''C. elegans'''''||'''celegans'''||afp,cfp||none||NA|
+
|'''''C. elegans'''''||'''celegans'''||afp,cfp||none||NA||
 
|-
 
|-
−
|'''''C. elegans'' other than Bristol'''|| cnonbristol ||afp,cfp||none||NA|
+
|'''''C. elegans'' other than Bristol'''|| cnonbristol ||afp,cfp||none||NA||
 
|-
 
|-
−
|'''Nematodes other than ''C. elegans'''''||nematode||afp,cfp||none||NA|
+
|'''Nematodes other than ''C. elegans'''''||nematode||afp,cfp||none||NA||
 
|-
 
|-
−
|'''Non-nematode species'''||nonnematode||afp,cfp||none||NA|
+
|'''Non-nematode species'''||nonnematode||afp,cfp||none||NA||
 
|-
 
|-
−
|'''Genes studied in this paper'''||genestudied||afp, cfp, tfp||geneace||
+
|'''Genes studied in this paper'''||genestudied||afp, cfp, tfp||geneace||||
 
|-
 
|-
−
|'''Newly cloned gene''' || genesymbol ||afp, cfp, jfp||geneace||
+
|'''Newly cloned gene''' || genesymbol ||afp, cfp, jfp||geneace||||
 
|-
 
|-
−
|'''Newly created allele'''||extvariation||afp, cfp, tfp, jfp||variation NS||home/acedb/karen/cur_status_sources/vargene_ref.txt|
+
|'''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||||
 
|-
 
|-
−
|'''Phenotype analysis''' || newmutant ||cfp, afp, svm ||postgres||postgres|
+
|'''Phenotype analysis''' || newmutant ||cfp, afp, svm ||postgres||postgres||
 
|-
 
|-
−
|'''Small-scale RNAi'''||rnai||afp, cfp, tfp, svm||citace||postgres|
+
|'''Small-scale RNAi'''||rnai||afp, cfp, tfp, svm||citace||postgres through the paper editor link /~postgres/cgi-bin/paper_editor.cgi||
 
|-
 
|-
−
|'''Large-scale RNAi'''||lsrnai||afp, cfp, tfp, svm||citace||postgres|
+
|'''Large-scale RNAi'''||lsrnai||afp, cfp, tfp, svm||citace||postgres through the paper editor link /~postgres/cgi-bin/paper_editor.cgi||
 
|-
 
|-
−
|'''Overexpression phenotype'''||overexpr||afp, cfp, svm||postgres||postgres via transgene-phenotype|
+
|'''Overexpression phenotype'''||overexpr||afp, cfp, svm||postgres||postgres via transgene-phenotype||
 
|-
 
|-
−
|'''Chemicals'''||chemicals (molecule?) ||afp, cfp||postgres|||
+
|'''Chemicals'''||chemicals (molecule?) ||afp, cfp||postgres||||
 
|-
 
|-
−
|'''Mosaic analysis'''||mosaic ||afp, cfp||?|||
+
|'''Mosaic analysis'''||mosaic ||afp, cfp||?||||
 
|-
 
|-
−
|'''Tissue or cell site of action'''|| siteaction ||afp, cfp||?|||
+
|'''Tissue or cell site of action'''|| siteaction ||afp, cfp||?||||
 
|-
 
|-
−
|'''Time of action''' || timeaction||afp, cfp||?|||
+
|'''Time of action''' || timeaction||afp, cfp||?||||
 
|-
 
|-
−
|'''Molecular function of a gene product'''||genefunc||afp, cfp||?|||
+
|'''Molecular function of a gene product'''||genefunc||afp, cfp||?||||
 
|-
 
|-
−
|'''Homolog of a human disease-associated gene.'''|| humdis ||afp, cfp||?|||
+
|'''Homolog of a human disease-associated gene.'''|| humdis ||afp, cfp||?||||
 
|-
 
|-
−
|'''Genetic interactions''' ||geneint||tfp, afp, cfp||postgres||postgres|
+
|'''Genetic interactions''' ||geneint||tfp, afp, cfp||postgres||postgres||
 
|-
 
|-
−
|'''Functional complementation'''||funccomp||afp, cfp||?||NA|
+
|'''Functional complementation'''||funccomp||afp, cfp||?||NA||
 
