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]]==
=A note to authors=
 
===''Congratulations on your paper being accepted by GENETICS for publication!''===
 
  
Now that your paper has been accepted, you have an opportunity to see your data incorporated into WormBase on a much faster time scale than data published in other journals. GENETICS has agreed to help you get your data into our database faster, by requesting that you fill out the following form before your paper hits the press, rather than us waiting for your paper to appear in Pubmed, which can take weeks to months.  In addition, by giving us just a bit more detailed information than we would ask of authors of papers from other journals, we can help your paper become a more comprehensive resource portal to worm biology.  <br>
+
==[[Mark Up Work Flow]]==
<br>
+
[[Media:slide1.jpg]]
To fill out the form,  either '''indicate by a check of the box''' if a specific data type exists in the body of your paper '''or list specific details''' that you use as part of your experiments.  In the latter case, when we ask for specific details, these will be objects that you have created or used during the course of your research, such as alleles, RNAi probes, antibodies, integrated transgenes, etc., which do not exist in WormBase already. Please enter the objects into the space provided. If you would rather upload a file, please contact kyook@caltech.edu. <br>
 
<br>
 
Thank you for your cooperation. We expect you to benefit greatly from participating in our data extraction and markup partnership with GENETICS, Textpresso and WormBase. <br>
 
<br>
 
  
 +
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>
  
Best Wishes,  
+
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> 
 +
 
 +
''The responsible party is noted before each step.'' <br>
 +
 
 +
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. 
 +
* 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/
 +
* 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.
 +
 
 +
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.
 +
* 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.
 +
 
 +
--[[User:Kyook|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."
 +
 
 +
[http://www.wormbase.org/wiki/index.php/Instructions_for_Genetics previous notes to authors]<br>
 +
--[[User:Kyook|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.
 +
 
 +
--[[User:Kyook|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).
 
   
 
   
WormBase <br>
+
The form URL is generated by Genetics through the doi ticket form.
http://wwww.wormbase.org<br>
+
 
wormbase-help@wormbase.org
+
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>
 +
 
 +
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.  
  
===Please click the box next to the type of data found in the body of your publication.===
+
Data curators are automatically alerted to the new data when the form is submitted.
If this is not a primary research article, please click here. You may ignore the fields below. Thank you.
 
Click the "?" to find out more about the data type.<br>
 
  
 +
==[http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 Sample GENETICS Firstpass form]==
  
----
+
==[[jfp postgres table details]]==
  
=Genetics First Pass form=
+
==[[Data types used on first-pass forms]]==
''"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"
 
| align="center" style="background:#f0f0f0;"|'''Actions'''
 
| 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;"|'''Instructions 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.||
 
|-
 
  
  
|||GENE IDENTIFICATION AND MAPPING:
 
|-
 
  
|||||->Enter genes studied in this paper||genestudied||->Please list any gene that is a focus of analysis in your paper.
+
[[Category:Curation]]
||
+
[[Category:GSA_markup]]
|-
 
|Needs to be fed to textpresso.||||Genes studied in this paper ->Enter genes cloned in the paper [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=genesymbol (flagged-done)]||genesymbol ||->Please list any gene in your paper that doesn't exist in WormBase already.||genenames@wormbase.org, vanauken@its.caltech.edu
 
|-
 
|Needs to be fed to textpresso, need to add curator contacts||||Newly cloned gene ->Enter new alleles||extvariation||->Please list any allele in your paper that doesn't exist in WormBase already.||
 
|-
 
|Needs to be fed to textpresso.||||Newly created alleles ->Enter new strains||NEW FIELD||->Please list any strain in your paper that doesn't exist in WormBase already.||
 
|-
 
|||||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
 
|-
 
|Needs to be fed to textpresso.||||New Balancers ->Enter new balancers||NEW FIELD||-> Please list any balancer in your paper that doesn't exist in WormBase already.|| genenames@wormbase.org
 
|-
 
|||GENE FUNCTION:
 
|-
 
|||->Mutant, overexpression, or chemical-based phenotypes||>keep sub data fields unhidden<
 
|-
 
|||||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 nonRNAi-based phenotype for a mutant. ||emsch@its.caltech.edu, garys@its.caltech.edu, jolenef@its.caltech.edu
 
|-
 
|||||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
 
|-
 
|||||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. The use of mutagens for the generation of mutants in genetic screens do not need to be indicated.|||
 
|-
 
|||New subheader section ->RNAi experimental details||>keep sub data fields unhidden<||||->If your paper reports RNAi experiments and the details for the probes used are not listed in supplemental materials, please enter the sequences or source of sequences used for these experiments so we can map these experiments in relation to the genome. You can enter this information in the form of standard primer pair names (e.g., sjj_ZK617.1, cenix:155-g4,  mv_CAA3346 or the library used), genomic coordinates of the primers (e.g. IV:11970667..12012891, ZK1067:13703..22295, MtDNA:4504..5613), or cDNA/EST/OST clone names (e.g. AF071375, yk275g9, OSTR215B4_1). Otherwise, please give us the sequences of the primers or the exact sequence of the entire RNAi probe.
 
