Difference between revisions of "Curation status"

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*[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi curation status]
 
*[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi curation status]
 
*[http://tazendra.caltech.edu/~postgres/cgi-bin/svm_results.cgi svm flagging status]
 
*[http://tazendra.caltech.edu/~postgres/cgi-bin/svm_results.cgi svm flagging status]
−
+
 
 +
===Other related pages===
 +
*[http://wiki.wormbase.org/index.php/First-pass_flagging_pipelines Overview of first pass flagging pipelines]
 +
**[http://wiki.wormbase.org/index.php/Textpresso Textpresso flagging pipelines] with postgres queries for individual data types
 +
**[http://wiki.wormbase.org/index.php/Genetics_Markup_by_Textpresso_and_First_Pass GSA first pass overview]
 +
*[http://wiki.wormbase.org/index.php/First-pass_schedule,_instructions,_automation Original first pass indexing page]
 +
**[http://wiki.wormbase.org/index.php/First-pass_to_Curation Brief summary of curator first pass pipeline, obsolete with new paper editor]
 +
*[http://wiki.wormbase.org/index.php/Datatypes_flagged Definition of data types flagged]
 +
''need a page for describing tagging a flag as false positive''
 +
 
 
===Datatypes, curation storage and source for generating curation status===
 
===Datatypes, curation storage and source for generating curation status===
 
{|| border="1" cellpadding="2"
 
{|| border="1" cellpadding="2"
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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||N/A||
+
|'''''C. elegans'''''||'''celegans'''||afp,cfp||none||NC||
 
|-
 
|-
−
|'''''C. elegans'' other than Bristol'''|| cnonbristol ||afp,cfp||none||N/A||
+
|'''''C. elegans'' other than Bristol'''|| cnonbristol ||afp,cfp||none||NC||
 
|-
 
|-
−
|'''Nematodes other than ''C. elegans'''''||nematode||afp,cfp||none||N/A||
+
|'''Nematodes other than ''C. elegans'''''||nematode||afp,cfp||none||NC||
 
|-
 
|-
−
|'''Non-nematode species'''||nonnematode||afp,cfp||none||N/A||
+
|'''Non-nematode species'''||nonnematode||afp,cfp||none||NC||
 
|-
 
|-
−
|'''Genes studied in this paper'''||genestudied||afp, cfp, tfp||geneace|||
+
|'''Genes studied in this paper'''||genestudied||afp, cfp, tfp||postgres? paper tables?||||
 
|-
 
|-
−
|'''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||old: home/acedb/karen/cur_status_sources/vargene_ref.txt; current:?||for paper-allele connections; Variation NS for latest variation curation
 
|-
 
|-
−
|'''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-phenotype table||this is the correct source
 
|-
 
|-
−
|'''Small-scale RNAi''' (less than 100 experiments reported)|| rnai||afp, cfp, tfp, svm||citace||postgres via paper checkout|
+
|'''Small-scale RNAi'''||rnai||afp, cfp, tfp, svm||citace||postgres through the paper editor link /~postgres/cgi-bin/paper_editor.cgi||
 
|-
 
|-
−
|'''Large-scale RNAi''' (more than 100 experiments reported)|| lsrnai||afp, cfp, tfp, svm||citace||postgres via paper checkout|
+
|'''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 (no specific table)||should be from postgres transgene-phenotype-paper
 
|-
 
|-
−
|'''Chemicals'''||chemicals (molecule?) ||afp, cfp||postgres|||
+
|'''Chemicals'''||chemicals (molecule?) ||afp, cfp, tfp||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, tfp||?||||
 
|-
 
|-
−
|'''Genetic interactions''' ||geneint||tfp, afp, cfp||postgres||postgres|
+
|'''Genetic interactions''' ||geneint||tfp, afp, cfp||postgres||postgres- interaction table||
 
|-
 
|-
−
|'''Functional complementation'''||funccomp||afp, cfp||?||N/A||
+
|'''Functional complementation'''||funccomp||afp, cfp||?||NC||
 
|-
 
|-
−
|'''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||
+
|'''Images'''||||tfp||postgres||postgres||
 
|-
 
|-
−
|'''Regulatory sequence features'''||seqfeat ||afp, cfp||?|||
+
|'''Alterations in gene expression by genetic or other treatment'''|| genereg ||afp, cfp||postgres||home/acedb/karen/cur_status_sources/regulation_ref.txt||
 
|-
 
|-
−
|PFM, PWM|| matrices||afp, cfp||? |||
+
|'''Regulatory sequence features'''||seqfeat ||afp, cfp||?||||
 
|-
 
|-
−
|'''Microarray'''|| microarray ||afp, cfp||citace?||/karen/cur_status_sources/microarray_ref.txt||
+
|'''PFM, PWM'''|| matrices||afp, cfp||?||||
 
|-
 
|-
−
|in vitro ''Protein analysis''|| invitro|| SVM?||?|||
+
|'''Microarray'''|| microarray ||afp, cfp||citace?||old: /karen/cur_status_sources/microarray_ref.txt; current:?||
 
|-
 
|-
−
|'''Domain analysis''' || domanal (populated with information previously in "structureinformation")||||?||N/A|
+
|'''in vitro ''Protein analysis'''''|| invitro|| tfp||?||||
 
|-
 
|-
−
|'''Covalent modification'''|| covalent||||?||N/A||
+
|'''Domain analysis''' || domanal (populated with information previously in "structureinformation")||||?||NC||
 
|-
 
|-
−
|'''Structural information'''|| structinfo||||?||N/A||
+
|'''Covalent modification'''|| covalent||||?||NC||
 
