Difference between revisions of "Curation status"

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afp = Author first pass
cfp = Curator first pass
tfp = Textpresso first pass
jpf = Journal first pass
SVM = Support Vector Machine

Revision as of 19:04, 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 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


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