Difference between revisions of "Genetics Markup by Textpresso and First Pass"

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[[http://www.wormbase.org/wiki/index.php/How_to_FirstPass back]]
 
[[http://www.wormbase.org/wiki/index.php/How_to_FirstPass back]]
 
----
 
----
−
=[[Instructions for Genetics]]=
+
==[[Mark up policy]]==
−
=[[Instructions for Authors]]=
 
  
−
----
+
==[[Mark Up Work Flow]]==
 +
[[Media:slide1.jpg]]
  
−
=Genetics First Pass Curator form=
+
this file diagrams the most recent and most detailed workflow we established, which includes editorial roles at Dartmouth. The steps below is a brief overview of the process. <br>
−
''"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.'''
 
  
−
{|| border="1" cellpadding="2"
+
These following steps outline the work flow for Textpresso markup starting with the acceptance of the paper by GENETICS and through to the incorporation of the paper into WB.<br>  
−
| align="center" style="background:#f0f0f0;"|'''Data type Section'''
 
−
| align="center" style="background:#f0f0f0;"|'''Data type'''
 
−
| align="center" style="background:#f0f0f0;"|'''PGdb name'''
 
−
| align="center" style="background:#f0f0f0;"|'''Description for author'''
 
−
| align="center" style="background:#f0f0f0;"|'''Curator Flagged'''
 
−
|-
 
−
|SPECIES:
 
−
|-
 
−
|||'''''C. elegans''''' ''default checked.''||celegans||Please uncheck if you are not reporting data for ''C. elegans''.||
 
−
|-
 
−
|||'''''C. elegans'' other than Bristol'''||cnonbristol ||Please indicate if data for ''C. elegans'' isolates other than N2 (Bristol) are presented in this paper.||
 
−
|-
 
−
|||'''Nematodes other than ''C. elegans'''''||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'''||nonnematode||Please indicate if data is presented for any non-nematode species.||
 
−
|-
 
  
 +
''The responsible party is noted before each step.'' <br>
  
−
|GENE IDENTIFICATION AND MAPPING:
+
Genetics (1) The paper gets accepted.
−
|-
 
  
−
|||'''Genes studied in this paper'''||genestudied||Please list any genes that were a focus of analysis in this research article.||
+
Genetics (2) A DOI is assigned to the paper
−
|-
+
 
−
|||'''Newly cloned gene''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=genesymbol (flagged-done)]||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
+
Genetics (3) A WBPaperID and URL are acquired through the ticketing form at: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_paper_ticket.cgi
−
|-
+
 
−
|||'''Newly created allele'''||extvariation||Please indicate if your paper reports the identification of any allele that doesn't exist in WormBase already.||
+
Genetics (4) The WBPaperID from the ticket issuer is attached to the XML
−
|-
+
 
−
|||||'''Genetic mapping data''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=mappingdata (flagged)]||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
+
Genetics (5)  the author is sent the generated URL to access the author form
−
|-
+
 
−
|GENE FUNCTION:
+
Author  (6) Authors provide the final source files and fills out the author first pass form within 48 hours of acceptance to GENETICS.
−
|-
+
* Author data populates journal first-pass tables in postgres, new objects are automatically added to the appropriate lexicon.  
−
|||'''Mutant, RNAi, overexpression, or chemical-based phenotypes''':||'''PLEASE SPECIFY DATA TYPE.'''
+
* New object data from the journal first-pass form is sent to Karen, who makes sure the information is entered correctly
−
|-
+
* New data goes to the appropriate data curator for acedb object creation.
−
|||'''Allele phenotype analysis''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=newmutant (flagged-done)]||newmutant ||Please indicate if your paper reports any phenotype for a mutant. ||emsch@its.caltech.edu, garys@its.caltech.edu, jolenef@its.caltech.edu  
+
* All other data populates author first-pass tables and paper is placed in the pipeline for first-pass curation (Juancarlos will make a filter so these papers will be prioritized for first-pass).
−
|-
+
−
|||'''Small-scale RNAi''' (less than 100 experiments reported) [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=rnai (flagged-done)]|| rnai||Please indicate if your paper reports gene knockdown phenotypes for less than 100 individual RNAi experiments.||garys@its.caltech.edu
+
DJS (Dartmouth Journal Services) (~5-8) sends the final source file (in XML format) to Arun - ''deposits XML on a web service?'' http://textpresso-dev.caltech.edu/gsa/worm/incoming_xml/
−
|-
+
* An e-mail is sent to the QC curator that a paper is coming and to expect a follow up e-mail with a link to the linked paper and entity table.
−
|||'''Large-scale RNAi''' (less than 100 experiments reported) [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=lsrnai (flagged-done)]||lsrnai||Please indicate if your paper reports gene knockdown phenotypes for more than 100 individual RNAi experiments.||raymond@its.caltech.edu
+
 
