Difference between revisions of "GO entity markup"

From WormBaseWiki
Jump to navigationJump to search
Line 44: Line 44:
 
==Papers that have been linked==
 
==Papers that have been linked==
 
Click on the associated links to see the various pages documenting the GO linking of that paper<br>
 
Click on the associated links to see the various pages documenting the GO linking of that paper<br>
WBPaper00038399 | [http://dev.textpresso.org/gsa/worm/html//128421.html WBPaper00038399_GO_linked_html] | [http://dev.textpresso.org/gsa/worm/first_pass_entity_link_tables/128421.html WBPaper00038399_GO_entity_list] | [[WBPaper00038399_GO_linking_comments]]<br>
+
 
 +
doi10.1534/genetics.111.128421 00038399 | [http://dev.textpresso.org/gsa/worm/html//128421.html GO_linked_html] | [http://dev.textpresso.org/gsa/worm/first_pass_entity_link_tables/128421.html GO_entity_list] | [[WBPaper00038399_GO_linking_comments]]<br>
 +
doi10.1534/genetics.111.130450 00038523 | [http://dev.textpresso.org/gsa/worm/html//130450.html GO_linked_html] | [http://dev.textpresso.org/gsa/worm/first_pass_entity_link_tables/130450.html GO_entity_list] | [[WBPaper00038523_GO_linking_comments]]<br>
 +
doi10.1534/genetics.111.131227 00038528 ''expected''<br>
 +
doi10.1534/genetics.111.131714 00039858 ''expected''<br>

Revision as of 19:06, 22 July 2011

Trial runs with linking GO terms in GSA papers

This project will be carried out in parallel with the normal markup pipeline with the following criteria:

  • markup is done on a separate textpresso machine -dev.textpresso.org (production machine is textpresso-dev.caltech.edu)
  • the papers will not be sent to DJS (there is no upload form set for this pipeline)
  • only the GO lexicon from AmiGo will be used
  • papers marked up will be papers that come through the normal pipeline (no retroactive markup will occur for now)
  • GO marked up papers will be sent to the GO linking crew: Kimberly, Ranjana, Daniela, Chris, Karen, and Paul
  • as with the normal pipeline a link to an entity table of all entities, the generated URL, and a brief description of the webpage will be included in the alert e-mail (see below)
  • all comments for the papers will be made available through this wiki.
  • all links are formed for WB GO pages, not AmiGo pages

e-mail alert from Arun

Once a paper has been received and run through the GO linking script on dev.textpresso.org, an e-mail message will be sent out to everyone on the GO linking crew. This message includes a link to the paper and to the entity table.


Forwarded message
From: <arunr@wormbase.org>
Date: Wed, Jul 13, 2011 at 10:14 AM
Subject: GSA auto-email: GSA 128421 linked file available
To: arunr@wormbase.org

This is an automatic email sent to you by the GSA pipeline.

ATTENTION: This is not the production file. This is only for testing GO term linking.

Responsible curator: Daniela Raciti

Linked file available for manual QC at
http://dev.textpresso.org/gsa/worm/html//128421.html

The entity table for this first pass/automatically linked article is available at
http://dev.textpresso.org/gsa/worm/first_pass_entity_link_tables/128421.html

Thank you!


known problems

  • Some GO terms do not have pages and WB displays a page with title 'Gene Ontology Search' for these URLs. See

http://www.wormbase.org/db/ontology/gene?name=GO%3A0001047;class=GO_term

    • these problem links have been color-coded in 'grey' in the entity table. The URL is live, but the page has no relevant content.

Papers that have been linked

Click on the associated links to see the various pages documenting the GO linking of that paper

doi10.1534/genetics.111.128421 00038399 | GO_linked_html | GO_entity_list | WBPaper00038399_GO_linking_comments
doi10.1534/genetics.111.130450 00038523 | GO_linked_html | GO_entity_list | WBPaper00038523_GO_linking_comments
doi10.1534/genetics.111.131227 00038528 expected
doi10.1534/genetics.111.131714 00039858 expected