Difference between revisions of "Texpresso/Author/Curator interim form"
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|||GENE IDENTIFICATION AND MAPPING: | |||GENE IDENTIFICATION AND MAPPING: | ||
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− | |||||<span style="color:#FF00FF">'''''C. elegans'' other than Bristol'''</span>|| '''new field'''|| celegans||Please indicate if ''C. elegans'' isolates other than Bristol are | + | |||||'''C. elegans''' <span style="color:#FF00FF">CHANGE NAME TO '''''C. elegans'' other than Bristol'''</span>|| '''new field'''|| celegans||<span style="color:#FF00FF">Please indicate if data for''C. elegans'' isolates other than 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 <span style="color:#FF00FF">''C. elegans''(italicize)</span>, e.g., ''C. briggsae'', ''Pristionchus pacificus'', ''Brugia malayi'', etc.|| | |||||'''Nematodes other than ''C. elegans'''''||nonntwo||nematodes||Please indicate if data is presented for any species other than <span style="color:#FF00FF">''C. elegans''(italicize)</span>, e.g., ''C. briggsae'', ''Pristionchus pacificus'', ''Brugia malayi'', etc.|| | ||
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|in progress||||'''Newly cloned gene''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=genesymbol (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 cloned gene''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=genesymbol (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|| | + | |in progress||||'''Newly created allele'''||''Extract allele''||extractedvariation||<span style="color:#FF00FF"> Please indicate if your paper reports the identification of any allele that doesn't exist in WormBase already.</span>|| |
|- | |- | ||
|||||'''Genetic mapping data''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=mappingdata (flagged)]||''mapping data''||mappingdata||Please indicate if your paper contains 3-factor interval mapping data, <span style="color:#FF00FF">i.e., genetic data only. Include Df or Dp data, but no SNP interval mapping.</span>||genenames@wormbase.org | |||||'''Genetic mapping data''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=mappingdata (flagged)]||''mapping data''||mappingdata||Please indicate if your paper contains 3-factor interval mapping data, <span style="color:#FF00FF">i.e., genetic data only. Include Df or Dp data, but no SNP interval mapping.</span>||genenames@wormbase.org | ||
|- | |- | ||
− | |||GENE FUNCTION: | + | |||GENE FUNCTION: <span style="color:#FF00FF"> The data fields in this section are changed and reordered.|| The new order of data fields are: Phenotype Analysis section (keep suborder), Mosaic Analysis, Cell or tissue site of action, Time of action, Gene function, and Homolog of a human disease-associated gene. |
|- | |- | ||
− | |||Phenotype Analysis <span style="color:#FF00FF">CHANGE TO: "Mutant, RNAi, overexpression, or chemical-based phenotypes" </span>:||<span style="color:#FF00FF">'''PLEASE SPECIFY DATA TYPE.''' (make pop up text instructions bolder and more noticeable)</span> | + | |||Phenotype Analysis <span style="color:#FF00FF">CHANGE NAME TO: "Mutant, RNAi, overexpression, or chemical-based phenotypes" </span>:||<span style="color:#FF00FF">'''PLEASE SPECIFY DATA TYPE.''' (make pop up text instructions bolder and more noticeable)</span> |
|- | |- | ||
|||||'''Allele phenotype analysis''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=newmutant (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 | |||||'''Allele phenotype analysis''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=newmutant (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 | ||
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|in progress||||'''Chemicals''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=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.||| | |in progress||||'''Chemicals''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=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.||| | ||
|- | |- | ||
− | ||| | + | |||<span style="color:#FF00FF">moved</span>||'''Mosaic analysis''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=mosaic (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 |
|- | |- | ||
− | |in progress||||'''Homolog of a human disease-associated gene''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=humandiseases (flagged)]||''Human Disease''|| humandiseases ||Please indicate if genes discussed in your paper are a homolog/ortholog of a human disease-related gene. | + | |||<span style="color:#FF00FF">moved</span>|| '''Tissue or cell site of action''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=site (flagged-done)]||''Site of action''|| site ||Please indicate if your paper reports anatomy (tissue or cell)-specific expression function for a gene.||raymond@its.caltech.edu |
+ | |- | ||
+ | |||<span style="color:#FF00FF">moved</span>||'''Developmental time of action '''<span style="color:#FF00FF">CHANGE NAME TO "Time of action"</span>||'''new field''' || timeofaction||Please indicate if your paper reports a temporal requirement for gene function.||raymond@its.caltech.edu | ||
