Difference between revisions of "WormBase-Caltech Weekly Calls"

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= Previous Years =
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[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
  
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[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
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 +
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
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 +
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
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[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
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 +
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
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 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 +
 +
  
  
2013 Meetings
+
= 2020 Meetings =
  
 +
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
[[WormBase-Caltech_Weekly_Calls_January_2013|January]]
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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
[[WormBase-Caltech_Weekly_Calls_February_2013|February]]
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
[[WormBase-Caltech_Weekly_Calls_March_2013|March]]
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
[[WormBase-Caltech_Weekly_Calls_April_2013|April]]
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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
[[WormBase-Caltech_Weekly_Calls_May_2013|May]]
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[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
[[WormBase-Caltech_Weekly_Calls_June_2013|June]]
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[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
[[WormBase-Caltech_Weekly_Calls_July_2013|July]]
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[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
  
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[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
  
= August 1, 2013 =
+
[[WormBase-Caltech_Weekly_Calls_October_2020|October]]
  
Quarterly Progress Reports
 
*Capturing curation stats from the Curation Status form
 
*What data types do we want to capture curation stats for that we are not currently?
 
*We have frequent database dumps that can be read for stats
 
*We can capture the stats table statically on a regular basis (daily)
 
** form at http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi
 
** cronjob to get data from "Curation Statistics Page" button at
 
** /home/acedb/cron/curation_stats/get_daily_curation_stats.pl
 
** deposits files every day at 5am to :
 
** /home/acedb/cron/curation_stats/files/
 
  
RNA-Seq and Tiling Array data
+
==Nov 5th, 2020==
*Data in SPELL
 
*Wen found a lot more non modENCODE data sets
 
*May use SVM for expression cluster data
 
*Gene IDs can be found from original paper or data set
 
*Up-to-date mapping to genes is not currently done
 
  
 +
===WS279 GAF 2.0 and disease files===
 +
*Valerio and Ranjana still working with the GAF 2.0 files to generate gene descriptions
 +
*Valerio and Ranjana will probably have a meeting with Magdalena to sort out the FTP file issues for gene descriptions
 +
*Will let Raymond know if the disease GAFs are okay after they test these for gene descriptions
 +
*Raymond needs the GAFs for WoBR
  
AMIGO2 (Wormbase Ontology Browser)
+
===Experimenting with addeding new citace data to the current WS release ===
*Raymond and Juancarlos have taken AMIGO2 infrastructure to make an ontology browser for integration into WormBase
+
*Wen will take the newest expression, physical interaction, and paper class from postgres, add them to WS279 to create a "WS279.1" version of ACeDB database. Then compare WS279.1 to WS279 by comparing the SimpleMine results generated from these two versions of ACeDB. The goal is to explore the possibility of notifying users some of the new curation since the data freeze for the WS build.
*GO Term [http://mangolassi.caltech.edu/~azurebrd/cgi-bin/testing/amigo/wobr/amigo.cgi focus page demo]
 
*Graph view shows path to root (DAG view)
 
*Inferred tree view shows:
 
**Ancestor terms, no annotation numbers
 
**Main term and children, with annotation numbers (inferred, term and descendant annotations)
 
**Annotation numbers link to list of genes
 
**Will not show "direct" annotations, only inferred
 
*Sibling term displays: list parents with option to expand to see siblings of the main term
 
*Separate [http://mangolassi.caltech.edu/~azurebrd/cgi-bin/testing/amigo/wobr/treeExpand.cgi expandable/collapsible tree] of ontology ("Browse entire ontology")
 
*Widget can be coded to integrate the ontology browser
 
  
 +
===MicroPub user webinar on Nov 9th===
 +
*Ranjana and Kimberly have conflicts--Alliance call and GO call. Anyway microPub team is running the show and they have other WormBasers to help as well.
  
