Difference between revisions of "Curation status"

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m (Created page with '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…')
 
 
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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"
 
| align="center" style="background:#f0f0f0;"|'''Data type'''
 
| align="center" style="background:#f0f0f0;"|'''Data type'''
−
| align="center" style="background:#f0f0f0;"|'''PGdb name'''
+
| align="center" style="background:#f0f0f0;"|'''afp PGdb name'''
−
| align="center" style="background:#f0f0f0;"|'''Pre-build storage db'''
+
| align="center" style="background:#f0f0f0;"|'''Flagging method(s)'''
−
| align="center" style="background:#f0f0f0;"|'''Curator Flagged'''
+
| align="center" style="background:#f0f0f0;"|'''Pre-build db storage of curated data'''
−
| align="center" style="background:#f0f0f0;"|'''Notes about field'''
+
| align="center" style="background:#f0f0f0;"|'''Curation status source'''
−
|-
+
| align="center" style="background:#f0f0f0;"|'''Notes/actions'''
−
|'''''C. elegans'''''||'''celegans'''||||||
 
−
|-
 
−
|||materials and methods||'''''C. elegans'' other than Bristol'''|| '''new field'''|| cnonbristol ||Check if data for ''C. elegans'' natural isolates other than N2 (Bristol) are reported.''e.g. Hawaiian, CB4855, CB4852, CB4507, LSJ1, etc.''||||
 
−
|-
 
−
|||materials and methods||'''Nematodes other than ''C. elegans'''''||nonntwo||nematode||Check if data is reported for any species other than ''C. elegans'', e.g., ''C. briggsae'', ''Pristionchus pacificus'', ''Brugia malayi'', etc. ||||
 
−
|-
 
−
|||materials and methods||'''Non-nematode species'''||'''new field'''||nonnematode||Check if data is reported for any non-nematode species.||||
 
−
|-
 
−
 
 
−
 
 
−
|||||colspan="6"|GENE IDENTIFICATION AND MAPPING:
 
 
|-
 
|-
−
 
+
|'''''C. elegans'''''||'''celegans'''||afp,cfp||none||NC||
−
|||||'''Genes studied in this paper'''||||genestudied||List any gene for which you report experimental results; do not include genetic markers.|||| '''Big text box, auto-opened.'''
 
 
|-
 
|-
−
|in progress||||'''Newly cloned gene''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=genesymbol (flagged-done)]||''Gene Symbol''|| genesymbol ||Check  if your paper reports a new symbol for a known locus or the name of a newly defined locus.||genenames@wormbase.org, vanauken@its.caltech.edu ||
+
|'''''C. elegans'' other than Bristol'''|| cnonbristol ||afp,cfp||none||NC||
 
|-
 
|-
−
|in progress||||'''Newly created allele'''||''Extract allele''||extvariation||Check if your paper reports the identification of any allele that doesn't exist in WormBase already.||||
+
|'''Nematodes other than ''C. elegans'''''||nematode||afp,cfp||none||NC||
 
|-
 
|-
−
|||||'''Genetic mapping data''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=mappingdata (flagged)]||''mapping data''||mappingdata||Check if your paper contains 3-factor interval mapping data, i.e., genetic data only. Include Df or Dp data, but no SNP interval mapping.||genenames@wormbase.org ||
+
|'''Non-nematode species'''||nonnematode||afp,cfp||none||NC||
 
|-
 
|-
−
|||||colspan="6"|GENE FUNCTION:
+
|'''Genes studied in this paper'''||genestudied||afp, cfp, tfp||postgres? paper tables?||||
 
|-
 
|-
−
|||||colspan="4"|'''Mutant, RNAi, overexpression, or chemical-based phenotypes''':||colspan="2"|'''PLEASE SPECIFY DATA TYPE.'''
+
|'''Newly cloned gene''' || genesymbol ||afp, cfp, jfp||geneace||||
 
|-
 
|-
−
|'''DONE'''||||'''Phenotype analysis''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=newmutant (flagged-done)]|| ''Mutant Phenotype''|| newmutant ||Check if your paper reports phenotype due to mutation or overexpression analysis. ||remove-'''emsch@its.caletch.edu''', garys@its.caltech.edu, jolenef@its.caltech.edu ||
+
|'''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
 