|-
 
|-
−
|'''Gene product interactions''' ||geneprod||afp, cfp||?|||
+
|'''Gene product interactions''' ||geneprod||afp, cfp||?||||
 
|-
 
|-
−
|'''New expression pattern for a gene'''|| otherexpr ||afp, cfp,SVM ||postgres||postgres|
+
|'''New expression pattern for a gene'''|| otherexpr ||afp, cfp,SVM ||postgres||postgres||
 
|-
 
|-
−
|'''Alterations in gene expression by genetic or other treatment'''|| genereg ||afp, cfp||postgres||home/acedb/karen/cur_status_sources/regulation_ref.txt|
+
|'''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||?||||
 
|-
 
|-
−
|PFM, PWM|| matrices||afp, cfp||? |||
+
|'''PFM, PWM'''|| matrices||afp, cfp||?||||
 
|-
 
|-
−
|'''Microarray'''|| microarray ||afp, cfp||citace?||/karen/cur_status_sources/microarray_ref.txt|
+
|'''Microarray'''|| microarray ||afp, cfp||citace?||/karen/cur_status_sources/microarray_ref.txt||
 
|-
 
|-
−
|in vitro ''Protein analysis''|| invitro|| SVM?||?|||
+
|'''in vitro ''Protein analysis'''''|| invitro|| SVM?||?||||
 
|-
 
|-
−
|'''Domain analysis''' || domanal (populated with information previously in "structureinformation")||||?||NA|
+
|'''Domain analysis''' || domanal (populated with information previously in "structureinformation")||||?||NA||
 
|-
 
|-
 
|'''Covalent modification'''|| covalent||||?||NA||
 
|'''Covalent modification'''|| covalent||||?||NA||
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|'''Structural information'''|| structinfo||||?||NA||
 
|'''Structural information'''|| structinfo||||?||NA||
 
|-
 
|-
−
|'''Mass spectrometry'''|| massspec||afp, cfp||Hinxton|||
+
|'''Mass spectrometry'''|| massspec||afp, cfp||Hinxton||||
 
|-
 
|-
−
|'''''C. elegans'' antibodies'''|| antibody ||tfp||postgres?||/karen/cur_status_sources/antibody_ref.txt|
+
|'''''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||
 
|-
 
|-
−
|'''Transgenes used as tissue markers'''|| marker||afp, cfp||postgres||postgres|
+
|'''Transgenes used as tissue markers'''|| marker||afp, cfp||postgres||postgres||
 
|-
 
|-
−
|'''Gene structure correction''' || structcorr (this use to be two different fields)||?||||
+
|'''Gene structure correction''' ||structcorr (this use to be two different fields)||?||||||
 
|-
 
|-
−
|'''Sequencing mutant alleles''' ||seqchange |||||||
+
|'''Sequencing mutant alleles''' ||seqchange ||afp, cfp||||||
 
|-
 
|-
−
|'''New SNPs'''||newsnp|||||||
+
|'''New SNPs'''||newsnp||afp, cfp||||||
 
|-
 
|-
−
|'''Ablation data'''||ablationdata |||||||
+
|'''Ablation data'''||ablationdata ||afp, cfp||||||
 
|-
 
|-
−
|'''Cell function'''||cellfunc|||||||
+
|'''Cell function'''||cellfunc||afp, cfp|||||||
 
|-
 
|-
−
|'''Phylogenetic data'''||phylogenetic||||||N/A||
+
|'''Phylogenetic data'''||phylogenetic||afp, cfp||||N/A||
 
|-
 
|-
−
|'''Other bioinformatics analysis'''||othersilico||||||N/A||
+
|'''Other bioinformatics analysis'''||othersilico||afp, cfp||||N/A||
 
|-
 
|-
−
|'''Supplemental materials'''||supplemental|||||||
+
|'''Supplemental materials'''||supplemental||afp, cfp||||||
 
|-
 
|-
−
|'''Comment'''||nocuratable|||||||
+
|'''Comment'''||nocuratable||afp, cfp||||||
 
