Difference between revisions of "Caltech documentation"

From WormBaseWiki
Jump to navigationJump to search
 
(140 intermediate revisions by 10 users not shown)
Line 1: Line 1:
== First pass curation ==
 
[[How to FirstPass]]
 
  
== Datatype curation ==
+
 
*[[Paper Pipeline]]
+
==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]]
 +
 
 +
== 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 Pattern]]
 +
*[[Gene Class Descriptions]]
 +
*[[Gene Interaction]]
 
*[[Gene Ontology]]
 
*[[Gene Ontology]]
 +
*[[Gene-Paper Associations]]
 
*[[Gene Regulation]]
 
*[[Gene Regulation]]
 +
*[[Generation of automated descriptions]]
 +
*[[Genotype]]
 +
*[[Life_Stage]]
 +
*[[Molecule]]
 +
*[[Movie]]
 +
*[[Paper Pipeline]]
 
*[[Phenotypes]]
 
*[[Phenotypes]]
*[[Process Pages]]
+
*[[Physical Interactions]]
 +
*[[Pictures]]
 +
*[[Relations Ontology]]
 +
*[[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]]
  
I. [[Phenote+ Phenotype Curation|Phenote+ Phenotype Curation]]
+
==Working Group==
#[[Installing Phenote|Installing Phenote]]
+
*[[Phenotype Ontology Development]]
#[[Phenote Fields|Phenote Fields for Variation-Phenotype]]  
+
*[[Community Curation]]
#[[Phenote .obo files|Phenote .obo files]]  
+
*[[LEGO Curation]]
#[[Phenote .ace citace upload|Phenote .ace citace upload]]
 
#[[Phenote quirks and bugs/fixes to request|Phenote quirks and bugs/fixes to request]]
 
#[[Postgres Query|Postgres Queries for the Variation-Phenotype Postgres table]]
 
  
II. [[Phenotype Ontology Changes by WS|Phenotype Ontology Changes by WS]]
+
==Curation Progress==
#[[WS193|WS193]]  
+
*[[Curation status|Curation status pages]]
#[[WS194|WS194]]
+
*[[New 2012 Curation Status|New 2012 Curation Status pages]]
  
III. [[Processing NBP alleles]]
+
==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 ==
 
*[[WormBase-Caltech Weekly Calls]]
 
*[[WormBase-Caltech Weekly Calls]]
  
== Software/Tool Development and Technical Issues ==
+
==Conference Calls==
 +
*[[November 25, 2009 - Sequence Curation Flags]]
 +
 
 +
== Phenote ==
 
*[[Phenote cgi wish list]]
 
*[[Phenote cgi 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]]
 +
*[[How to make a new Textpresso category]]
 +
*[[Textpresso Central]]
 +
 +
==SVMs for First Pass Curation==
 +
*[[What are SVMs?]]
 +
*[[SVM Guidelines]]
 +
*[[WormBase SVMs]]
 +
*[[dictyBase]]
 +
*[[FlyBase]]
 +
 +
==GSA markup==
 +
* [http://wiki.wormbase.org/index.php/Genetics_Markup_by_Textpresso_and_First_Pass GSA Markup Workflow]
 +
* [[GSA Markup SOP]]
 +
* [[GSA linking pipeline | Pipeline image]]
 +
* [[Linking_script_pipeline | Linking scripts]]
 +
* [[Entity classes and problems]]
 +
** [[Example marked up papers]]
 +
** [[Markup excerpts]]
 +
*[[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]]
 +
 +
 +
==Requested details for the Citace upload report==
 +
[[Citace_upload_report]]
 +
 +
==Release note requests from Caltech==
 +
[[Release note requests]]

Latest revision as of 04:47, 8 December 2020


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