|-
 
|-
−
|'''Mass spectrometry'''|| massspec||afp, cfp||Hinxton|||
+
|'''Structural information'''|| structinfo||||?||NC||
 
|-
 
|-
−
|'''''C. elegans'' antibodies'''|| antibody ||tfp||postgres?||/karen/cur_status_sources/antibody_ref.txt||
+
|'''Mass spectrometry'''|| massspec||afp, cfp||Hinxton||||
 
|-
 
|-
−
|'''Integrated transgenes'''||transgene||tfp, jfp ||postgres||postgres|
+
|'''''C. elegans'' antibodies'''|| antibody ||tfp||postgres||old:/karen/cur_status_sources/antibody_ref.txt; current:?||
 
|-
 
|-
−
|'''Transgenes used as tissue markers'''|| marker||afp, cfp||postgres||postgres|
+
|'''Integrated transgenes'''||transgene||tfp, jfp ||postgres||postgres||
 
|-
 
|-
−
|'''Gene structure correction''' || structcorr (this use to be two different fields)|||||||
+
|'''Transgenes used as tissue markers'''|| marker||afp, cfp||postgres||postgres||
 
|-
 
|-
−
|'''Sequencing mutant alleles''' ||seqchange |||||||
+
|'''Gene structure correction''' ||structcorr (this use to be two different fields)||svm||Hinxton||||
 
|-
 
|-
−
|'''New SNPs'''||newsnp|||||||
+
|'''Sequencing mutant alleles''' ||seqchange ||afp, cfp||||||
 
|-
 
|-
−
|'''Ablation data'''||ablationdata |||||||
+
|'''New SNPs'''||newsnp||afp, cfp||||||
 
|-
 
|-
−
|'''Cell function'''||cellfunc|||||||
+
|'''Ablation data'''||ablationdata ||afp, cfp||||||
 
|-
 
|-
−
|'''Phylogenetic data'''||phylogenetic||||||N/A||
+
|'''Cell function'''||cellfunc||afp, cfp|||||||
 
|-
 
|-
−
|'''Other bioinformatics analysis'''||othersilico||||||N/A||
+
|'''Phylogenetic data'''||phylogenetic||afp, cfp||||NC||
 
|-
 
|-
−
|'''Supplemental materials'''||supplemental|||||||
+
|'''Other bioinformatics analysis'''||othersilico||afp, cfp||||NC||
 
|-
 
|-
−
|'''Comment'''||nocuratable|||||||
+
|'''Supplemental materials'''||supplemental||afp, cfp||||||
 
|-
 
|-
−
|'''Feedback'''||comment|||||||
+
|'''Comment'''||nocuratable||afp, cfp||||||
 
|-
 
|-
−
|'''Strain'''||?||jfp, afp??||textpresso, postgres??|||
+
|'''Feedback'''||comment||afp, cfp||||||
 
|-
 
|-
−
|'''Rearrangements'''||?||jfp, afp?||textpresso, postgres?|||
+
|'''Strain'''||?||jfp||textpresso (GSA), postgres-afp table||||
 
|-
 
|-
−
|'''Cell/anatomy terms and synonyms'''||?||jfp, afp??||textpresso, postgres?||/karen/cur_status_sources
+
|'''Rearrangements'''||?||jfp||textpresso (GSA), postgres-afp table||||
−
/anatomy_ref.txt|
 
 
|-
 
|-
−
|'''New phenotype'''||?||jfp, afp??||textpresso, postgres||phenotype obo? |
+
|'''Cell/anatomy terms and synonyms'''||?||jfp ||textpresso (GSA), postgres-afp table||old: /karen/cur_status_sources/anatomy_ref.txt; current:?||
 +
|-
 +
|'''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
 +
 +
NC = Not actively curated

Latest revision as of 08:24, 24 October 2014

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

Other related pages

need a page for describing tagging a flag as false positive

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 NC
C. elegans other than Bristol cnonbristol afp,cfp none NC
Nematodes other than C. elegans nematode afp,cfp none NC
Non-nematode species nonnematode afp,cfp none NC
Genes studied in this paper genestudied afp, cfp, tfp postgres? paper tables?
Newly cloned gene genesymbol afp, cfp, jfp geneace
Newly created allele extvariation afp, cfp, tfp, jfp variation NS old: home/acedb/karen/cur_status_sources/vargene_ref.txt; current:? for paper-allele connections; Variation NS for latest variation curation
Genetic mapping data mappingdata cfp, afp geneace
Phenotype analysis newmutant cfp, afp, svm postgres postgres-phenotype table this is the correct source
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 (no specific table) should be from postgres transgene-phenotype-paper
Chemicals chemicals (molecule?) afp, cfp, tfp 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, tfp ?
Genetic interactions geneint tfp, afp, cfp postgres postgres- interaction table
Functional complementation funccomp afp, cfp ? NC
Gene product interactions geneprod afp, cfp ?
New expression pattern for a gene otherexpr afp, cfp, SVM postgres postgres
Images tfp 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? old: /karen/cur_status_sources/microarray_ref.txt; current:?
in vitro Protein analysis invitro tfp ?
Domain analysis domanal (populated with information previously in "structureinformation") ? NC
Covalent modification covalent ? NC
Structural information structinfo ? NC
Mass spectrometry massspec afp, cfp Hinxton
C. elegans antibodies antibody tfp postgres old:/karen/cur_status_sources/antibody_ref.txt; current:?
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) svm Hinxton
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 NC
Other bioinformatics analysis othersilico afp, cfp NC
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 old: /karen/cur_status_sources/anatomy_ref.txt; current:?
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

NC = Not actively curated

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