Difference between revisions of "Caltech documentation"
From WormBaseWiki
Jump to navigationJump to search| (71 intermediate revisions by 7 users not shown) | |||
| Line 1: | Line 1: | ||
| − | |||
| − | == | + | |
| − | * | + | ==First-pass flagging== |
| + | * [[First-pass flagging pipelines|First-pass flagging pipelines]] | ||
* Instructions for the first pass curator: | * Instructions for the first pass curator: | ||
**[[First-pass to Curation|Quick summary]] | **[[First-pass to Curation|Quick summary]] | ||
| Line 14: | Line 14: | ||
*[[Schedule for Presentations]] | *[[Schedule for Presentations]] | ||
| − | == Datatype | + | *[[WormBase Literature Curation Workflow]] |
| + | |||
| + | == Citace == | ||
| + | *[[citace data assignments]] | ||
| + | |||
| + | == Datatype == | ||
| + | <div style="column-count:3;-moz-column-count:3;-webkit-column-count:3"> | ||
*[[Antibody]] | *[[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]] | *[[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== | ==postgres== | ||
*[[WBGene information and status pipeline]] | *[[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 41: | Line 81: | ||
*[[November 25, 2009 - Sequence Curation Flags]] | *[[November 25, 2009 - Sequence Curation Flags]] | ||
| − | == | + | == Phenote == |
*[[Phenote cgi wish list]] | *[[Phenote cgi wish list]] | ||
| − | *[[Ontology Annotator | + | |
| + | ==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 57: | 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]] | ||
| − | ** [[ | + | ** [[Example marked up papers]] |
** [[Markup excerpts]] | ** [[Markup excerpts]] | ||
*[[Future Entities for markup]] | *[[Future Entities for markup]] | ||
*[[GSA Markup Meeting Notes]] | *[[GSA Markup Meeting Notes]] | ||
| + | *[[GO entity markup]] | ||
==User Guide 2010== | ==User Guide 2010== | ||
[[User Guide 2010:TOC |Table of Contents]] | [[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 17:36, 25 April 2023
Contents
- 1 First-pass flagging
- 2 Automation and Text Mining Approaches
- 3 Citace
- 4 Datatype
- 5 Paper Categorization
- 6 Paper ID Conversion CGI
- 7 Working Group
- 8 Curation Progress
- 9 postgres
- 10 Caltech weekly meetings
- 11 Conference Calls
- 12 Phenote
- 13 Ontology Annotator
- 14 Textpresso
- 15 SVMs for First Pass Curation
- 16 GSA markup
- 17 User Guide 2010
- 18 Interesting, Not-yet-modelled Data Index
- 19 Requested details for the Citace upload report
- 20 Release note requests from Caltech
First-pass flagging
- First-pass flagging pipelines
- Instructions for the first pass curator:
- Datatypes flagged through the first-pass forms: Datatypes flagged
Automation and Text Mining Approaches
Citace
Datatype
- Antibody
- Automated gene descriptions 2.0
- Concise Descriptions
- Construct
- Evidence Code Ontology
- Expression Cluster
- Expression Pattern
- Gene Class Descriptions
- Gene Interaction
- Gene Ontology
- Gene-Paper Associations
- Gene Regulation
- Generation of automated descriptions
- Genotype
- Life_Stage
- Molecule
- Movie
- Paper Pipeline
- Phenotypes
- Physical Interactions
- Pictures
- Relations Ontology
- RNAi
- Sequence Feature
- Strain
- Topic_pages
- Transgenes
- Disease and Drugs
- Drugs
- Variation Concise Descriptions
Paper Categorization
Paper ID Conversion CGI
Working Group
Curation Progress
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
Conference Calls
Phenote
Ontology Annotator
Textpresso
SVMs for First Pass Curation
GSA markup
- GSA Markup Workflow
- GSA Markup SOP
- Pipeline image
- Linking scripts
- Entity classes and problems
- Future Entities for markup
- GSA Markup Meeting Notes
- GO entity markup
User Guide 2010
Interesting, Not-yet-modelled Data Index
