Difference between revisions of "Caltech documentation"

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[[User Guide 2010:TOC | Table of Contents]]
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==First-pass flagging==
 
==First-pass flagging==
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== Datatype ==
 
== Datatype ==
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<div style="column-count:3;-moz-column-count:3;-webkit-column-count:3">
 
*[[Antibody]]
 
*[[Antibody]]
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*[[Automated gene descriptions 2.0]]
 
*[[Concise Descriptions]]
 
*[[Concise Descriptions]]
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*[[Construct]]
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*[[Evidence Code Ontology]]
 
*[[Expression Pattern]]
 
*[[Expression Pattern]]
 
*[[Gene Class Descriptions]]
 
*[[Gene Class Descriptions]]
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*[[Gene-Paper Associations]]
 
*[[Gene-Paper Associations]]
 
*[[Gene Regulation]]
 
*[[Gene Regulation]]
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*[[Generation of automated descriptions]]
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*[[Genotype]]
 
*[[Life_Stage]]
 
*[[Life_Stage]]
 
*[[Molecule]]
 
*[[Molecule]]
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*[[Physical Interactions]]
 
*[[Physical Interactions]]
 
*[[Pictures]]
 
*[[Pictures]]
*[[Process pages]]
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*[[Relations Ontology]]
 
*[[RNAi]]
 
*[[RNAi]]
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*[[Sequence Feature]]
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*[[Strain]]
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*[[Topic_pages]]
 
*[[Transgenes]]
 
*[[Transgenes]]
 
*[[Disease and Drugs]]
 
*[[Disease and Drugs]]
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*[[Drugs]]
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*[[VariationConciseDescriptions | Variation Concise Descriptions]]
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</div>
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 +
==Paper Categorization==
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*[[WormBase Paper Categorization]]
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 +
==Paper ID Conversion CGI==
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*[[Paper_ID_conversion_CGI]]
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 +
==Working Group==
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*[[Phenotype Ontology Development]]
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*[[Community Curation]]
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*[[LEGO Curation]]
  
 
==Curation Progress==
 
==Curation Progress==
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==postgres==
 
==postgres==
 
*[[WBGene information and status pipeline]]
 
*[[WBGene information and status pipeline]]
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*[[Source and maintenance of non-WBGene info]]
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*[[OA forms, tables, scripts, etc]]
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*[[Postgres queries]]
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*[[Updating Postgres with New WS Information]]
  
 
== Caltech weekly meetings ==
 
== Caltech weekly meetings ==
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==Ontology Annotator==
 
==Ontology Annotator==
*[[Ontology Annotator]]
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*[[Ontology Annotator | Overview]]
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**[[Ontology_Annotator#Batch_upload_to_OA_from_tab-delimited_file | Batch upload data to OA]]
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**[[Ontology_Annotator#Problems | Problems]]
  
 
==Textpresso==
 
==Textpresso==
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* [http://wiki.wormbase.org/index.php/Genetics_Markup_by_Textpresso_and_First_Pass GSA Markup Workflow]
 
* [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]]
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* [[GSA linking pipeline | Pipeline image]]
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* [[Linking_script_pipeline | Linking scripts]]
 
* [[Entity classes and problems]]  
 
* [[Entity classes and problems]]  
** [[Papers that have been markedup]]
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** [[Example marked up papers]]
 
** [[Markup excerpts]]
 
** [[Markup excerpts]]
 
*[[Future Entities for markup]]
 
*[[Future Entities for markup]]
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[[INDI]]
 
[[INDI]]
  
==Release note requests for Wormbase@EBI team==
 
 
====For Phenotype====
 
Contact persons: Karen Yook
 
 
*In particular how many genes have been annotated with a phenotype
 
**through RNAi observed phenotype (ignore phenotype not observed for this class)
 
**through variation phenotype (include observed and not observed)
 
**through overexpression (transgene-phenotype)
 
 
The problem with this query is that I need to know this information broken down for genes with alleles, and need to filter out snps from the variation class and filter out all MM, WGS mutations as well.  It would be good to have a list of all putative coding changing snps, but I do not want to mix up granular gene function characterization efforts  with large scale sequencing projects that do not focus on gene-phenotype analysis. 
 
 
*I would like to also get this list of genes with alleles and no phenotype.
 
 
====For Disease====
 
 
Contact Persons: Paul Davis, Ranjana Kishore
 
  
*number of genes with 'Disease info' tag
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==Requested details for the Citace upload report==
*number of genes with 'Potential model' tag
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[[Citace_upload_report]]
*number of genes with 'Experimental model' tag
 
*number of Disease Ontology terms (DO) terms in database
 
*number of DO terms linked to genes (add DO terms used in Potential_model and Experimental_model tags)
 
  
[[Category:Curation]]
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==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