Difference between revisions of "Texpresso/Author/Curator interim form"
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| align="center" style="background:#f0f0f0;"|'''Description for author''' | | align="center" style="background:#f0f0f0;"|'''Description for author''' | ||
| align="center" style="background:#f0f0f0;"|'''Curator Flagged''' | | align="center" style="background:#f0f0f0;"|'''Curator Flagged''' | ||
+ | | align="center" style="background:#f0f0f0;"|'''Notes about field''' | ||
|- | |- | ||
− | |||||colspan=" | + | |||||colspan="6"|SPECIES: |
|- | |- | ||
|||materials and methods||'''''C. elegans''''' ''default checked.''||'''new field'''||'''celegans'''||Please uncheck if you are not reporting data for ''C. elegans''.|| | |||materials and methods||'''''C. elegans''''' ''default checked.''||'''new field'''||'''celegans'''||Please uncheck if you are not reporting data for ''C. elegans''.|| | ||
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− | |||||colspan=" | + | |||||colspan="6"|GENE IDENTIFICATION AND MAPPING: |
|- | |- | ||
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|||||'''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, i.e., genetic data only. Include Df or Dp data, but no SNP interval mapping.||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, i.e., genetic data only. Include Df or Dp data, but no SNP interval mapping.||genenames@wormbase.org | ||
|- | |- | ||
− | |||||colspan=" | + | |||||colspan="6"|GENE FUNCTION: |
|- | |- | ||
− | |||||colspan=" | + | |||||colspan="4"|'''Mutant, RNAi, overexpression, or chemical-based phenotypes''':||colspan="2"|'''PLEASE SPECIFY DATA TYPE.''' |
|- | |- | ||
|||||'''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. ||emsch@its.caltech.edu, garys@its.caltech.edu, jolenef@its.caltech.edu | |||||'''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. ||emsch@its.caltech.edu, garys@its.caltech.edu, jolenef@its.caltech.edu | ||
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|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''|| humdis ||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 | |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''|| humdis ||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 | ||
|- | |- | ||
− | |||||colspan=" | + | |||||colspan="6"|INTERACTIONS: |
|- | |- | ||
|''Andrei may do this''||||'''Genetic interactions''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=geneinteractions (flagged-done)]||''Gene interactions'' ||geneint||''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 | |''Andrei may do this''||||'''Genetic interactions''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=geneinteractions (flagged-done)]||''Gene interactions'' ||geneint||''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 | ||
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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'' ||geneprod||Please indicate if your paper reports data on protein-protein, RNA-protein, DNA-protein or Y2H interactions, etc.|| 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'' ||geneprod||Please indicate if your paper reports data on protein-protein, RNA-protein, DNA-protein or Y2H interactions, etc.|| emsch@its.caltech.edu | ||
|- | |- | ||
− | |||||colspan=" | + | |||||colspan="6"|REGULATION OF GENE EXPRESSION: |
|- | |- | ||
|||||'''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''|| otherexpr ||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''|| otherexpr ||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 | ||
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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 | ||
|- | |- | ||
− | |||||colspan=" | + | |||||colspan="6"|PROTEIN FUNCTION AND STRUCTURE: |
|- | |- | ||
|||materials and methods; results||'''Protein analysis ''in vitro'''''[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=invitro (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.|| | |||materials and methods; results||'''Protein analysis ''in vitro'''''[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=invitro (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.|| | ||
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|||materials and methods; results||'''Covalent modification''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=covalent (flagged)]||''Covalent modification'' || covalent|| Please indicate if your paper reports on post-translational modifications as assayed by mutagenesis or ''in vitro'' analysis|| | |||materials and methods; results||'''Covalent modification''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=covalent (flagged)]||''Covalent modification'' || covalent|| Please indicate if your paper reports on post-translational modifications as assayed by mutagenesis or ''in vitro'' analysis|| | ||
|- | |- | ||
− | |||materials and methods; results||'''Structural information'''[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=structureinformation (flagged)]||''Structure information''|| structinfo||Please indicate if your paper reports NMR or X-ray crystallographic information.|| | + | |||materials and methods; results||'''Structural information'''[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=structureinformation (flagged)]||''Structure information''|| structinfo||Please indicate if your paper reports NMR or X-ray crystallographic information.|||| besides structure info (e.g. x-ray crystallography data) Andrei also includes structure-function data (e.g. mutation at Ser-321 compromises folding, binding, etc.) |
