Difference between revisions of "Texpresso/Author/Curator interim form"

From WormBaseWiki
Jump to navigationJump to search
Line 17: Line 17:
 
|||||<span style="color:#FF00FF"> add new field'''''C. elegans'''''</span> which is default checked.||'''new field'''||'''celegans'''||<span style="color:#FF00FF"> Please uncheck if you are not reporting data for ''C. elegans''.||
 
|||||<span style="color:#FF00FF"> add new field'''''C. elegans'''''</span> which is default checked.||'''new field'''||'''celegans'''||<span style="color:#FF00FF"> Please uncheck if you are not reporting data for ''C. elegans''.||
 
|-
 
|-
|||||'''''C. elegans'' other than Bristol'''<span style="color:#FF00FF"> CHANGE TO "''C. elegans'' other than N2 (Bristol)"</span> <span style="color:#008080"> remove default 'on'</span> || '''new field'''|| <span style="color:#FF00FF">celegansnonbristol or what ever you want to call it</span>||<span style="color:#FF00FF"> Please indicate if data for ''C. elegans'' isolates other than N2 (Bristol) are presented in this paper.</span>||
+
|||||'''''C. elegans'' other than Bristol'''<span style="color:#FF00FF"> CHANGE TO "''C. elegans'' other than N2 (Bristol)"</span> <span style="color:#008080"> remove default 'on'</span> || '''new field'''|| <span style="color:#FF00FF">cnonbristol </span>||<span style="color:#FF00FF"> Please indicate if data for ''C. elegans'' isolates other than N2 (Bristol) are presented in this paper.</span>||
 
|-
 
|-
|||||'''Nematodes other than ''C. elegans'''''||nonntwo||nematodes||Please indicate if data is presented for any species other than ''C. elegans'', e.g., ''C. briggsae'', ''Pristionchus pacificus'', ''Brugia malayi'', etc. ||
+
|||||'''Nematodes other than ''C. elegans'''''||nonntwo||nematode||Please indicate if data is presented for any species other than ''C. elegans'', e.g., ''C. briggsae'', ''Pristionchus pacificus'', ''Brugia malayi'', etc. ||
 
|-
 
|-
|||||'''Non-nematode species'''||'''new field'''||'''new field'''||<span style="color:#FF00FF"> Please indicate if data is presented for any non-nematode species.</span>||
+
|||||'''Non-nematode species'''||'''new field'''||nonnematode||<span style="color:#FF00FF"> Please indicate if data is presented for any non-nematode species.</span>||
 
|-
 
|-
  

Revision as of 05:16, 14 March 2009

[back]

New First Pass Curator form

"flagged" = WBPapers that have been flagged for that particular data type but not curated yet or not assessed for curation status yet; "flagged-done" = WBPapers that have been flagged and curated. These papers can be used as a source for verified curation flag examples.

Click the "?" to find out more about the data type.

