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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{|| 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'''
 
|-
 
|-
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|'''''C. elegans'''''||'''celegans'''||||||
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|'''''C. elegans'''''||'''celegans'''||afp,cfp||none||N/A||
 
|-
 
|-
−
|||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.''||||
+
|'''''C. elegans'' other than Bristol'''|| cnonbristol ||afp,cfp||none||N/A||
 
|-
 
|-
−
|||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. ||||
+
|'''Nematodes other than ''C. elegans'''''||nematode||afp,cfp||none||N/A||
 
|-
 
|-
−
|||materials and methods||'''Non-nematode species'''||'''new field'''||nonnematode||Check if data is reported for any non-nematode species.||||
+
|'''Non-nematode species'''||nonnematode||afp,cfp||none||N/A||
 
|-
 
|-
−
 
+
|'''Genes studied in this paper'''||genestudied||afp, cfp, tfp||geneace|||
−
 
 
−
|||||colspan="6"|GENE IDENTIFICATION AND MAPPING:
 
 
|-
 
|-
−
 
+
|'''Newly cloned gene''' || genesymbol ||afp, cfp, jfp||geneace|||
−
|||||'''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 ||
+
|'''Newly created allele'''||extvariation||afp, cfp, tfp, jfp||variation NS||home/acedb/karen/cur_status_sources/vargene_ref.txt||
 
|-
 
|-
−
|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.||||
+
|'''Genetic mapping data'''||mappingdata||cfp, afp||geneace|||
 
|-
 
|-
−
|||||'''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 ||
+
|'''Phenotype analysis''' || newmutant ||cfp, afp, svm ||postgres||postgres|
 
|-
 
|-
−
|||||colspan="6"|GENE FUNCTION:
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|'''Small-scale RNAi''' (less than 100 experiments reported)|| rnai||afp, cfp, tfp, svm||citace||postgres via paper checkout|
 
|-
 
|-
−
|||||colspan="4"|'''Mutant, RNAi, overexpression, or chemical-based phenotypes''':||colspan="2"|'''PLEASE SPECIFY DATA TYPE.'''
+
|'''Large-scale RNAi''' (more than 100 experiments reported)|| lsrnai||afp, cfp, tfp, svm||citace||postgres via paper checkout|
 
|-
 
|-
−
|'''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 ||
+
|'''Overexpression phenotype'''||overexpr||afp, cfp, svm||postgres||postgres via transgene-phenotype|
 
|-
 
|-
−
|'''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||
+
|'''Chemicals'''||chemicals (molecule?) ||afp, cfp||postgres|||
 
|-
 
|-
−
|'''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||
+
|'''Mosaic analysis'''||mosaic ||afp, cfp||?|||
 
|-
 
|-
−
|'''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||
+
|'''Tissue or cell site of action'''|| siteaction ||afp, cfp||?|||
 
|-
 
|-
−
|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.||||
+
|'''Time of action''' || timeaction||afp, cfp||?|||
 
|-
 
|-
−
|||||'''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 ||
+
|'''Molecular function of a gene product'''||genefunc||afp, cfp||?|||
 
|-
 
|-
−
|||||'''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 ||
+
|'''Homolog of a human disease-associated gene.'''|| humdis ||afp, cfp||?|||
 
|-
 
|-
−
|||||'''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||
+
|'''Genetic interactions''' ||geneint||tfp, afp, cfp||postgres||postgres|
 
|-
 
|-
−
|||||'''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''' ||
+
|'''Functional complementation'''||funccomp||afp, cfp||?||N/A||
 
|-
 
|-
−
|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 ||
+
|'''Gene product interactions''' ||geneprod||afp, cfp||?|||
 
|-
 
|-
−
|||||colspan="6"|INTERACTIONS:
+
|'''New expression pattern for a gene'''|| otherexpr ||afp, cfp,SVM ||postgres||postgres|
 
|-
 
|-
−
|||||'''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''' ||
+
|'''Alterations in gene expression by genetic or other treatment'''|| genereg ||afp, cfp||postgres||/home/acedb/karen/cur_status_sources/regulation_ref.txt||
 
|-
 
|-
−
|||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.|| ||
+
|'''Regulatory sequence features'''||seqfeat ||afp, cfp||?|||
 
|-
 
|-
−
|||||'''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''' ||
+
|PFM, PWM|| matrices||afp, cfp||? |||
 
|-
 
|-
−
|||||colspan="6"|REGULATION OF GENE EXPRESSION:
+
|'''Microarray'''|| microarray ||afp, cfp||citace?||/karen/cur_status_sources/microarray_ref.txt||
 
