Difference between revisions of "Curation status"
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| align="center" style="background:#f0f0f0;"|'''Notes/actions''' | | align="center" style="background:#f0f0f0;"|'''Notes/actions''' | ||
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− | |'''''C. elegans'''''||'''celegans'''||afp,cfp||none|| | + | |'''''C. elegans'''''||'''celegans'''||afp,cfp||none||NC|| |
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− | |'''''C. elegans'' other than Bristol'''|| cnonbristol ||afp,cfp||none|| | + | |'''''C. elegans'' other than Bristol'''|| cnonbristol ||afp,cfp||none||NC|| |
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− | |'''Nematodes other than ''C. elegans'''''||nematode||afp,cfp||none|| | + | |'''Nematodes other than ''C. elegans'''''||nematode||afp,cfp||none||NC|| |
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− | |'''Non-nematode species'''||nonnematode||afp,cfp||none|| | + | |'''Non-nematode species'''||nonnematode||afp,cfp||none||NC|| |
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|'''Genes studied in this paper'''||genestudied||afp, cfp, tfp||geneace|||| | |'''Genes studied in this paper'''||genestudied||afp, cfp, tfp||geneace|||| | ||
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|'''Genetic interactions''' ||geneint||tfp, afp, cfp||postgres||||postgres- interaction table | |'''Genetic interactions''' ||geneint||tfp, afp, cfp||postgres||||postgres- interaction table | ||
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− | |'''Functional complementation'''||funccomp||afp, cfp||?|| | + | |'''Functional complementation'''||funccomp||afp, cfp||?||NC|| |
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|'''Gene product interactions''' ||geneprod||afp, cfp||?|||| | |'''Gene product interactions''' ||geneprod||afp, cfp||?|||| | ||
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|'''in vitro ''Protein analysis'''''|| invitro|| SVM?||?|||| | |'''in vitro ''Protein analysis'''''|| invitro|| SVM?||?|||| | ||
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− | |'''Domain analysis''' || domanal (populated with information previously in "structureinformation")||||?|| | + | |'''Domain analysis''' || domanal (populated with information previously in "structureinformation")||||?||NC|| |
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− | |'''Covalent modification'''|| covalent||||?|| | + | |'''Covalent modification'''|| covalent||||?||NC|| |
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− | |'''Structural information'''|| structinfo||||?|| | + | |'''Structural information'''|| structinfo||||?||NC|| |
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|'''Mass spectrometry'''|| massspec||afp, cfp||Hinxton|||| | |'''Mass spectrometry'''|| massspec||afp, cfp||Hinxton|||| | ||
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|'''Cell function'''||cellfunc||afp, cfp||||||| | |'''Cell function'''||cellfunc||afp, cfp||||||| | ||
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− | |'''Phylogenetic data'''||phylogenetic||afp, cfp|||| | + | |'''Phylogenetic data'''||phylogenetic||afp, cfp||||NC|| |
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− | |'''Other bioinformatics analysis'''||othersilico||afp, cfp|||| | + | |'''Other bioinformatics analysis'''||othersilico||afp, cfp||||NC|| |
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|'''Supplemental materials'''||supplemental||afp, cfp|||||| | |'''Supplemental materials'''||supplemental||afp, cfp|||||| | ||
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SVM = Support Vector Machine | SVM = Support Vector Machine | ||
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+ | NC = Not actively curated |
Revision as of 22:15, 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
- Overview of first pass flagging pipelines
- Textpresso flagging pipelines with postgres queries for individual data types
- GSA first pass overview
- Original first pass indexing page
- 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
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 | 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 | this is the correct source to get paper-allele connection |
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 | should be from postgres transgene-phenotype-paper | |
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- 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 | |
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") | ? | NC | ||
Covalent modification | covalent | ? | NC | ||
Structural information | structinfo | ? | NC | ||
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 | 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 | /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
NC = Not actively curated