|- | |- | ||
− | |||||'''Mass spectrometry''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=massspec (flagged-done)]||''Mass Spec''|| massspec||Please indicate if your paper reports data from any mass spec analysis | + | |||||'''Mass spectrometry''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=massspec (flagged-done)]||''Mass Spec''|| massspec||Please indicate if your paper reports data from any mass spec analysis; keywords: mass spectrometry, peptide, (and any one of the following:) MASCOT, SEQUEST, X!Tandem, OMSSA, MassMatrix.||gw3@sanger.ac.uk, worm-bug@sanger.ac.uk||From Gary "I receive the Mass Spec data. I've been receiving a high proportion of false positives. This is because I'm only interested in papers that report the peptide sequences that the mass-spec fragments match. These peptides are usually created by one of the programs: MASCOT, SEQUEST, X!Tandem, OMSSA, MassMatrix. So, the Description field should be: |
+ | Keywords: mass spectrometry, peptide, (and any one of the following:) MASCOT, SEQUEST, X!Tandem, OMSSA, MassMatrix | ||
+ | |||
+ | Examples of info sent to data curator | ||
+ | |||
+ | "Supplemental Legends | ||
+ | Supplemental Table 1 Library of synthetic C. elegans FLP and NLP peptides." | ||
+ | |||
+ | "The MS/MS data of all 10 SCX fractions were transformed into pkl files or peak list files using the Proteinlynx software (Waters-Micromass). These text files were subsequently submitted to a Mascot search on an in-house server to identify the peptides. This bioinformatics program matches the fragmentation data from the peak list files against our home-made database containing all known ABC precursors. Individual ions with Probability Based Mowse Scores above the threshold required for identity or extensive homology (p < 0.05) were further manually explored and annotated to gain sequence information. " | ||
+ | |||
|- | |- | ||
− | |||||colspan=" | + | |||||colspan="6"|'''REAGENTS''':|| |
|- | |- | ||
|'''DONE'''||||'''''C. elegans'' antibodies''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=antibody (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'''||||'''''C. elegans'' antibodies''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=antibody (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 | ||
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|||||'''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 | |||||'''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 | ||
|- | |- | ||
− | |||||colspan=" | + | |||||colspan="6"|GENOME SEQUENCE DATA: |
|- | |- | ||
− | |||||'''Gene structure correction''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=structurecorrectionsanger (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, wormticket@watson.wustl.edu | + | |||||'''Gene structure correction''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=structurecorrectionsanger (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, wormticket@watson.wustl.edu|| |
+ | the authors may or may not state explicitly that let's say there is a | ||
+ | novel exon. if i see a gene studied in some detail (e.g. new gene was | ||
+ | cloned or gene structure is drawn in fig.), than i check amino acid | ||
+ | length for the protein with the data in WB, and i will eyeball the | ||
+ | diagrams of gene structures to see if there are obvious diffs. these | ||
+ | are quick checks but they catch an occasional gene structure change | ||
+ | not listed in the text. | ||
|- | |- | ||
|||||'''Sequencing mutant alleles''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=sequencechange (flagged)]||''Sequence change''||seqchange ||Please indicate if your paper reports new sequence data for any mutation.||genenames@wormbase.org | |||||'''Sequencing mutant alleles''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=sequencechange (flagged)]||''Sequence change''||seqchange ||Please indicate if your paper reports new sequence data for any mutation.||genenames@wormbase.org |
Revision as of 17:57, 22 June 2009
[back]
Instructions for curators
Feature Requests
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 | Paper Section | Data type | Old fp curation form name | PGdb name | Description for author | Curator Flagged | Notes about field | |
SPECIES: | ||||||||
materials and methods | C. elegans default checked. | new field | celegans | Please uncheck if you are not reporting data for C. elegans. | ||||
materials and methods | C. elegans other than Bristol | new field | cnonbristol | Please indicate if data for C. elegans isolates other than N2 (Bristol) are presented in this paper.e.g. Hawaiian, CB4855, CB4852, CB4507, LSJ1, etc. | ||||
materials and methods | 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. | ||||
materials and methods | 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 | extvariation | 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. | |||||||