|-
 
|-
−
|'''DONE'''||||'''Small-scale RNAi''' (less than 100 experiments reported) [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=rnai (flagged-done)]||''RNAi''|| rnai||Check if your paper reports gene knockdown phenotypes for less than 100 individual RNAi experiments.||garys@its.caltech.edu||
+
|'''Genetic mapping data'''||mappingdata||cfp, afp||geneace||||
 
|-
 
|-
−
|'''DONE''' ''will be part of small scale RNAi pipeline''||||'''Large-scale RNAi''' (less than 100 experiments reported) [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=lsrnai (flagged-done)]||''Large-Scale RNAi''|| lsrnai||Check if your paper reports gene knockdown phenotypes for more than 100 individual RNAi experiments.||raymond@its.caltech.edu||
+
|'''Phenotype analysis''' || newmutant ||cfp, afp, svm ||postgres||postgres-phenotype table||this is the correct source
 
|-
 
|-
−
|'''DONE''' through phenotype analysis||||'''Overexpression phenotype''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=overexpression (flagged)]||''Overexpression''|| overexpr||Check if your paper reports an abnormal phenotype based on the overexpression of a gene or gene construct. E.g., ""...constitutively activated SCD-2(neu*) receptor caused 100% of animals to arrest in the first larval stage (L1)..." ||remove-'''emsch@its.caletch.edu''', garys@its.caltech.edu, jolenef@its.caltech.edu||
+
|'''Small-scale RNAi'''||rnai||afp, cfp, tfp, svm||citace||postgres through the paper editor link /~postgres/cgi-bin/paper_editor.cgi||
 
|-
 
|-
−
|in progress||materials and methods; results||'''Chemicals''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=chemicals (flagged)]||''Chemicals''|| chemicals ||Check if the effects of small molecules, chemicals, or drugs were studied on worms. E.g., paraquat, butanone, benzaldehyde, aldicarb, etc. Mutagens used for the generation of mutant in genetic screens do not need to be indicated.||||
+
|'''Large-scale RNAi'''||lsrnai||afp, cfp, tfp, svm||citace||postgres through the paper editor link /~postgres/cgi-bin/paper_editor.cgi||
 
|-
 
|-
−
|||||'''Mosaic analysis''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=mosaic (flagged-done)]||''Mosaic analysis''||mosaic ||Check if your paper reports cell specific gene function based on mosaic analysis, e.g. extra-chromosomal transgene loss in a particular cell lineage leads to loss of mutant rescue, etc. ||raymond@its.caltech.edu ||
+
|'''Overexpression phenotype'''||overexpr||afp, cfp, svm||postgres||postgres (no specific table)||should be from postgres transgene-phenotype-paper
 
|-
 
|-
−
|||||'''Tissue or cell site of action''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=site (flagged-done)]||''Site of action''|| siteaction ||Check if your paper reports anatomy-specific function for a gene.||raymond@its.caltech.edu ||
+
|'''Chemicals'''||chemicals (molecule?) ||afp, cfp, tfp||postgres||||
 
|-
 
|-
−
|||||'''Time of action'''||'''new field''' || timeaction||Check if your paper reports a temporal requirement for gene function, that is, if gene activity was assayed, for example, through temperature-shift experiments.||raymond@its.caltech.edu||
+
|'''Mosaic analysis'''||mosaic ||afp, cfp||?||||
 
|-
 
|-
−
|||||'''Molecular function of a gene product'''[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=genefunction (flagged-done)]||''Gene function''||genefunc||Check if your paper discusses a new function for a known or newly defined gene.||remove '''emsch@its.caletch.edu''' ||
+
|'''Tissue or cell site of action'''|| siteaction ||afp, cfp||?||||
 
|-
 
|-
−
|in progress||||'''Homolog of a human disease-associated gene.'''[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=humandiseases (flagged)]||''Human Disease''|| humdis ||Check if genes discussed in your paper are a homolog/ortholog of a human disease-related gene or if your study models some aspect of a human disease.||ranjana@its.caltech.edu ||
+
|'''Time of action''' || timeaction||afp, cfp||?||||
 
|-
 
|-
−
|||||colspan="6"|INTERACTIONS:
+
|'''Molecular function of a gene product'''||genefunc||afp, cfp||?||||
 