|-
 
|Need more specific data here.||||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 tell us the sequences or source of sequences used for RNAi experiments so we can map these experiments in relation to the genome.  ||garys@its.caltech.edu
 
|-
 
|||||Large-scale RNAi (more 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
 
|-
 
|||||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
 
|-
 
|||||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
 
|-
 
|||||Time of action||timeaction||Please indicate if your paper reports a temporal requirement for gene function.||raymond@its.caltech.edu
 
|-
 
|||||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
 
|-
 
|||||Homolog of a human disease-associated gene. [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=humandiseases (flagged)]||humdis ||Please indicate if any gene reported in your paper is 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 [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 used concurrent with other RNAi-treatments or mutations.||emsch@its.caltech.edu
 
|-
 
|||||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.''||
 
|-
 
|||||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
 
|-
 
|||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)]||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
 
|-
 
|||||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
 
|-
 
|||||Regulatory sequence features  [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=sequencefeatures (flagged)]
 
||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)||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[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
 
|-
 
|||PROTEIN FUNCTION AND STRUCTURE:
 
|-
 
|Needs to be fed to textpresso.||||New Protein->Enter new protein||NEW FIELD||->Please list any protein that doesn't exist in WormBase already.||
 
|-
 
|||||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, reconstitution studies, etc.||
 
|-
 
|||||Domain analysis||domanal ||Please indicate if your paper reports on a function of a particular domain within a protein.||
 
|-
 
|||||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||
 
|-
 
|||||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.||
 
|-
 
|||||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 
 
|-
 
|||REAGENTS:||
 
|-
 
|||||''C. elegans'' antibodies ->Enter ''C. elegans'' antibodies [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=antibody (flagged-done)]|| antibody ||->Please list any new or known antibody created by your lab or another researcher's lab, that is used in this paper; do not check this box if antibodies were commercially bought.''||wchen@its.caltech.edu
 
|-
 
|Needs to be fed to Textpresso.||||Integrated transgene ->Enter integrated transgenes [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=transgene (flagged-done)] ||transgene||->Please list any integrated transgene used in this paper that doesn't exist in WormBase already, especially if the transgene does not have a canonical name.'' ||wchen@its.caltech.edu
 
|-
 
|||||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
 
|-
 
|||GENOME SEQUENCE DATA:
 
|-
 
|||||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
 
|-
 
|||||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
 
|-
 
|Needs to be fed to textpresso.||||New SNPs [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=newsnp (flagged)]||newsnp||->Please list any SNP reported in your paper that doesn't exist in WormBase already.||dblasiar@watson.wustl.edu, tbieri@watson.wustl.edu
 
|-
 
|||CELL DATA:
 
|-
 
|Needs to be fed to textpresso and Raymond||||New cell/anatomy name-> Enter new cell/anatomy term||NEW FIELD (was on the ancient curator first pass form)||->Please list any C. elegans cell or anatomy part reported in your paper that doesn't exist in WormBase already.||
 
|-
 
|||||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
 
|-
 
|||||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
 
|-
 
|||IN SILICO DATA:
 
|-
 
||||||Phylogenetic data||phylogenetic||Please indicate if your paper reports any phylogenetic analysis.||
 
|-
 
||||||Other bioinformatics analysis||othersilico||Please indicate if your paper reports any bioinformatic data not indicated anywhere else on this form.||
 
|-
 
|||OTHER:
 
|-
 
|||||Supplemental materials [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=supplemental (flagged-done)]||supplemental||Please attach supplemental material.||qwang@its.caltech.edu
 
|-
 
|||||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.||
 
|-
 
|Needs to go to Cecilia and Textpresso||||Authors->Enter authors||NEW FIELD||->Please list the e-mail address of any author on your paper that needs to be added to the WormBase database. These authors will receive a separate request from us for more information.||
 
|-
 
|||||Any feedback? ->Feedback||comment||->Please give us feedback on this form or on any topic pertinent to how we can better extract data from your paper. ||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