−
|-
+
Automatic (8) the paper is run through the linking script. 
−
|||'''Overexpression phenotype''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=overexpression (flagged)]||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
+
* The script links all the objects in wormbase and the ones provided by the author first pass form
−
|-
+
* The linked file is deposited here http://textpresso-dev.caltech.edu/gsa/worm/html/
−
|||'''Chemicals''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=chemicals (flagged)]||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.|||
+
* An initial entity link table is created and deposited in http://textpresso-dev.caltech.edu/gsa/worm/first_pass_entity_link_tables/
−
|-
+
* QC curator receives a link to the linked XML in a QCFast interface and a link to the entity table.
−
|||'''Mosaic analysis''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=mosaic (flagged-done)]||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
+
 
−
|-
+
Juancarlos (~9) gets XML from Arun, populates bibliography information for WormBase.''?''
−
|||'''Tissue or cell site of action''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=site (flagged-done)]||siteaction ||Please indicate if your paper reports anatomy-specific function for a gene.||raymond@its.caltech.edu
+
 
−
|-
+
Script (10) sends markup back to DJS, this action is prompted by a submit button on QCFast.  
−
|||'''Time of action'''||timeaction||Please indicate if your paper reports a temporal requirement for gene function.||raymond@its.caltech.edu
+
* A final entity table is created http://textpresso-dev.caltech.edu/gsa/worm/entity_link_tables/
−
|-
+
* An e-mail is sent to the curator that the file has been deposited and includes a link to the final entity table.
−
|||'''Molecular function of a gene product'''[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=genefunction (flagged-done)]||genefunc||Please indicate if your paper discusses a new function for a known or newly defined gene.||emsch@its.caltech.edu
+
 
−
|-
+
--[[User:Kyook|kjy]] 19:44, 19 April 2012 (UTC)
−
|||'''Homolog of a human disease-associated gene.''' CHANGE TO '''Relevance to a human disease.'''[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=humandiseases (flagged)]||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
+
 
−
|-
+
==Instructions for Genetics==
−
|INTERACTIONS:
+
The following are instructions to the journal and to the authors.
−
|-
+
 
−
|||'''Genetic interactions''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=geneinteractions (flagged-done)]||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
+
===Note to authors:===
−
|-
+
The following message is sent to authors by GENETICS upon acceptance of their paper and after the DOI has been assigned and WBPaperID retrieved.
−
|||'''Functional complementation''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=functionalcomplementation (flagged)]||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.||
+
 
−
|-
+
"GENETICS is working with textpresso (www.textpresso.org) and WormBase (www.wormbase.org) to create links between genetic and genomic objects that are in your paper to the appropriate page in WormBase. These links will be included in both the online full text and PDF formats of your paper.
−
|||'''Gene product interactions''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=geneproduct (flagged-done)]||geneprod||Please indicate if your paper reports data on protein-protein, RNA-protein, DNA-protein or Y2H interactions, etc.|| emsch@its.caltech.edu
+
 
