Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
  
= 2014 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
== January 9, 2014 ==
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
=== AGENDA ===
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
* Apologies from Mary Ann - in Strasboug. Might try and Skype in. - Mary Ann joined in at the end of the call.
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
* Curation of protein complexes - will wait until Chris can join in.
 
* Set up a time next week to go over what more needs to be done for the construct/variation/transgene class - Main people being Mary Ann, Daniela, Chris, and Karen, others are welcome. Visit the construct model requests [http://wiki.wormbase.org/index.php/WormBase_Model:Construct here]
 
* Raymond gave an update on WObr. Juancarlos has learned enough Catalyst to create a workable ontology browser on the caltech wormbase sandbox.
 
**The browser can accommodate all ontologies used by Caltech curators (all GO, Phenotype, Anatomy, Life Stage, Disease)
 
**A browser will be on each respective ontology page;
 
***direct and indirect gene connections will be displayed in a list format
 
***there was a request that the gene connections to ontology terms display the indirect annotations with direct annotations in parenths
 
**various ontology browsers can be in their own widgets where desired.
 
**still need to set up the search function from the main wb search
 
*  Caltech Models due Thursday 16 January 2014
 
* Caltech WS242 data due into Citace by Tuesday Jan 28.
 
*  Biocuration 2014
 
**http://biocuration2014.events.oicr.on.ca/biocuration
 
**M. Tuli, X. Wang interested in attending.
 
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
== January 16, 2014 ==
 
  
=== AGENDA ===
 
* WOBr discussion
 
* Author-person issues
 
* Timeline for construct model
 
* Topic Curation
 
  
  
=== Author/Person issues ===
+
= 2020 Meetings =
*User was looking for papers for a specific person
 
*Person was an author, but did not have a WBPerson object
 
*Cecilia will contact user
 
*Make author names searchable? ~32,000 authors without a person object
 
*How many authors (without a WBPerson) have multiple (5+?) papers?
 
*Proposal 1: make WBPersons for authors with 5 or more articles, and/or sort results of a search by number of publications
 
*Proposal 2: Search for WBPerson (no autocomplete function); if no WBPerson, look up authors (prioritized search)
 
  
 +
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
=== Timeline for ?Construct model ===
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
*For WS243?
 
*Mapping primers used for expression constructs or reporters
 
*Integration of sequence features
 
*Examples of the new Crispr/CAS (genome editing) alleles (curated with flanking sequences)
 
*AddGene plasmids etc.
 
*Karen will move ahead with the ?Construct model just for the context of genome-editing alleles
 
*Other contexts can be added later
 
  
 +
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
=== Topic Curation ===
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
*Is there a way to update curators if a new paper is added to the current focus topic?
 
*No, but curators can just send around an e-mail and/or query through the topic OA and curation status form
 
  
 +
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
=== WormBase Ontology Browser (WOBr) ===
+
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
*Juancarlos can now modify WormBase widgets, but would need to learn how ACEDB is handled, if required
 
*We want to workout a pipeline for widget/website modifications, proposals etc.
 
*WOBr is not working off of ACEDB
 
*Note: WOBr is going to be a widget on the Ontology Term page (all other ACEDB-based info will be present on page)
 
*General structure:
 
**Testing site: http://juancarlos.wormbase.org/tools/ontology_browser
 
**Two entry points: 1. Homepage "Tools" menu (tree-like view from root terms), 2. Specific ontology term page (WOBr widget)
 
**Data present: ontology term objects, associated genes
 
*Association files needed: Disease, Life stage
 
*Curators are now testing and commenting on WOBr
 
*Difficult to implement: display of evidence codes, sorting by species
 
**Will consider for second generation WOBr
 
*Do we want species-specific WOBr? C. elegans WOBr? Yes, probably; not clear how to implement
 
**WormBase ontologies are currently species-agnostic
 
**Maybe we should have species-specific ontology terms/pages
 
*When displaying the number of associated gene products, we could/should? distinguish the number of gene products from C. elegans versus other species (or ALL species)
 
*Direct vs. indirect/inferred annotations, how to display at different points? Ignore numbers for ancestor terms? Speed is an issue
 
*The new Solr update may allow for precalculated/precached number calculations, which should improve speed
 
  
 +
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
== January 23, 2014 ==
+
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
  
=== AGENDA ===
+
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
  
*  Biocuration 2014
+
[[WormBase-Caltech_Weekly_Calls_October_2020|October]]
** Mary Ann's flights are booked.
 
