Curation status
From WormBaseWiki
Revision as of 01:19, 4 June 2011 by Kyook (talk | contribs) (→Datatypes, curation storage and source for generating curation status)
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 |