−
|-
+
If you want any genes, alleles, transgenes, CGC-destined strains, anatomy terms, etc.,  discovered or described in your paper to be linked to WormBase please enter the names of these objects using the form at the following link:
−
|'''REGULATION OF GENE EXPRESSION''':
+
http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00040237&passwd=1317224998.8903801
−
|-
+
 
−
|||'''New expression pattern for a gene''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=expression (flagged-done)]||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
+
Follow the examples carefully as your submitted data will be processed automatically. If you would rather upload a file, please contact kyook@caltech.edu.
−
|-
+
 
−
|||'''Alterations in gene expression by genetic or other treatment''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=generegulation (flagged-done)]|| 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
+
Thank you for your help."
−
|-
+
 
−
|||'''Regulatory sequence features'''  [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=sequencefeatures (flagged)]
+
[http://www.wormbase.org/wiki/index.php/Instructions_for_Genetics previous notes to authors]<br>
−
||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
+
--[[User:Kyook|kjy]] 19:40, 2 December 2011 (UTC)
−
|-
+
 
−
|||'''Position frequency matrix (PFM)''' or '''Position weight matrix (PWM)'''||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
+
===Note to GENETICS:===
−
|-
+
 
−
|||'''Microarray'''[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=microarray (flagged-done)]||microarray ||Please indicate if your paper reports any microarray data.||wchen@its.caltech.edu
+
This form (link sent) represents a user-friendly interface to a postgres database table stored at WormBase Caltech.
−
|-
+
 
−
|PROTEIN FUNCTION AND STRUCTURE:
+
Once the authors hit 'flag' (the button at the bottom of the page) their data will:
−
|-
+
 
−
|||'''Protein analysis ''in vitro'''''[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=invitro (flagged)]||invitro ||Please indicate if your paper reports any ''in vitro'' protein analysis such as kinase assays, agonist pharmacological studies, ''in vitro'' reconstitution studies, etc.||
+
* be added to Arun's object markup list, so new objects can be marked up in the paper along with known WB objects. NOTE: these objects will need to be entered correctly and cleanly as everything that appears on his markup list will be linked.  
−
|-
+
* populate the postgres table and the corresponding first pass paper curation form used by fp curators
−
|||'''Domain analysis'''||domanal (populated with information previously in "structureinformation")||Please indicate if your paper reports on a function of a particular domain within a protein.||
+
* be marked in our first pass curation list as having author data, therefore marked for priority curation
−
|-
+
 
−
|||'''Covalent modification''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=covalent (flagged)]||covalent|| Please indicate if your paper reports on post-translational modifications as assayed by mutagenesis or ''in vitro'' analysis||
+
The WB QC curator will receive an e-mail alerting them to the submitted data, at which point it will be checked over to make sure it is in the proper format for Arun's scripts and corrected if needed.
−
|-
+
 
−
|||'''Structural information'''[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=structureinformation (flagged)]||structinfo||Please indicate if your paper reports NMR or X-ray crystallographic information.||
+
We won't be able to take uploaded tables for the data types; the parsing of this data will be problematic for Texptresso as we anticipate people uploading the data in many different formats. Nonetheless, if they do want to upload a file, for data that doesn't exist in their supplemental materials, they are welcome to contact one of us (kyook@caltech.edu, for now) to do that.
−
|-
+
 
−
|||'''Mass spectrometry''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=massspec (flagged-done)]||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 
+
--[[User:Kyook|kjy]] 19:53, 2 December 2011 (UTC)
−
|-
+
 
−
|'''REAGENTS''':||
+
==Journal first-pass form (jfp) : GENETICS papers only==
−
|-
+
This is not a postgres table but is a form that collects extra data from Genetics authors, which is then stored in our author first pass table (afp).
−
|||'''''C. elegans'' antibodies''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=antibody (flagged-done)]|| 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
+
−
|-
+
The form URL is generated by Genetics through the doi ticket form.  
−
|||'''Integrated transgenes''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=transgene (flagged-done)] ||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
+
 
