Difference between revisions of "Caltech documentation"

From WormBaseWiki
Jump to navigationJump to search
 
(96 intermediate revisions by 8 users not shown)
Line 1: Line 1:
==First Pass Curation==
 
*[[First-pass flagging pipelines]]
 
*[[First-pass to Curation]]
 
*[[Data types used on first-pass forms]]
 
  
== Datatype Curation ==
+
 
 +
==First-pass flagging==
 +
* [[First-pass flagging pipelines|First-pass flagging pipelines]]
 +
* Instructions for the first pass curator:
 +
**[[First-pass to Curation|Quick summary]]
 +
**[[First-pass_schedule,_instructions,_automation|Detailed instructions]]
 +
* Datatypes flagged through the first-pass forms: [[Datatypes flagged]]
 +
 
 +
==Automation and Text Mining Approaches==
 +
 
 +
*[[Curation Tasks]]
 +
 
 +
*[[Schedule for Presentations]]
 +
 
 +
*[[WormBase Literature Curation Workflow]]
 +
 
 +
== Citace ==
 
*[[citace data assignments]]
 
*[[citace data assignments]]
 +
 +
== Datatype ==
 +
<div style="column-count:3;-moz-column-count:3;-webkit-column-count:3">
 +
*[[Antibody]]
 +
*[[Automated gene descriptions 2.0]]
 
*[[Concise Descriptions]]
 
*[[Concise Descriptions]]
 +
*[[Construct]]
 +
*[[Evidence Code Ontology]]
 +
*[[Expression Cluster]]
 +
*[[Expression Pattern]]
 +
*[[Gene Class Descriptions]]
 +
*[[Gene Interaction]]
 
*[[Gene Ontology]]
 
*[[Gene Ontology]]
 
*[[Gene-Paper Associations]]
 
*[[Gene-Paper Associations]]
 
*[[Gene Regulation]]
 
*[[Gene Regulation]]
 +
*[[Generation of automated descriptions]]
 +
*[[Genotype]]
 +
*[[Life_Stage]]
 +
*[[Molecule]]
 +
*[[Movie]]
 
*[[Paper Pipeline]]
 
*[[Paper Pipeline]]
 
*[[Phenotypes]]
 
*[[Phenotypes]]
 +
*[[Physical Interactions]]
 +
*[[Pictures]]
 +
*[[Relations Ontology]]
 
*[[RNAi]]
 
*[[RNAi]]
 +
*[[Sequence Feature]]
 +
*[[Strain]]
 +
*[[Topic_pages]]
 +
*[[Transgenes]]
 +
*[[Disease and Drugs]]
 +
*[[Drugs]]
 +
*[[VariationConciseDescriptions | Variation Concise Descriptions]]
 +
</div>
 +
 +
==Paper Categorization==
 +
*[[WormBase Paper Categorization]]
 +
 +
==Paper ID Conversion CGI==
 +
*[[Paper_ID_conversion_CGI]]
 +
 +
==Working Group==
 +
*[[Phenotype Ontology Development]]
 +
*[[Community Curation]]
 +
*[[LEGO Curation]]
 +
 +
==Curation Progress==
 +
*[[Curation status|Curation status pages]]
 +
*[[New 2012 Curation Status|New 2012 Curation Status pages]]
 +
 +
==postgres==
 +
*[[WBGene information and status pipeline]]
 +
*[[Source and maintenance of non-WBGene info]]
 +
*[[OA forms, tables, scripts, etc]]
 +
*[[Postgres queries]]
 +
*[[Updating Postgres with New WS Information]]
  
 
== Caltech weekly meetings ==
 
== Caltech weekly meetings ==
Line 20: Line 81:
 
*[[November 25, 2009 - Sequence Curation Flags]]
 
*[[November 25, 2009 - Sequence Curation Flags]]
  
== Software/tool development and technical issues ==
+
== Phenote ==
 
*[[Phenote cgi wish list]]
 
*[[Phenote cgi wish list]]
*[[Ontology Annotator wish list]]
+
 
 +
==Ontology Annotator==
 +
*[[Ontology Annotator | Overview]]
 +
**[[Ontology_Annotator#Batch_upload_to_OA_from_tab-delimited_file | Batch upload data to OA]]
 +
**[[Ontology_Annotator#Problems | Problems]]
  
 
==Textpresso==
 
==Textpresso==
 
*[[Textpresso]]
 
*[[Textpresso]]
 
*[[How to make a new Textpresso category]]
 
*[[How to make a new Textpresso category]]
 +
*[[Textpresso Central]]
  
 
==SVMs for First Pass Curation==
 
==SVMs for First Pass Curation==
Line 36: Line 102:
  
 
==GSA markup==
 
==GSA markup==
 +
* [http://wiki.wormbase.org/index.php/Genetics_Markup_by_Textpresso_and_First_Pass GSA Markup Workflow]
 
* [[GSA Markup SOP]]
 
* [[GSA Markup SOP]]
* [[GSA linking pipeline]]
+
* [[GSA linking pipeline | Pipeline image]]
 +
* [[Linking_script_pipeline | Linking scripts]]
 
* [[Entity classes and problems]]  
 
* [[Entity classes and problems]]  
** [[Papers that have been markedup]]
+
** [[Example marked up papers]]
 
** [[Markup excerpts]]
 
** [[Markup excerpts]]
 
*[[Future Entities for markup]]
 
*[[Future Entities for markup]]
 +
*[[GSA Markup Meeting Notes]]
 +
*[[GO entity markup]]
 +
 +
==User Guide 2010==
 +
[[User Guide 2010:TOC |Table of Contents]]
 +
 +
==Interesting, Not-yet-modelled Data Index==
 +
[[INDI]]
 +
  
==Process Pages==
+
==Requested details for the Citace upload report==
*[[Overview of process pages]]
+
[[Citace_upload_report]]
**[[Example process pages]]
 
*[[WBProcess Model build]]
 
  
==Molecule Pages==
+
==Release note requests from Caltech==
*[[Overview of molecule pages]]
+
[[Release note requests]]
**[[Molecule papers]]
 
**[[Example molecule pages]]
 
*[[Molecule model build]]
 

Latest revision as of 17:36, 25 April 2023


First-pass flagging

Automation and Text Mining Approaches

Citace

Datatype

Paper Categorization

Paper ID Conversion CGI

Working Group

Curation Progress

postgres

Caltech weekly meetings

Conference Calls

Phenote

Ontology Annotator

Textpresso

SVMs for First Pass Curation

GSA markup

User Guide 2010

Table of Contents

Interesting, Not-yet-modelled Data Index

INDI


Requested details for the Citace upload report

Citace_upload_report

Release note requests from Caltech

Release note requests