Paper Categorization
+
===WS280 deadlines===
*Word frequency
+
*Caltech files due for citace: Dec 15th, 2020
**We chose papers from the Author First Pass (AFP) list with 'stress'
 
**About 40 papers in list, varied topics ('stress' is a broad term)
 
**Curation essentially now complete for most data types
 
**Expanding beyond AFP?
 
*Chris will draw up preliminary tree of topics and send around
 
**We can discuss, edit, and expand as a group
 
**We want to 1) Collect positive and negative training papers and 2) Manually generate a list of key words to use for training
 
*Todd proposes for paper pages on WormBase:
 
**Show a table of flagged data types for a paper?
 
**Give users a sense of where paper is in the curation pipeline
 
  
  
 +
==Nov 12th, 2020==
 +
=== Cynthia Kenyon tool ===
 +
* developed a new tool for the worm, complete with tutorials, for analyzing gene expression data using Gene Module analysis.
 +
* tool at http://genemodules.org
 +
* add link outs from the gene expression widget or add in general WB tools?
 +
* if we want to incorporate we need to have it updated.
 +
* are they maintaining it?
 +
* there's no RNAseq, can be outdated
 +
* maybe good to add a blog post
  
= August 8, 2013 =
+
=== Graphical curation tool update===
 +
* We will show a live demo on the current state of the graphical curation tool
  
New Spica now has a closed (private) 'citace' account
+
=== Curating to human genes in ACEDB ===
*citpub account is accessible to everyone with password
+
* Karen requested option to curate constructs with human genes
*People can create their own spica accounts
+
* Would we need to change our human genes in ACEDB? For example, migrate from Ensembl IDs to HGNC IDs as primary keys?
*Personal accounts are encouraged so as to avoid saving changes to citpub database
+
* Will discuss on next site-wide call
  
 +
=== GAF (and GAF-like) file headers ===
 +
* GO GAF files (on FTP, WS279) for WormBase now in 2.2 format with header like
 +
!gaf-version: 2.2
 +
!generated-by: WormBase
 +
!date-generated: 2020-10-30
 +
! WB annotations 00015014
 +
* For files that can migrate to 2.2 format (e.g. always require column 4 qualifier) we could adopt a similar header
 +
* For other files (that cannot always have a qualifier in column 4), we could stick to 2.0 format with a header like:
 +
!gaf-version: 2.0
 +
!generated-by: WormBase
 +
!date-generated: 2020-10-30
 +
* Current need is to include information about format specification, possibly in addition to other extra header content.
 +
* New proposed headers:
 +
!project-URL: https://wormbase.org
 +
!specification-URL: https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md
 +
OR
 +
!specification-URL: https://wiki.wormbase.org/index.php/WormBase_gene_association_file
 +
!project-release: WS279
 +
* Could repurpose the Wiki page: https://wiki.wormbase.org/index.php/WormBase_gene_association_file from internal docs only to include user guide info, including how our GAF-like files deviate in format from standard GAF
  
Worm Ontology Browser
 
*Raymond has set up a server
 
*Browsing should be faster now
 
*Should be transferable to the Amazon cloud
 
*Raymond will establish a WormBase development environment
 
  
 +
== Nov 19, 2020 ==
  
Curation priorities
+
=== Webinars ===
*Paper categorization
+
* JBrowse webinar tomorrow (Friday)
*Depth vs breadth of topics (number of papers?)
+
** Ranjana will host; Wen will provide tech support; Daniela will collect user questions from chat in Google Doc; Chris will write staff answers to questions in Google Doc
**'Stress' has been a pilot topic, but is a very broad topic
+
* Background slides put together for when audience is waiting
**Will work on generating subcategories of 'Stress' on the [http://wiki.wormbase.org/index.php/WormBase_Paper_Categorization Paper Categorization Wiki] page
+
* Wen will start the meeting at 9:30am Pacific; can run a test poll
**Curators can analyze the Author First Pass list of 'Stress' papers as well as entire backlog/corpus
+
* Questions will be collected in Google Doc; answers can be written into the Google Doc in real time; we can use the Google Doc as a reference to assemble FAQs later
*Goals of 'covering' a topic?
 
**'Complete' and vetted process page, Wikipathway
 
**Promote 'featured processes' on WormBase for a given release
 
*We should collect positive and negative papers (for a given topic) for SVM training
 
  
 +
=== Alaska ===
 +
* Is Eduardo still working on it?
 +
* He replied to a user asking about Alaska
 +
* Is it still running? Maintained?
 +
* Can we tell what usage it gets?
 +
* Is it useful for the Alliance? Maybe can write it into grant?
 +
* Is it commercially viable? Maybe someone can write an SBIR grant proposal?
  