+ | |- | ||
+ | |||<span style="color:#FF00FF">reordered</span>||'''Gene function''' <span style="color:#FF00FF"> CHANGE NAME TO '''Molecular function of a gene product'''</span> [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=genefunction (flagged-done)]||''Gene function''||genefunction||Please indicate if your paper discusses a new function for a known or a newly defined gene.||emsch@its.caltech.edu | ||
+ | |- | ||
+ | |in progress||<span style="color:#FF00FF">reordered</span>||'''Homolog of a human disease-associated gene''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=humandiseases (flagged)]||''Human Disease''|| humandiseases ||Please indicate if genes discussed in your paper are a homolog/ortholog of a human disease-related gene. | ||
||ranjana@its.caltech.edu | ||ranjana@its.caltech.edu | ||
|- | |- | ||
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|||||'''Gene product interactions''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=geneproduct (flagged-done)]||''Gene product interaction'' ||geneproduct ||<span style="color:#FF00FF">Please indicate if your paper reports data on protein-protein, RNA-protein, DNA-protein, or Y2H interactions, etc.</span>|| emsch@its.caltech.edu | |||||'''Gene product interactions''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=geneproduct (flagged-done)]||''Gene product interaction'' ||geneproduct ||<span style="color:#FF00FF">Please indicate if your paper reports data on protein-protein, RNA-protein, DNA-protein, or Y2H interactions, etc.</span>|| emsch@its.caltech.edu | ||
|- | |- | ||
− | |||GENE EXPRESSION AND FUNCTION <span style="color:#FF00FF">CHANGE TO "REGULATION OF GENE EXPRESSION"</span>: | + | |||GENE EXPRESSION AND FUNCTION <span style="color:#FF00FF"> CHANGE NAME TO "REGULATION OF GENE EXPRESSION"</span>: |
|- | |- | ||
− | |||||'''New expression pattern for a gene''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=expression (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 | + | |||||'''New expression pattern for a gene''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=expression (flagged-done)]||''expression pattern data''|| otherexpression ||<span style="color:#FF00FF">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.</span>||wchen@its.caltech.edu, vanauken@its.caltech.edu |
|- | |- | ||
− | |in progress||||'''Alterations in gene expression by genetic background or other treatment''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=generegulation (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 background, exposure to chemicals or temperature or any other experimental treatment.||xdwang@its.caltech.edu | + | |in progress||||'''Alterations in gene expression by genetic background or other treatment'''<span style="color:#FF00FF"> CHANGE NAME TO "Alterations in gene expression by genetic or other treatment" </span> [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=generegulation (flagged-done)]||''Gene regulation on expression level'' || generegulation ||<span style="color:#FF00FF"> Please indicate if your paper reports changes or lack of changes in gene expression levels or patterns due to genetic background, exposure to chemicals or temperature, or any other experimental treatment.</span>||xdwang@its.caltech.edu |
|- | |- | ||
|||||'''Regulatory sequence features''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=sequencefeatures (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 | |||||'''Regulatory sequence features''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=sequencefeatures (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 | + | |||||'''Position frequency matrix (PFM)''' or '''Position weight matrix (PWM)'''||'''new field''' || matrices||<span style="color:#FF00FF"> 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.</span>||xdwang@its.caltech.edu, emsch@its.caltech.edu |
− | |||
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− | |||
− | |||
− | |||
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+ | |||
|||||'''Microarray'''[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=microarray (flagged-done)]||''Microarray''|| microarray ||Please indicate if your paper reports any microarray data.||wchen@its.caltech.edu | |||||'''Microarray'''[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=microarray (flagged-done)]||''Microarray''|| microarray ||Please indicate if your paper reports any microarray data.||wchen@its.caltech.edu | ||
|- | |- | ||
|||PROTEIN FUNCTION AND STRUCTURE: | |||PROTEIN FUNCTION AND STRUCTURE: | ||
|- | |- | ||
