Difference between revisions of "Curation status"
Line 4: | Line 4: | ||
*[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi curation status] | *[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi curation status] | ||
*[http://tazendra.caltech.edu/~postgres/cgi-bin/svm_results.cgi svm flagging status] | *[http://tazendra.caltech.edu/~postgres/cgi-bin/svm_results.cgi svm flagging status] | ||
+ | |||
+ | === SVM status form=== | ||
+ | |||
+ | A form intended to analyze SVM data has been developed | ||
+ | http://mangolassi.caltech.edu/~postgres/cgi-bin/svm_results.cgi | ||
+ | |||
+ | Before moving on with the SVM form curators have to reach a consensus on how the analysis should be done. Should we keep track on SVM analysis on single documents or combined documents? In other words, do we keep the supplementary material separated or do we merge everything in a combined PDF file that will then be scanned by SVM? | ||
+ | |||
+ | Please add/edit below pros and cons on having the analysis performed on single documents(i.e. .main; .sup1; .sup2..) | ||
+ | |||
+ | * Pros | ||
+ | ** specificity -> curators don't have to scan through all the supplementary materials but could open just the relevant document | ||
+ | |||
+ | * Cons of having it to single documents: | ||
+ | ** We cannot perform statistics on what has been done so far | ||
+ | ** Curators have to record in the OA in which document was the info. e.g.: dropdown .sup1. Is it really time consuming? | ||
===Other related pages=== | ===Other related pages=== |
Revision as of 02:06, 18 September 2012
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.
Contents
Current status forms
SVM status form
A form intended to analyze SVM data has been developed http://mangolassi.caltech.edu/~postgres/cgi-bin/svm_results.cgi
Before moving on with the SVM form curators have to reach a consensus on how the analysis should be done. Should we keep track on SVM analysis on single documents or combined documents? In other words, do we keep the supplementary material separated or do we merge everything in a combined PDF file that will then be scanned by SVM?
Please add/edit below pros and cons on having the analysis performed on single documents(i.e. .main; .sup1; .sup2..)
- Pros
- specificity -> curators don't have to scan through all the supplementary materials but could open just the relevant document
- Cons of having it to single documents:
- We cannot perform statistics on what has been done so far
- Curators have to record in the OA in which document was the info. e.g.: dropdown .sup1. Is it really time consuming?
- 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 | postgres? paper tables? | ||
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 | for paper-allele connections; Variation NS for latest variation curation |
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 | postgres (no specific table) | should be from postgres transgene-phenotype-paper |
Chemicals | chemicals (molecule?) | afp, cfp, tfp | 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, tfp | ? | ||
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 | |
Images | tfp | 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 | tfp | ? | ||
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