Curator's should check CGIs
+
=== Server space ===
*Submission forms and other CGIs may have been altered
+
* No new space in Chen building
 +
* Many servers will stay in a server room where they are currently
 +
* Other servers we will need to see if they can be moved to Chen
 +
* Paul may have some space for servers in his lab designated space (or his own office)
 +
* It may be possible to move some machines over to the WB space in Chen as soon as we can get a key, but may have to wait until the official move in late January

Latest revision as of 17:52, 19 November 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings



2020 Meetings

January

February

March

April

May

June

July

August

September

October


Nov 5th, 2020

WS279 GAF 2.0 and disease files

  • Valerio and Ranjana still working with the GAF 2.0 files to generate gene descriptions
  • Valerio and Ranjana will probably have a meeting with Magdalena to sort out the FTP file issues for gene descriptions
  • Will let Raymond know if the disease GAFs are okay after they test these for gene descriptions
  • Raymond needs the GAFs for WoBR

Experimenting with addeding new citace data to the current WS release

  • Wen will take the newest expression, physical interaction, and paper class from postgres, add them to WS279 to create a "WS279.1" version of ACeDB database. Then compare WS279.1 to WS279 by comparing the SimpleMine results generated from these two versions of ACeDB. The goal is to explore the possibility of notifying users some of the new curation since the data freeze for the WS build.

MicroPub user webinar on Nov 9th

  • Ranjana and Kimberly have conflicts--Alliance call and GO call. Anyway microPub team is running the show and they have other WormBasers to help as well.

WS280 deadlines

  • Caltech files due for citace: Dec 15th, 2020


Nov 12th, 2020

Cynthia Kenyon tool

  • developed a new tool for the worm, complete with tutorials, for analyzing gene expression data using Gene Module analysis.
  • tool at http://genemodules.org
  • add link outs from the gene expression widget or add in general WB tools?
  • if we want to incorporate we need to have it updated.
  • are they maintaining it?
  • there's no RNAseq, can be outdated
  • maybe good to add a blog post

Graphical curation tool update

  • We will show a live demo on the current state of the graphical curation tool

Curating to human genes in ACEDB

  • Karen requested option to curate constructs with human genes
  • Would we need to change our human genes in ACEDB? For example, migrate from Ensembl IDs to HGNC IDs as primary keys?
  • Will discuss on next site-wide call

GAF (and GAF-like) file headers

  • GO GAF files (on FTP, WS279) for WormBase now in 2.2 format with header like
!gaf-version: 2.2
!generated-by: WormBase
!date-generated: 2020-10-30
! WB annotations 00015014
  • For files that can migrate to 2.2 format (e.g. always require column 4 qualifier) we could adopt a similar header
  • For other files (that cannot always have a qualifier in column 4), we could stick to 2.0 format with a header like:
!gaf-version: 2.0
!generated-by: WormBase
!date-generated: 2020-10-30
  • Current need is to include information about format specification, possibly in addition to other extra header content.
  • New proposed headers:
!project-URL: https://wormbase.org
!specification-URL: https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md

OR

!specification-URL: https://wiki.wormbase.org/index.php/WormBase_gene_association_file
!project-release: WS279


Nov 19, 2020

Webinars

  • JBrowse webinar tomorrow (Friday)
    • Ranjana will host; Wen will provide tech support; Daniela will collect user questions from chat in Google Doc; Chris will write staff answers to questions in Google Doc
  • Background slides put together for when audience is waiting
  • Wen will start the meeting at 9:30am Pacific; can run a test poll
  • Questions will be collected in Google Doc; answers can be written into the Google Doc in real time; we can use the Google Doc as a reference to assemble FAQs later

Alaska

  • Is Eduardo still working on it?
  • He replied to a user asking about Alaska
  • Is it still running? Maintained?
  • Can we tell what usage it gets?
  • Is it useful for the Alliance? Maybe can write it into grant?
  • Is it commercially viable? Maybe someone can write an SBIR grant proposal?

Server space

  • No new space in Chen building
  • Many servers will stay in a server room where they are currently
  • Other servers we will need to see if they can be moved to Chen
  • Paul may have some space for servers in his lab designated space (or his own office)
  • It may be possible to move some machines over to the WB space in Chen as soon as we can get a key, but may have to wait until the official move in late January