−
|-
+
The purpose of the genetics first pass form is to collect data objects that do not exist in WB already so that Arun can mark-up the Genetics paper and provide links for these objects.<br>
−
|||'''Transgenes used as tissue markers'''||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
+
 
−
|-
+
New entities (postgres table) are collected for the following data types:
−
|GENOME SEQUENCE DATA:
+
*gene (genesymbol)
−
|-
+
*variations (extvariation)
−
|||'''Gene structure correction''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=structurecorrectionsanger (flagged)]|| 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
+
*CGC-sent strains (newstrains)
−
|-
+
*integrated transgene (transgene)
−
|||'''Sequencing mutant alleles''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=sequencechange (flagged)]||seqchange ||Please indicate if your paper reports new sequence data for any mutation.||genenames@wormbase.org
+
*balancers
−
|-
+
*cell/anatomy(newcell)
−
|||'''New SNPs''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=newsnp (flagged)]||newsnp||Please indicate if your paper reports a SNP that does not already exist in WormBase.||dblasiar@watson.wustl.edu, tbieri@watson.wustl.edu
+
*phenotype
−
|-
+
 
−
|CELL DATA:
+
All of these fields, except genesymbol, do not show on the normal afp_form.  We opted to make a hybrid of the afp_form for the Genetics authors so that they would not be requested to fill out another WB generated form for us after their paper was published and because we needed this extra information from them asap.
−
|-
+
 
−
|||'''Ablation data''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=ablationdata (flagged-done)]||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
+
It is also my understanding that these authors would be required to fill out the form as part of the publication process, so this was an opportunity to have 100% author feedback for paper flagging.
−
|-
+
 
−
|||'''Cell function''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=cellfunction (flagged-done)]||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
+
Data curators are automatically alerted to the new data when the form is submitted.
−
|-
+
 
−
|IN SILICO DATA:
+
==[http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 Sample GENETICS Firstpass form]==
−
|-
+
 
−
||||'''Phylogenetic data'''||phylogenetic||Please indicate if your paper reports any phylogenetic analysis.||
+
==[[jfp postgres table details]]==
−
|-
+
 
−
||||'''Other bioinformatics analysis'''||othersilico||Please indicate if your paper reports any bioinformatic data not indicated anywhere else on this form.||
+
==[[Data types used on first-pass forms]]==
−
|-
+
 
−
|OTHER:
+
 
−
|-
+
 
−
|||'''Supplemental materials''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=supplemental (flagged-done)]||supplemental||Please indicate if your paper has supplemental material.||qwang@its.caltech.edu
+
 
−
|-
+
[[Category:Curation]]
−
|||'''NONE of the aforementioned data types are in this research article'''  [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=comment (flagged)]||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.||
+
[[Category:GSA_markup]]
−
|-
 
−
|||'''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.''' ||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
 
−
|-
 
−
|}
 

Latest revision as of 20:36, 23 July 2013

[back]

Mark up policy

Mark Up Work Flow

Media:slide1.jpg

this file diagrams the most recent and most detailed workflow we established, which includes editorial roles at Dartmouth. The steps below is a brief overview of the process.

These following steps outline the work flow for Textpresso markup starting with the acceptance of the paper by GENETICS and through to the incorporation of the paper into WB.

The responsible party is noted before each step.

Genetics (1) The paper gets accepted.

Genetics (2) A DOI is assigned to the paper

Genetics (3) A WBPaperID and URL are acquired through the ticketing form at: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_paper_ticket.cgi

Genetics (4) The WBPaperID from the ticket issuer is attached to the XML

Genetics (5) the author is sent the generated URL to access the author form

Author (6) Authors provide the final source files and fills out the author first pass form within 48 hours of acceptance to GENETICS.

