Curation status
From WormBaseWiki
Jump to navigationJump to searchA 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