|-
 
|-
−
|||||'''Genetic interactions''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=geneinteractions (flagged-done)]||''Gene interactions'' ||geneint||''Check if your paper reports the analysis of more than one gene at a time, e.g., double, triple, etc. mutants, including experiments where RNAi was concurrent with other RNAi-treatments or mutations.''||remove '''emsch@its.caletch.edu''' ||
+
|'''Homolog of a human disease-associated gene.'''|| humdis ||afp, cfp, tfp||?||||
 
|-
 
|-
−
|||materials and methods (tools); results||'''Functional complementation''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=functionalcomplementation (flagged)]||''Functional Complementation'' ||funccomp||Check if your paper reports functional redundancy between separate genes, e.g. the rescue of ''gen-A'' by overexpression of ''gen-B'' or any other extragenic sequence.|| ||
+
|'''Genetic interactions''' ||geneint||tfp, afp, cfp||postgres||postgres- interaction table||
 
|-
 
|-
−
|||||'''Gene product interactions''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=geneproduct (flagged-done)]||''Gene product interaction'' ||geneprod||Check if your paper reports data on protein-protein, RNA-protein, DNA-protein or Y2H interactions, etc.|| remove '''emsch@its.caletch.edu''' ||
+
|'''Functional complementation'''||funccomp||afp, cfp||?||NC||
 
|-
 
|-
−
|||||colspan="6"|REGULATION OF GENE EXPRESSION:
+
|'''Gene product interactions''' ||geneprod||afp, cfp||?||||
 
|-
 
|-
−
|some SVM (not great)||||'''New expression pattern for a gene''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=expression (flagged-done)]||''expression pattern data''|| otherexpr ||Check if your paper reports new temporal or spatial (e.g., tissue, subcellular, etc.) data on the pattern of expression of any gene in a wild-type background. You can include:  reporter gene analysis, antibody staining, ''In situ'' hybridization, RT-PCR, Western or Northern blot data.||wchen@its.caltech.edu, vanauken@its.caltech.edu||
+
|'''New expression pattern for a gene'''|| otherexpr ||afp, cfp, SVM ||postgres||postgres||
 
|-
 
|-
−
|some SVM (not great)||||'''Alterations in gene expression by genetic or other treatment''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=generegulation (flagged-done)]||''Gene regulation on expression level'' || genereg ||Check if your paper reports changes or lack of changes in gene expression levels or patterns due to genetic, chemical, temperature, or any other experimental treatment.||xdwang@its.caltech.edu ||
+
|'''Images'''||||tfp||postgres||postgres||
 
|-
 
|-
−
|||||'''Regulatory sequence features''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=sequencefeatures (flagged)]||''Sequence features'' ||seqfeat ||Check if your paper reports any gene expression regulatory elements, e.g., DNA/RNA elements required for gene expression,  promoters, introns, UTR's, DNA binding sites, etc.||xdwang@its.caltech.edu, worm-bug@sanger.ac.uk, stlouis@wormbase.org ||
+
|'''Alterations in gene expression by genetic or other treatment'''|| genereg ||afp, cfp||postgres||home/acedb/karen/cur_status_sources/regulation_ref.txt||
 
|-
 
|-
−
|||||'''Position frequency matrix (PFM)''' or '''Position weight matrix (PWM)'''||'''new field''' || matrices||Check if your paper reports PFMs or PWMs, which are typically used to define regulatory sites in genomic DNA (e.g., bound by transcription factors) or mRNA (e.g., bound by translational factors or miRNA). PFMs define simple nucleotide frequencies, while PWMs are scaled logarithmically against a background frequency.||xdwang@its.caltech.edu, remove- '''emsch@its.caletch.edu''' ||
+
|'''Regulatory sequence features'''||seqfeat ||afp, cfp||?||||
 
|-
 
|-
−
|||||'''Microarray'''[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=microarray (flagged-done)]||''Microarray''|| microarray ||Check if your paper reports any microarray data.||wchen@its.caltech.edu ||
+
|'''PFM, PWM'''|| matrices||afp, cfp||?||||
 
|-
 
|-
−
|||||colspan="6"|PROTEIN FUNCTION AND STRUCTURE:
+
|'''Microarray'''|| microarray ||afp, cfp||citace?||old: /karen/cur_status_sources/microarray_ref.txt; current:?||
 