** Shall we ask for a WormBase booth/helpdesk table?
 
  
=== Biocuration Meeting April 2014, OICR, Toronto, CA ===
 
  
* http://biocuration2014.events.oicr.on.ca/biocuration
+
==Nov 5th, 2020==
* Mary Ann going
 
* Xiaodong may go, present info presented at IWM
 
* Wen considering, may want to see what's up for RNAseq etc.
 
* February 10, 2014 is abstract deadline, March registration deadline
 
* More WormBase curators?
 
* Registration discount for "International Society for Biocuration" members
 
  
=== Topic Curation ===
+
===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
  
* Considerations for WS243
+
===Experimenting with addeding new citace data to the current WS release ===
* Innate immunity, response to pathogens?
+
*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.
* Good to work on something for which a WormBook chapter exists
 
* Jonathan Ewbank, "Signaling in the immune response" 2006 WormBook chapter
 
* Creg Darby, "Interactions with microbial pathogens" 2005 WormBook chapter
 
* Action items: Look over two WormBook chapters, collect relevant genes and send to EBI/Hinxton, collect relevant papers
 
* What are the distinct challenges for EBI/Hinxton? Is it the number of genes? Number of protein coding genes? Are we sticking to "Core" species only? Which ones?
 
  
=== Upload ===
+
===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.
  
* Tuesday morning 10am, 1-28-2014 deadline
+
===WS280 deadlines===
* Models available tomorrow (Friday 1-24-2014)
+
*Caltech files due for citace: Dec 15th, 2020
  
  
== January 30, 2014 ==
+
==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
  
=== AGENDA ===
+
=== Graphical curation tool update===
* lin-15
+
* We will show a live demo on the current state of the graphical curation tool
* Models deadline
 
* Curating pseudogenes
 
* Part-time help
 
  
=== lin-15 - Creating a page for it ===
+
=== Curating to human genes in ACEDB ===
<pre>
+
* Karen requested option to curate constructs with human genes
Karen:
+
* Would we need to change our human genes in ACEDB? For example, migrate from Ensembl IDs to HGNC IDs as primary keys?
*Should it be considered a gene or can we fix up it up better as an operon?
+
* Will discuss on next site-wide call
It has been assigned to operon CEOPX140, but searching for
 
lin-15 in the operon class does not work, is there an other_name tag in the operon
 
class to store 'lin-15'.
 
*'lin-15' is frequently published object. Although many people in the field know
 
that it is a complex locus comprised of two separate genes, lin-15A and lin-15B,
 
many people do not.
 
*There are many lin-15AB alleles, e.g., n765. Where in WB can we see that one
 
allele affects more than one gene, is this something a lin-15 operon page can
 
display?
 
  
</pre>
+
=== GAF (and GAF-like) file headers ===
<pre>
+
* GO GAF files (on FTP, WS279) for WormBase now in 2.2 format with header like
Mary Ann:
+
!gaf-version: 2.2
*There are no plans to kill the lin-15 gene object at this time.
+
!generated-by: WormBase
*I agree that the operon object is rather vague. That it is the lin-15 operon
+
!date-generated: 2020-10-30
could currently only be curated in the Description tag, which is not ideal.  
+
! WB annotations 00015014
Should we propose a Name (or similar) tag for the ?Operon model?
+
* For files that can migrate to 2.2 format (e.g. always require column 4 qualifier) we could adopt a similar header
*The operon object is linked from lin-15A and lin-15B and is visible in the
+
* For other files (that cannot always have a qualifier in column 4), we could stick to 2.0 format with a header like:
Overview on their respective Gene Summary pages.  
+
!gaf-version: 2.0
</pre>
+
!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
  
<pre>
 
Tim Schedl:
 
I think there should be a lin-15 page that explains the original allele/
 
why it was called lin-15 and then refers the user to the lin-15A and lin-15B
 
pages.  The lin-15 page need not have any/much other information, although
 
a description of the define allele would be useful. 
 
