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

• curation status
• svm flagging status

Other related pages

• 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
  • Brief summary of curator first pass pipeline, obsolete with new paper editor
• 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	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)	svm	Hinxton
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