|-
 
|-
−
|Kimberly said to remove this ||materials and methods; results||'''Protein analysis ''in vitro'''''[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=invitro (flagged)]||in vitro ''Protein analysis''|| invitro ||Check if your paper reports any ''in vitro'' protein analysis such as kinase assays, agonist pharmacological studies, ''in vitro'' reconstitution studies, etc.|| ||
+
|'''in vitro ''Protein analysis'''''|| invitro|| tfp||?||||
 
|-
 
|-
−
|||materials and methods; results||'''Domain analysis'''||'''new field''' || domanal (populated with information previously in "structureinformation")||Check if your paper reports on a function of a particular domain within a protein.||||
+
|'''Domain analysis''' || domanal (populated with information previously in "structureinformation")||||?||NC||
 
|-
 
|-
−
|||materials and methods; results||'''Covalent modification''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=covalent (flagged)]||''Covalent modification'' || covalent|| Check if your paper reports on post-translational modifications as assayed by mutagenesis or ''in vitro'' analysis||||
+
|'''Covalent modification'''|| covalent||||?||NC||
 
|-
 
|-
−
|||materials and methods; results||'''Structural information'''[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=structureinformation (flagged)]||''Structure information''|| structinfo||Check if your paper reports NMR or X-ray crystallographic information.|||| besides structure info (e.g. x-ray crystallography data) Andrei also includes structure-function data (e.g. mutation at Ser-321 compromises folding, binding, etc.)
+
|'''Structural information'''|| structinfo||||?||NC||
 
|-
 
|-
−
|||||'''Mass spectrometry''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=massspec (flagged-done)]||''Mass Spec''|| massspec||Check if your paper reports data from any mass spec analysis; keywords: mass spectrometry, peptide, (and any one of the following:) MASCOT, SEQUEST, X!Tandem, OMSSA, MassMatrix.||gw3@sanger.ac.uk, worm-bug@sanger.ac.uk||From Gary "...only interested in papers that report the peptide sequences that the mass-spec fragments match. These peptides are usually created by one of the programs: MASCOT, SEQUEST, X!Tandem, OMSSA, MassMatrix. So, the Description field should be:
+
|'''Mass spectrometry'''|| massspec||afp, cfp||Hinxton||||
−
Keywords: mass spectrometry, peptide, (and any one of the following:) MASCOT, SEQUEST, X!Tandem, OMSSA, MassMatrix
 
−
 
 
 
|-
 
|-
−
|||||colspan="6"|'''REAGENTS''':
+
|'''''C. elegans'' antibodies'''|| antibody ||tfp||postgres||old:/karen/cur_status_sources/antibody_ref.txt; current:?||
 
|-
 
|-
−
|'''DONE'''||||'''''C. elegans'' antibodies''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=antibody (flagged-done)]||''Extract Antibody''|| antibody ||Check if your paper reports the use of new or known antibodies created by your lab or someone else's lab; do not check this box if antibodies were commercially bought.||wchen@its.caltech.edu ||
+
|'''Integrated transgenes'''||transgene||tfp, jfp ||postgres||postgres||
 
|-
 
|-
−
|'''DONE'''||||'''Integrated transgenes''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=transgene (flagged-done)] ||''Transgene''||transgene||Check if integrated transgenes were used in this paper. If the transgene does not have a canonical name, please list it in the "Add Information text area" ||wchen@its.caltech.edu ||
+
|'''Transgenes used as tissue markers'''|| marker||afp, cfp||postgres||postgres||
 
|-
 
|-
−
|||||'''Transgenes used as tissue markers'''||''Marker''|| marker||Check if reporters (integrated transgenes) were used to mark certain tissues,  subcellular structures, or life stages, etc. as a reference point to assay gene function or location.||wchen@its.caltech.edu, vanauken@its.caltech.edu ||
+
|'''Gene structure correction''' ||structcorr (this use to be two different fields)||svm||Hinxton||||
 
|-
 
|-
−
|||||colspan="6"|GENOME SEQUENCE DATA:
+
|'''Sequencing mutant alleles''' ||seqchange ||afp, cfp||||||
 
|-
 
|-
−
|||||'''Gene structure correction''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=structurecorrectionsanger (flagged)]||''Sanger Gene Structure Correction'' and ''St. Louis Gene Structure Correction''|| structcorr (this use to be two different fields)||Check if your paper reports a gene structure that is different from the one in WormBase, e.g.,  different splice-site, SL1 instead of SL2, etc.||worm-bug@sanger.ac.uk, wormticket@watson.wustl.edu||
+
|'''New SNPs'''||newsnp||afp, cfp||||||
−
the authors may or may not state explicitly that let's say there is a
 
