Instructions for Genetics
back to Genetics Markup by Textpresso and First Pass
Contents
"Note to GENETICS":
This form represents a user-friendly interface to a postgres database table stored here 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
I will receive an e-mail alerting me to the submitted data, at which point I will check it over to make sure it is in the proper format for Arun's scripts and correct whatever needs to be corrected, (should probably have some stall here to make sure entered data is in the right format).
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. If we required that data be uploaded in a certain format, then there is no benefit for them to upload a table versus cutting and pasting the data into the box area on the form.
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. The ultimate goal is to have this pipeline automated to get away from manual flagging of the data types. If it turns out that there will always have to be a curator that receives data, which has to be manually parsed, then it is not the ideal situation, but it is doable and in the end still a step forward for literature curation.
Current "Note to authors":
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.
--kjy 19:34, 2 December 2011 (UTC)
Revised "Note to authors":
Congratulations on your paper being accepted by GENETICS for publication!
GENETICS is working with Textpresso (www.textpresso.org) and WormBase (www.wormbase.org) to create links from the online version of your paper to objects in WormBase. As you may be reporting genes, alleles, reagents, etc., that are novel and would not be found in WormBase yet, Textpresso will be unable to link these new objects unless you tell us what they are. Please use the form provided below to enter the names of these objects. This information will also be sent to WormBase where these objects will be entered into our database to be available in the next possible release of our database
Please follow the examples carefully as your data will be processed automatically. Errors in data submission may result in the need for an extended period of proofreading.
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.
Best Wishes,
WormBase http://wwww.wormbase.org wormbase-help@wormbase.org
Please click the box next to the type of data found in the body of your publication. Click the "?" to find out more about the data type.
Original "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.
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.
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.
Best Wishes,
WormBase
http://wwww.wormbase.org
wormbase-help@wormbase.org
Please click the box next to the type of data found in the body of your publication.
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.