|-
 
|-
−
|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||
+
|in vitro ''Protein analysis''|| invitro|| SVM?||?|||
 
|-
 
|-
−
|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 ||
+
|'''Domain analysis''' || domanal (populated with information previously in "structureinformation")||||?||N/A|
 
|-
 
|-
−
|||||'''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 ||
+
|'''Covalent modification'''|| covalent||||?||N/A||
 
|-
 
|-
−
|||||'''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''' ||
+
|'''Structural information'''|| structinfo||||?||N/A||
 
|-
 
|-
−
|||||'''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 ||
+
|'''Mass spectrometry'''|| massspec||afp, cfp||Hinxton|||
 
|-
 
|-
−
|||||colspan="6"|PROTEIN FUNCTION AND STRUCTURE:
+
|'''''C. elegans'' antibodies'''|| antibody ||tfp||postgres?||/karen/cur_status_sources/antibody_ref.txt||
 
|-
 
|-
−
|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.|| ||
+
|'''Integrated transgenes'''||transgene||tfp, jfp ||postgres||postgres|
 
|-
 
|-
−
|||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.||||
+
|'''Transgenes used as tissue markers'''|| marker||afp, cfp||postgres||postgres|
 
|-
 
|-
−
|||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||||
+
|'''Gene structure correction''' || structcorr (this use to be two different fields)|||||||
 
|-
 
|-
−
|||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.)
+
|'''Sequencing mutant alleles''' ||seqchange |||||||
 
|-
 
|-
−
|||||'''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:
+
|'''New SNPs'''||newsnp|||||||
−
Keywords: mass spectrometry, peptide, (and any one of the following:) MASCOT, SEQUEST, X!Tandem, OMSSA, MassMatrix
 
−
 
 
 
|-
 
|-
−
|||||colspan="6"|'''REAGENTS''':
+
|'''Ablation data'''||ablationdata |||||||
 
|-
 
|-
−
|'''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 ||
+
|'''Cell function'''||cellfunc|||||||
 
|-
 
|-
−
|'''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 ||
+
|'''Phylogenetic data'''||phylogenetic||||||N/A||
 
|-
 
|-
−
|||||'''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 ||
+
|'''Other bioinformatics analysis'''||othersilico||||||N/A||
 
|-
 
|-
−
|||||colspan="6"|GENOME SEQUENCE DATA:
+
|'''Supplemental materials'''||supplemental|||||||
 
|-
 
|-
−
|||||'''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||
+
|'''Comment'''||nocuratable|||||||
−
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||
+
|'''Feedback'''||comment|||||||
 
|-
 
|-
−
|||||'''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||
+
|'''Strain'''||?||jfp, afp??||textpresso, postgres??|||
 
|-
 
|-
−
|||||colspan="5"|CELL DATA:
+
|'''Rearrangements'''||?||jfp, afp?||textpresso, postgres?|||
 
|-
 
|-
−
|||||'''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 ||
+
|'''Cell/anatomy terms and synonyms'''||?||jfp, afp??||textpresso, postgres?||/karen/cur_status_sources
 +
/anatomy_ref.txt|
 
|-
 
|-
−
|||||'''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 ||
+
|'''New phenotype'''||?||jfp, afp??||textpresso, postgres||phenotype obo? |
−
|-
 
−
|||||colspan="5" |IN SILICO DATA:
 
−
|-
 
−
||||||'''Phylogenetic data'''||'''new field'''||phylogenetic||Check if your paper reports any phylogenetic analysis.||||
 
−
|-
 
−
||||||'''Other bioinformatics analysis'''||'''new field'''||othersilico||Check if your paper reports any bioinformatic data not indicated anywhere else on this form.||||
 
−
|-
 
−
|||||colspan="5"|OTHER:
 
−
|-
 
−
|||||'''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 ||
 
−
|-
 
−
|||||'''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.||||
 
−
|-
 
−
|||||'''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||
 
 
|-
 
|-
 
|}
 
|}

Revision as of 01:19, 4 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 N/A
C. elegans other than Bristol cnonbristol afp,cfp none N/A
Nematodes other than C. elegans nematode afp,cfp none N/A
Non-nematode species nonnematode afp,cfp none N/A
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
Small-scale RNAi (less than 100 experiments reported) rnai afp, cfp, tfp, svm citace
Large-scale RNAi (more than 100 experiments reported) 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 ? N/A
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 /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") ?
Covalent modification covalent ? N/A
Structural information structinfo ? N/A
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
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
Retrieved from "https://wiki.wormbase.org/index.php?title=Curation_status&oldid=11023"