−
novel exon. if i see a gene studied in some detail (e.g. new gene was
 
−
cloned or gene structure is drawn in fig.), than i check amino acid
 
−
length for the protein with the data in WB, and i will eyeball the
 
−
diagrams of gene structures to see if there are obvious diffs. these
 
−
are quick checks but they catch an occasional gene structure change
 
−
not listed in the text.
 
 
|-
 
|-
−
|||||'''Sequencing mutant alleles''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=sequencechange (flagged)]||''Sequence change''||seqchange ||Check if your paper reports new sequence data for any mutation.||genenames@wormbase.org||
+
|'''Ablation data'''||ablationdata ||afp, cfp||||||
 
|-
 
|-
−
|||||'''New SNPs''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=newsnp (flagged)]||''Extract New SNP''||newsnp||Check if your paper reports a SNP that does not already exist in WormBase.||dblasiar@watson.wustl.edu, tbieri@watson.wustl.edu||
+
|'''Cell function'''||cellfunc||afp, cfp|||||||
 
|-
 
|-
−
|||||colspan="5"|CELL DATA:
+
|'''Phylogenetic data'''||phylogenetic||afp, cfp||||NC||
 
|-
 
|-
−
|||||'''Ablation data''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=ablationdata (flagged-done)]||''Ablation data''||ablationdata ||Check if your paper reports data from an assay involving any cell or anatomical unit being ablated by laser or by other means (e.g., by expressing a cell-toxic protein).||raymond@its.caltech.edu ||
+
|'''Other bioinformatics analysis'''||othersilico||afp, cfp||||NC||
 
|-
 
|-
−
|||||'''Cell function''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=cellfunction (flagged-done)]||''Cell function''||cellfunc||Check if your paper reports a function for any anatomical part (e.g., cell, tissue, etc.), which has not been indicated elsewhere on this form.||raymond@its.caltech.edu ||
+
|'''Supplemental materials'''||supplemental||afp, cfp||||||
 
|-
 
|-
−
|||||colspan="5" |IN SILICO DATA:
+
|'''Comment'''||nocuratable||afp, cfp||||||
 
|-
 
|-
−
||||||'''Phylogenetic data'''||'''new field'''||phylogenetic||Check if your paper reports any phylogenetic analysis.||||
+
|'''Feedback'''||comment||afp, cfp||||||
 
|-
 
|-
−
||||||'''Other bioinformatics analysis'''||'''new field'''||othersilico||Check if your paper reports any bioinformatic data not indicated anywhere else on this form.||||
+
|'''Strain'''||?||jfp||textpresso (GSA), postgres-afp table||||
 
|-
 
|-
−
|||||colspan="5"|OTHER:
+
|'''Rearrangements'''||?||jfp||textpresso (GSA), postgres-afp table||||
 
|-
 
|-
−
|||||'''Supplemental materials''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=supplemental (flagged-done)]||''Supplemental material''||supplemental||Check if your paper has supplemental material.||qwang@its.caltech.edu ||
+
|'''Cell/anatomy terms and synonyms'''||?||jfp ||textpresso (GSA), postgres-afp table||old: /karen/cur_status_sources/anatomy_ref.txt; current:?||
 
|-
 
|-
−
|||||'''NONE of the aforementioned data types are in this research article''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=comment (flagged)]||'''Comment'''||nocuratable||Check if none of the above pertains to your paper. Feel free to list the data type most pertinent to your research paper in the "Add information" text area.||||
+
|'''New phenotype'''||?||jfp||textpresso (GSA), postgres-afp table||?||
−
|-
 
−
|||||'''Any feedback? Please feel free to give us feedback for this form or for any other topic pertinent to how we can better extract data from your paper.''' ||'''new field'''||comment||Comments from all authors and curators are accessible through the "Comment" button at the bottom of the page.||kyook@caltech.edu, vanauken@caltech.edu||
 
 
|-
 
|-
 
|}
 
|}
 +
 +
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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