|-
 
|-
−
|'''Feedback'''||comment|||||||
+
|'''Feedback'''||comment||afp, cfp||||||
 
|-
 
|-
−
|'''Strain'''||?||jfp, afp??||textpresso, postgres??|||
+
|'''Strain'''||?||jfp||textpresso (GSA), postgres-afp table||||
 
|-
 
|-
−
|'''Rearrangements'''||?||jfp, afp?||textpresso, postgres?|||
+
|'''Rearrangements'''||?||jfp||textpresso (GSA), postgres-afp table||||
 
|-
 
|-
−
|'''Cell/anatomy terms and synonyms'''||?||jfp, afp??||textpresso, postgres?||/karen/cur_status_sources
+
|'''Cell/anatomy terms and synonyms'''||?||jfp ||textpresso (GSA), postgres-afp table||/karen/cur_status_sources/anatomy_ref.txt||
−
/anatomy_ref.txt|
 
 
|-
 
|-
−
|'''New phenotype'''||?||jfp, afp??||textpresso, postgres||phenotype obo? |
+
|'''New phenotype'''||?||jfp||textpresso (GSA), postgres-afp table||?||
 
|-
 
|-
 
|}
 
|}
  
−
afp = Author first pass
+
afp = Author first pass table
  
−
cfp = Curator first pass
+
cfp = Curator first pass table
  
−
tfp = Textpresso first pass
+
tfp = Textpresso first pass table
  
−
jpf = Journal first pass
+
jpf = Journal first pass form = afp first pass table
  
 
SVM = Support Vector Machine
 
SVM = Support Vector Machine

Revision as of 19:48, 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 Notes/actions
C. elegans celegans afp,cfp none NA
C. elegans other than Bristol cnonbristol afp,cfp none NA
Nematodes other than C. elegans nematode afp,cfp none NA
Non-nematode species nonnematode afp,cfp none NA
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 home/acedb/karen/cur_status_sources/vargene_ref.txt
Genetic mapping data mappingdata cfp, afp geneace
Phenotype analysis newmutant cfp, afp, svm postgres postgres
Small-scale RNAi rnai afp, cfp, tfp, svm citace postgres through the paper editor link /~postgres/cgi-bin/paper_editor.cgi
Large-scale RNAi lsrnai afp, cfp, tfp, svm citace postgres through the paper editor link /~postgres/cgi-bin/paper_editor.cgi
Overexpression phenotype overexpr afp, cfp, svm postgres postgres via transgene-phenotype
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 postgres
Functional complementation funccomp afp, cfp ? NA
Gene product interactions geneprod afp, cfp ?
New expression pattern for a gene otherexpr afp, cfp,SVM postgres postgres
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 ?
PFM, PWM matrices afp, cfp ?
Microarray microarray afp, cfp citace? /karen/cur_status_sources/microarray_ref.txt
in vitro Protein analysis invitro SVM? ?
Domain analysis domanal (populated with information previously in "structureinformation") ? NA
Covalent modification covalent ? NA
Structural information structinfo ? NA
Mass spectrometry massspec afp, cfp Hinxton
C. elegans antibodies antibody tfp postgres? /karen/cur_status_sources/antibody_ref.txt
Integrated transgenes transgene tfp, jfp postgres postgres
Transgenes used as tissue markers marker afp, cfp postgres postgres
Gene structure correction structcorr (this use to be two different fields) ?
Sequencing mutant alleles seqchange afp, cfp
New SNPs newsnp afp, cfp
Ablation data ablationdata afp, cfp
Cell function cellfunc afp, cfp
Phylogenetic data phylogenetic afp, cfp N/A
Other bioinformatics analysis othersilico afp, cfp N/A
Supplemental materials supplemental afp, cfp
Comment nocuratable afp, cfp
Feedback comment afp, cfp
Strain ? jfp textpresso (GSA), postgres-afp table
Rearrangements ? jfp textpresso (GSA), postgres-afp table
Cell/anatomy terms and synonyms ? jfp textpresso (GSA), postgres-afp table /karen/cur_status_sources/anatomy_ref.txt
New phenotype ? jfp textpresso (GSA), postgres-afp table ?

afp = Author first pass table

cfp = Curator first pass table

tfp = Textpresso first pass table

jpf = Journal first pass form = afp first pass table

SVM = Support Vector Machine

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