  • Author data populates journal first-pass tables in postgres, new objects are automatically added to the appropriate lexicon.
  • New object data from the journal first-pass form is sent to Karen, who makes sure the information is entered correctly
  • New data goes to the appropriate data curator for acedb object creation.
  • All other data populates author first-pass tables and paper is placed in the pipeline for first-pass curation (Juancarlos will make a filter so these papers will be prioritized for first-pass).

DJS (Dartmouth Journal Services) (~5-8) sends the final source file (in XML format) to Arun - deposits XML on a web service? http://textpresso-dev.caltech.edu/gsa/worm/incoming_xml/

  • An e-mail is sent to the QC curator that a paper is coming and to expect a follow up e-mail with a link to the linked paper and entity table.

Automatic (8) the paper is run through the linking script.

Juancarlos (~9) gets XML from Arun, populates bibliography information for WormBase.?

Script (10) sends markup back to DJS, this action is prompted by a submit button on QCFast.

--kjy 19:44, 19 April 2012 (UTC)

Instructions for Genetics

The following are instructions to the journal and to the authors.

Note to authors:

The following message is sent to authors by GENETICS upon acceptance of their paper and after the DOI has been assigned and WBPaperID retrieved.

"GENETICS is working with textpresso (www.textpresso.org) and WormBase (www.wormbase.org) to create links between genetic and genomic objects that are in your paper to the appropriate page in WormBase. These links will be included in both the online full text and PDF formats of your paper.

If you want any genes, alleles, transgenes, CGC-destined strains, anatomy terms, etc., discovered or described in your paper to be linked to WormBase please enter the names of these objects using the form at the following link: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00040237&passwd=1317224998.8903801

Follow the examples carefully as your submitted data will be processed automatically. If you would rather upload a file, please contact kyook@caltech.edu.

Thank you for your help."

previous notes to authors
--kjy 19:40, 2 December 2011 (UTC)

Note to GENETICS:

This form (link sent) represents a user-friendly interface to a postgres database table stored at WormBase Caltech.

Once the authors hit 'flag' (the button at the bottom of the page) their data will:

  • be added to Arun's object markup list, so new objects can be marked up in the paper along with known WB objects. NOTE: these objects will need to be entered correctly and cleanly as everything that appears on his markup list will be linked.
  • populate the postgres table and the corresponding first pass paper curation form used by fp curators
  • be marked in our first pass curation list as having author data, therefore marked for priority curation

The WB QC curator will receive an e-mail alerting them to the submitted data, at which point it will be checked over to make sure it is in the proper format for Arun's scripts and corrected if needed.

We won't be able to take uploaded tables for the data types; the parsing of this data will be problematic for Texptresso as we anticipate people uploading the data in many different formats. Nonetheless, if they do want to upload a file, for data that doesn't exist in their supplemental materials, they are welcome to contact one of us (kyook@caltech.edu, for now) to do that.

--kjy 19:53, 2 December 2011 (UTC)

Journal first-pass form (jfp) : GENETICS papers only

This is not a postgres table but is a form that collects extra data from Genetics authors, which is then stored in our author first pass table (afp).

The form URL is generated by Genetics through the doi ticket form.

The purpose of the genetics first pass form is to collect data objects that do not exist in WB already so that Arun can mark-up the Genetics paper and provide links for these objects.

New entities (postgres table) are collected for the following data types:

  • gene (genesymbol)
  • variations (extvariation)
  • CGC-sent strains (newstrains)
  • integrated transgene (transgene)
  • balancers
  • cell/anatomy(newcell)
  • phenotype

All of these fields, except genesymbol, do not show on the normal afp_form. We opted to make a hybrid of the afp_form for the Genetics authors so that they would not be requested to fill out another WB generated form for us after their paper was published and because we needed this extra information from them asap.

It is also my understanding that these authors would be required to fill out the form as part of the publication process, so this was an opportunity to have 100% author feedback for paper flagging.

Data curators are automatically alerted to the new data when the form is submitted.

Sample GENETICS Firstpass form

jfp postgres table details

Data types used on first-pass forms

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