Difference between revisions of "Curation status"

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NC = Not actively curated
NC = Not actively curated
===Datatypes for Textpresso String Searches===
Enter your datatype here, and the URL where the data is.
Sequence feature -> http://textpresso-dev.caltech.edu/regulatory_region/fullcorpus_result20141023    I will talk to Yuling and see if the URL can be date-agnostic
Transgene -> http://textpresso-dev.caltech.edu/transgene/transgenes_in_regular_papers.out
Variation -> http://textpresso-dev.caltech.edu/gsa/worm/alleles/  [index of results]  [newfile docs are svm results]

Revision as of 20:29, 23 October 2014

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

Other related pages

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 old: home/acedb/karen/cur_status_sources/vargene_ref.txt; current:? 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? old: /karen/cur_status_sources/microarray_ref.txt; current:?
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 old:/karen/cur_status_sources/antibody_ref.txt; current:?
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 old: /karen/cur_status_sources/anatomy_ref.txt; current:?
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