Automation status Data type Section Data type Current fp curation form name PGdb name Description for author Curator Flagged
add new section called SPECIES:
add new fieldC. elegans which is default checked. new field celegans Please uncheck if you are not reporting data for C. elegans.
C. elegans other than Bristol CHANGE TO "C. elegans other than N2 (Bristol)" remove default 'on' new field cnonbristol Please indicate if data for C. elegans isolates other than N2 (Bristol) are presented in this paper.
Nematodes other than C. elegans nonntwo nematode Please indicate if data is presented for any species other than C. elegans, e.g., C. briggsae, Pristionchus pacificus, Brugia malayi, etc.
Non-nematode species new field nonnematode Please indicate if data is presented for any non-nematode species.
GENE IDENTIFICATION AND MAPPING:
Genes studied in this paper new field genestudied Please use text box below to list any genes that were a focus of analysis in this research article. This information actually is the same info that a curator would enter through the WBpaper editor page, so it should get tied to that pipeline somehow. Also the text box for this data field should be auto-opened.
in progress Newly cloned gene (flagged-done) Gene Symbol genesymbol Please indicate if your paper reports a new symbol for a known locus or the name of a newly defined locus. genenames@wormbase.org, vanauken@its.caltech.edu
in progress Newly created allele Extract allele extractedvariation Please indicate if your paper reports the identification of any allele that doesn't exist in WormBase already.
Genetic mapping data (flagged) mapping data mappingdata Please indicate if your paper contains 3-factor interval mapping data, i.e., genetic data only. Include Df or Dp data, but no SNP interval mapping. genenames@wormbase.org
GENE FUNCTION:
Mutant, RNAi, overexpression, or chemical-based phenotypes: PLEASE SPECIFY DATA TYPE.
Allele phenotype analysis (flagged-done) Mutant Phenotype newmutant Please indicate if your paper reports any phenotype for a mutant. emsch@its.caltech.edu, garys@its.caltech.edu, jolenef@its.caltech.edu
in progress Small-scale RNAi (less than 100 experiments reported) (flagged-done) RNAi rnai Please indicate if your paper reports gene knockdown phenotypes for less than 100 individual RNAi experiments. garys@its.caltech.edu
Large-scale RNAi (less than 100 experiments reported) (flagged-done) Large-Scale RNAi lsrnai Please indicate if your paper reports gene knockdown phenotypes for more than 100 individual RNAi experiments. raymond@its.caltech.edu
Overexpression phenotype (flagged) Overexpression overexpression Please indicate if your paper reports an abnormal phenotype based on the overexpression of a gene or gene construct. E.g., ""...constitutively activated SCD-2(neu*) receptor caused 100% of animals to arrest in the first larval stage (L1)..." "\" marks are showing on the page emsch@its.caltech.edu, garys@its.caltech.edu
in progress Chemicals (flagged) Chemicals chemicals Please indicate if the effects of small molecules, chemicals, or drugs were studied on worms. E.g., paraquat, butanone, benzaldehyde, aldicarb, etc. Mutagens used for the generation of mutant in genetic screens do not need to be indicated.
Mosaic analysis (flagged-done) Mosaic analysis mosaic Please indicate if your paper reports cell specific gene function based on mosaic analysis, e.g. extra-chromosomal transgene loss in a particular cell lineage leads to loss of mutant rescue, etc. raymond@its.caltech.edu
Tissue or cell site of action (flagged-done) Site of action siteofaction Please indicate if your paper reports anatomy-specific function for a gene. raymond@its.caltech.edu
Time of action new field timeofaction Please indicate if your paper reports a temporal requirement for gene function. raymond@its.caltech.edu
Molecular function of a gene product(flagged-done) Gene function genefunction Please indicate if your paper discusses a new function for a known or newly defined gene. emsch@its.caltech.edu
in progress Homolog of a human disease-associated gene. CHANGE TO Relevance to a human disease. (flagged) Human Disease humandiseases Please indicate if genes discussed in your paper are a homolog/ortholog of a human disease-related gene or if your study models some aspect of a human disease. ranjana@its.caltech.edu
INTERACTIONS:
Genetic interactions (flagged-done) Gene interactions geneinteractions Please indicate if your paper reports the analysis of more than one gene at a time, e.g., double, triple, etc. mutants, including experiments where RNAi was concurrent with other RNAi-treatments or mutations. emsch@its.caltech.edu
Functional complementation (flagged) Functional Complementation fxncomp Please indicate if your paper reports functional redundancy between separate genes, e.g. the rescue of gen-A by overexpression of gen-B or any other extragenic sequence.
Gene product interactions (flagged-done) Gene product interaction geneproduct Please indicate if your paper reports data on protein-protein, RNA-protein, DNA-protein or Y2H interactions, etc. emsch@its.caltech.edu
REGULATION OF GENE EXPRESSION:
New expression pattern for a gene (flagged-done) expression pattern data otherexpression Please indicate if your paper reports new temporal or spatial (e.g., tissue, subcellular, etc.) data on the pattern of expression of any gene in a wild-type background. You can include: reporter gene analysis, antibody staining, In situ hybridization, RT-PCR, Western or Northern blot data. wchen@its.caltech.edu, vanauken@its.caltech.edu