− | |||||'''Protein analysis ''in vitro'''''[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=invitro (flagged)]||in vitro ''Protein analysis''|| invitro ||<span style="color:#FF00FF">Please indicate if your paper reports any ''in vitro'' protein analysis such as kinase assays, agonist pharmacological studies, ''in vitro'' reconstitution studies, etc.</span>|| | + | |||||'''Protein analysis ''in vitro'''''[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=invitro (flagged)]||in vitro ''Protein analysis''|| invitro ||<span style="color:#FF00FF"> Please indicate if your paper reports any ''in vitro'' protein analysis such as kinase assays, agonist pharmacological studies, ''in vitro'' reconstitution studies, etc.</span>|| |
|- | |- | ||
|||||'''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.|| | |||||'''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.|| | ||
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|'''DONE'''||||'''Integrated transgenes''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=transgene (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 | |'''DONE'''||||'''Integrated transgenes''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=transgene (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 | ||
|- | |- | ||
− | |||||'''Cell or tissue reporter <span style="color:#FF00FF">CHANGE TO "Transgenes used as tissue markers"</span>''' ||''Marker''|| marker||<span style="color:#FF00FF">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.</span>||wchen@its.caltech.edu, vanauken@its.caltech.edu | + | |||||'''Cell or tissue reporter <span style="color:#FF00FF"> CHANGE NAME TO "Transgenes used as tissue markers"</span>''' ||''Marker''|| marker||<span style="color:#FF00FF">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.</span>||wchen@its.caltech.edu, vanauken@its.caltech.edu |
|- | |- | ||
|||GENOME SEQUENCE DATA: | |||GENOME SEQUENCE DATA: |
Revision as of 23:40, 12 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.
Automation status | Data type Section | Data type | Current fp curation form name | PGdb name | Description for author | Curator Flagged |
GENE IDENTIFICATION AND MAPPING: | ||||||
C. elegans CHANGE NAME TO C. elegans other than Bristol | new field | celegans | Please indicate if data forC. elegans isolates other than Bristol are presented in this paper. | |||
Nematodes other than C. elegans | nonntwo | nematodes | Please indicate if data is presented for any species other than C. elegans(italicize), e.g., C. briggsae, Pristionchus pacificus, Brugia malayi, etc. | |||
Genes studied in this paper | new field | rgngene | 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: The data fields in this section are changed and reordered. | The new order of data fields are: Phenotype Analysis section (keep suborder), Mosaic Analysis, Cell or tissue site of action, Time of action, Gene function, and Homolog of a human disease-associated gene. | |||||
Phenotype Analysis CHANGE NAME TO: "Mutant, RNAi, overexpression, or chemical-based phenotypes" : | PLEASE SPECIFY DATA TYPE. (make pop up text instructions bolder and more noticeable) | |||||
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. | ||
moved | 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 | |
moved | Tissue or cell site of action (flagged-done) | Site of action | site | Please indicate if your paper reports anatomy (tissue or cell)-specific expression function for a gene. | raymond@its.caltech.edu | |
moved | Developmental time of action CHANGE NAME TO "Time of action" | new field | timeofaction | Please indicate if your paper reports a temporal requirement for gene function. | raymond@its.caltech.edu | |
reordered | Gene function CHANGE NAME TO Molecular function of a gene product (flagged-done) | Gene function | genefunction | Please indicate if your paper discusses a new function for a known or a newly defined gene. | emsch@its.caltech.edu | |
in progress | reordered | Homolog of a human disease-associated gene (flagged) | Human Disease | humandiseases | Please indicate if genes discussed in your paper are a homolog/ortholog of a human disease-related gene. | 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 | functionalcomplementation | 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 | ||
GENE EXPRESSION AND FUNCTION CHANGE NAME TO "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 | Alterations in gene expression by genetic background or other treatment CHANGE NAME TO "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 background, exposure to chemicals or 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 | ||
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 | structureinformation | 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 | ||
Tools used for obtaining an expression pattern for a new gene CHANGE TO OWN SECTION CALLED "REAGENTS": | ||||||
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 | |
Cell or tissue reporter CHANGE NAME TO "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 | structurecorrectionsanger (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 | 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. "\" marks are showing on the page | |||
Comment (flagged) | new field | 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. | this should go to someone |