Phenotype analysis (flagged-done) | Mutant Phenotype | newmutant | Please indicate if your paper reports any phenotype. | emsch@its.caltech.edu, garys@its.caltech.edu, jolenef@its.caltech.edu | ||||
DONE | 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 | |||
DONE will be part of small scale RNAi pipeline | 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 | overexpr | 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)..." | emsch@its.caltech.edu, garys@its.caltech.edu, jolenef@its.caltech.edu | ||||
in progress | materials and methods; results | 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 | siteaction | Please indicate if your paper reports anatomy-specific function for a gene. | raymond@its.caltech.edu | ||||
Time of action | new field | timeaction | 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 | genefunc | 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.(flagged) | Human Disease | humdis | 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: | ||||||||
Andrei may do this | Genetic interactions (flagged-done) | Gene interactions | geneint | 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 | |||
materials and methods (tools); results | Functional complementation (flagged) | Functional Complementation | funccomp | 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 | geneprod | 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 | otherexpr | 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 or other treatment (flagged-done) | Gene regulation on expression level | genereg | 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 | seqfeat | 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: | ||||||||
materials and methods; results | 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. | ||||
materials and methods; results | Domain analysis | new field | domanal (populated with information previously in "structureinformation") | Please indicate if your paper reports on a function of a particular domain within a protein. | ||||
materials and methods; results | Covalent modification (flagged) | Covalent modification | covalent | Please indicate if your paper reports on post-translational modifications as assayed by mutagenesis or in vitro analysis | ||||
materials and methods; results | Structural information(flagged) | Structure information | structinfo | Please indicate if your paper reports NMR or X-ray crystallographic information. | besides structure info (e.g. x-ray crystallography data) Andrei also includes structure-function data (e.g. mutation at Ser-321 compromises folding, binding, etc.) | |||
Mass spectrometry (flagged-done) | Mass Spec | massspec | Please indicate if your paper reports data from any mass spec analysis; keywords: mass spectrometry, peptide, (and any one of the following:) MASCOT, SEQUEST, X!Tandem, OMSSA, MassMatrix. | gw3@sanger.ac.uk, worm-bug@sanger.ac.uk | From Gary "I receive the Mass Spec data. I've been receiving a high proportion of false positives. This is because I'm only interested in papers that report the peptide sequences that the mass-spec fragments match. These peptides are usually created by one of the programs: MASCOT, SEQUEST, X!Tandem, OMSSA, MassMatrix. So, the Description field should be:
Keywords: mass spectrometry, peptide, (and any one of the following:) MASCOT, SEQUEST, X!Tandem, OMSSA, MassMatrix Examples of info sent to data curator "Supplemental Legends Supplemental Table 1 Library of synthetic C. elegans FLP and NLP peptides." "The MS/MS data of all 10 SCX fractions were transformed into pkl files or peak list files using the Proteinlynx software (Waters-Micromass). These text files were subsequently submitted to a Mascot search on an in-house server to identify the peptides. This bioinformatics program matches the fragmentation data from the peak list files against our home-made database containing all known ABC precursors. Individual ions with Probability Based Mowse Scores above the threshold required for identity or extensive homology (p < 0.05) were further manually explored and annotated to gain sequence information. " | |||
REAGENTS: | ||||||||
DONE | 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, wormticket@watson.wustl.edu |
the authors may or may not state explicitly that let's say there is a novel exon. if i see a gene studied in some detail (e.g. new gene was cloned or gene structure is drawn in fig.), than i check amino acid length for the protein with the data in WB, and i will eyeball the diagrams of gene structures to see if there are obvious diffs. these are quick checks but they catch an occasional gene structure change not listed in the text. | |||
Sequencing mutant alleles (flagged) | Sequence change | seqchange | 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 | ||||
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 | cellfunc | 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. | |||||
Any feedback? 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 | Comments from all authors and curators are accessible through the "Comment" button at the bottom of the page. | kyook@caltech.edu, vanauken@caltech.edu |