Just killing the lin-15 page might lead to confusion for someone who
 
does not know the history (which is the majority of current worm researchers).
 
</pre>
 
  
* Mary Ann would like to attribute as many strains as possible to lin-15A or lin-15B
+
== Nov 19, 2020 ==
* lin-15 is the only gene/locus with ONLY a "Public_name"
 
* Can lin-15 be the CGC name? What about synonyms/"Other_names"
 
* Should the operon of lin-15 be called "lin-15"? Can we apply descriptions to operons?
 
* Proposal: create a "Name" tag for operons?
 
* Important: We need a page for the "lin-15" entity, for historical reasons at least, either as a gene or an operon (something else?)
 
* Allele attribution, e.g. n765? others?
 
  
=== Models deadline ===
+
=== Webinars ===
* Models deadline first conference call of the (upload) month?
+
* JBrowse webinar tomorrow (Friday)
* Proposal to EBI
+
** 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
** First conference call of the "Upload" month (3rd conference call of the cycle, usually), finalize models
+
* Background slides put together for when audience is waiting
** Paul Davis has 1 week to finish the models.wrm file and tag it for the official release
+
* Wen will start the meeting at 9:30am Pacific; can run a test poll
** Once tagged, the "final" models.wrm file can be tested by curators for ~1 week before data upload for citace build by Wen
+
* 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
** So, for example, on the current calendar we are on, we would have the following dates:
 
*** WS243 model submission deadline : March 6th, 2014
 
*** Paul finishes tagging WS243 models.wrm: March 13th, 2014
 
*** Curators can test official WS243 models.wrm file: March 14th, 2014 - March 24th, 2014
 
*** CITace data upload for WS243: March 25th, 2014
 
*** WS244 model submission deadline: May 1st, 2014
 
*** Paul finishes tagging WS244 models.wrm: May 8th, 2014
 
*** Curators can test official WS244 models.wrm file: May 9th, 2014 - May 26th, 2014
 
*** CITace data upload for WS244: May 27th, 2014
 
  
=== Curating Pseudogenes (Kimberly) ===
+
=== Alaska ===
*Two cases have come up recently wrt functional annotation of pseudogenes.
+
* Is Eduardo still working on it?
*drh-2 - a Dicer-related helicase for which there is apparently protein evidence and some functional studies (although it is part of an operon)
+
* He replied to a user asking about Alaska
***klp-10 - a kinesin-related protein that lacks a critical motif was recently converted to a pseudogene
+
* Is it still running? Maintained?
*Pseudogene status is listed discreetly under Type in the summary box display, but I wonder if we need to communicate this information more prominently and/or explain the classification in the concise description (CD). 
+
* Can we tell what usage it gets?
*Typically, we haven't written CDs for genes WB classifies as pseudogenes, but in the case of drh-2, there are papers that suggest it is functional. 
+
* Is it useful for the Alliance? Maybe can write it into grant?
*How best to reconcile all this data?  Should we contact authors of the papers? What should we do with experimental data attached to pseudogenes?
+
* Is it commercially viable? Maybe someone can write an SBIR grant proposal?
*Consensus: users should have access to all relevant information, including any conflicting evidence (in a concise description) and why a gene should or shouldn't be considered a pseudogene
 
  
=== Part-time help ===
+
=== Server space ===
* Part-time help (undergrads, etc.); Paul was wondering if we thought we could use any
+
* No new space in Chen building
* Mary Ann: allele curation, check through papers for true positives (appropriate for undergrads)
+
* Many servers will stay in a server room where they are currently
** Could undergrads at Caltech use the Hinxton curation tools? Would they need a "sponsored" account or something?
+
* Other servers we will need to see if they can be moved to Chen
** Or, more simply, papers could be scanned for data and results sent to Mary Ann
+
* Paul may have some space for servers in his lab designated space (or his own office)
* Karen: downloading papers and supplemental information (high school students could do this)
+
* 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