in progress reorder Alterations in gene expression by genetic or other treatment (flagged-done) Gene regulation on expression level generegulation Please indicate if your paper reports changes or lack of changes in gene expression levels or patterns due to genetic, chemical, temperature, or any other experimental treatment. xdwang@its.caltech.edu
Regulatory sequence features (flagged) Sequence features sequencefeatures Please indicate if your paper reports any gene expression regulatory elements, e.g., DNA/RNA elements required for gene expression, promoters, introns, UTR's, DNA binding sites, etc. xdwang@its.caltech.edu, worm-bug@sanger.ac.uk, stlouis@wormbase.org
Position frequency matrix (PFM) or Position weight matrix (PWM) new field matrices Please indicate if your paper reports PFMs or PWMs, which are typically used to define regulatory sites in genomic DNA (e.g., bound by transcription factors) or mRNA (e.g., bound by translational factors or miRNA). PFMs define simple nucleotide frequencies, while PWMs are scaled logarithmically against a background frequency. xdwang@its.caltech.edu, emsch@its.caltech.edu
reorder Microarray(flagged-done) Microarray microarray Please indicate if your paper reports any microarray data. wchen@its.caltech.edu
PROTEIN FUNCTION AND STRUCTURE:
Protein analysis in vitro(flagged) in vitro Protein analysis invitro Please indicate if your paper reports any in vitro protein analysis such as kinase assays, agonist pharmacological studies, in vitro reconstitution studies, etc.
Domain analysis new field domainanalysis note, should be populated with information previously in "structureinformation" Please indicate if your paper reports on a function of a particular domain within a protein.
Covalent modification (flagged) Covalent modification covalent Please indicate if your paper reports on post-translational modifications as assayed by mutagenesis or in vitro analysis
Structural information(flagged) Structure information structinfo Please indicate if your paper reports NMR or X-ray crystallographic information.
Mass spectrometry (flagged-done) Mass Spec massspec Please indicate if your paper reports data from any mass spec analysis e.g., LCMS, COSY, HRMS, etc. gw3@sanger.ac.uk, worm-bug@sanger.ac.uk
REAGENTSremove period:
in progress C. elegans antibodies (flagged-done) Extract Antibody antibody Please indicate if your paper reports the use of new or known antibodies created by your lab or someone else's lab; do not check this box if antibodies were commercially bought. wchen@its.caltech.edu
DONE Integrated transgenes (flagged-done) Transgene transgene Please indicate if integrated transgenes were used in this paper. If the transgene does not have a canonical name, please list it in the "Add Information text area" wchen@its.caltech.edu
Transgenes used as tissue markers Marker marker Please indicate if reporters (integrated transgenes) were used to mark certain tissues, subcellular structures, or life stages, etc. as a reference point to assay gene function or location. wchen@its.caltech.edu, vanauken@its.caltech.edu
GENOME SEQUENCE DATA:
Gene structure correction (flagged) Sanger Gene Structure Correction and St. Louis Gene Structure Correction structcorr (this use to be two different fields) Please indicate if your paper reports a gene structure that is different from the one in WormBase, e.g., different splice-site, SL1 instead of SL2, etc. worm-bug@sanger.ac.uk
Sequencing mutant alleles (flagged) Sequence change sequencechange Please indicate if your paper reports new sequence data for any mutation. genenames@wormbase.org
New SNPs (flagged) Extract New SNP newsnp Please indicate if your paper reports a SNP that does not already exist in WormBase. dblasiar@watson.wustl.edu, tbieri@watson.wustl.edu
retired? ? Extract SNP verified by St. Louis (flagged) Extract SNP verified by St.Louis "fig.2: two SNPs mentioned"; any SNP mentioned; "For nekl-1, cDNA clones indicated that the predicted gene annotation was incorrect." dblasiar@watson.wustl.edu, tbieri@watson.wustl.edu
CELL DATA:
Ablation data (flagged-done) Ablation data ablationdata Please indicate if your paper reports data from an assay involving any cell or anatomical unit being ablated by laser or by other means (e.g., by expressing a cell-toxic protein). raymond@its.caltech.edu
Cell function (flagged-done) Cell function cellfunction Please indicate if your paper reports a function for any anatomical part (e.g., cell, tissue, etc.), which has not been indicated elsewhere on this form. raymond@its.caltech.edu
IN SILICO DATA:
Phylogenetic data new field phylogenetic Please indicate if your paper reports any phylogenetic analysis.
Other bioinformatics analysis new field othersilico Please indicate if your paper reports any bioinformatic data not indicated anywhere else on this form.
OTHER:
Supplemental materials (flagged-done) Supplemental material supplemental Please indicate if your paper has supplemental material. qwang@its.caltech.edu
NONE of the aforementioned data types are in this research article (flagged) Comment nocuratable Please indicate if none of the above pertains to your paper. Feel free to list the data type most pertinent to your research paper in the "Add information" text area.
Comment. CHANGE TO Comment. Please feel free to give us feedback for this form or for any other topic pertinent to how we can better extract data from your paper. new field comment Will you set up an archive/wiki feedback page to collate all of these comments with an alert when changes/additions to the page are made? Perhaps a new author_form_feedback@its.caltech.edu for alerts from the form, with a link to a wormbase-wide accessible site that contains the comments.