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 ==
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
=== AGENDA ===
 
* WOBr discussion
 
* Author-person issues
 
* Timeline for construct model
 
* Topic Curation
 
  
 +
= 2021 Meetings =
 +
== January 14th, 2021 ==
  
=== Author/Person issues ===
+
===PubMed LinkOut to WormBase Paper Pages (Kimberly) ===
*User was looking for papers for a specific person
+
* Other databases [https://www.ncbi.nlm.nih.gov/projects/linkout/doc/nonbiblinkout.html link out from PubMed] to their respective paper pages
*Person was an author, but did not have a WBPerson object
+
* For example, https://pubmed.ncbi.nlm.nih.gov/20864032/ links out to GO and MGI paper pages
*Cecilia will contact user
+
* Would like to set this up for WormBase and ultimately for the Alliance, but this will require some developer help
*Make author names searchable? ~32,000 authors without a person object
+
* Work on this next month (after AFP and GO grant submissions)?
*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)
 
  
 +
===Update cycle for HGNC data in the OA (Ranjana) ===
 +
*Juancarlos had these questions for us:
 +
<pre style="white-space: pre-wrap;
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=== Timeline for ?Construct model ===
+
There's a script here that repopulates the postgres obo_*_hgnc tables
*For WS243?
+
based off of Chris and Wen's data
*Mapping primers used for expression constructs or reporters
+
/home/postgres/work/pgpopulation/obo_oa_ontologies/populate_obo_hgnc.pl
*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
 
  
 
+
It's not on a cronjob, because I think the files are not updated that
=== Topic Curation ===
+
oftenDo we want to run this every night, or run it manually when
*Is there a way to update curators if a new paper is added to the current focus topic?
+
the files get re-generated ? Or run every night, and check if the
*No, but curators can just send around an e-mail and/or query through the topic OA and curation status form
+
files's timestamps have changed, then repopulate postgres ?
 
 
 
 
=== WormBase Ontology Browser (WOBr) ===
 
*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
 
 
 
 
 
== January 23, 2014 ==
 
 
 
=== AGENDA ===
 
 
 
* Biocuration 2014
 
** 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
 
* 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 ===
 
 
 
* Considerations for WS243
 
* Innate immunity, response to pathogens?
 
* 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 ===
 
 
 
* Tuesday morning 10am, 1-28-2014 deadline
 
* Models available tomorrow (Friday 1-24-2014)
 
 
 
 
 
== January 30, 2014 ==
 
 
 
=== AGENDA ===
 
* lin-15
 
* Models deadline
 
* Curating pseudogenes
 
* Part-time help
 
 
 
=== lin-15 - Creating a page for it ===
 
<pre>
 
Karen:
 
*Should it be considered a gene or can we fix up it up better as an operon?  
 
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>
 
</pre>
<pre>
 
Mary Ann:
 
*There are no plans to kill the lin-15 gene object at this time.
 
*I agree that the operon object is rather vague. That it is the lin-15 operon
 
could currently only be curated in the Description tag, which is not ideal.
 
Should we propose a Name (or similar) tag for the ?Operon model?
 
*The operon object is linked from lin-15A and lin-15B and is visible in the
 
Overview on their respective Gene Summary pages.
 
</pre>
 
 
<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
 
* 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 ===
+
===Minutes===
* Models deadline first conference call of the (upload) month?
+
====PubMed LinkOut to WormBase Paper Pages====
* Proposal to EBI
 
** First conference call of the "Upload" month (3rd conference call of the cycle, usually), finalize models
 
** Paul Davis has 1 week to finish the models.wrm file and tag it for the official release
 
** Once tagged, the "final" models.wrm file can be tested by curators for ~1 week before data upload for citace build by Wen
 
  
=== Curating Pseudogenes (Kimberly) ===
+
====Update cycle for HGNC data in the OA====
*Two cases have come up recently wrt functional annotation of pseudogenes.
+
*We will update when Alliance updates the data
*drh-2 - a Dicer-related helicase for which there is apparently protein evidence and some functional studies (although it is part of an operon)
+
*Juancarlos will set it to check the timestamps and if they change will do an update for the OAs
***klp-10 - a kinesin-related protein that lacks a critical motif was recently converted to a pseudogene
 
*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). 
 
*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. 
 
*How best to reconcile all this data?  Should we contact authors of the papers?  What should we do with experimental data attached to pseudogenes?
 
*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 ===
+
====CENGEN====
* Part-time help (undergrads, etc.); Paul was wondering if we thought we could use any
+
*Wen, Daniela, and Raymond will look at the datasets to work out how to incorporate. Start simple.
* Mary Ann: allele curation, check through papers for true positives (appropriate for undergrads)
+
*We will make links to pages on their site.
** Could undergrads at Caltech use the Hinxton curation tools? Would they need a "sponsored" account or something?
 
** Or, more simply, papers could be scanned for data and results sent to Mary Ann
 
* Karen: downloading papers and supplemental information (high school students could do this)
 

Latest revision as of 20:03, 14 January 2021

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2021 Meetings

January 14th, 2021

PubMed LinkOut to WormBase Paper Pages (Kimberly)

  • Other databases link out from PubMed to their respective paper pages
  • For example, https://pubmed.ncbi.nlm.nih.gov/20864032/ links out to GO and MGI paper pages
  • Would like to set this up for WormBase and ultimately for the Alliance, but this will require some developer help
  • Work on this next month (after AFP and GO grant submissions)?

Update cycle for HGNC data in the OA (Ranjana)

  • Juancarlos had these questions for us:

There's a script here that repopulates the postgres obo_*_hgnc tables
based off of Chris and Wen's data
/home/postgres/work/pgpopulation/obo_oa_ontologies/populate_obo_hgnc.pl 

It's not on a cronjob, because I think the files are not updated that
often.  Do we want to run this every night, or run it manually when
the files get re-generated ?  Or run every night, and check if the
files's timestamps have changed, then repopulate postgres ?

Minutes

PubMed LinkOut to WormBase Paper Pages

Update cycle for HGNC data in the OA

  • We will update when Alliance updates the data
  • Juancarlos will set it to check the timestamps and if they change will do an update for the OAs

CENGEN

  • Wen, Daniela, and Raymond will look at the datasets to work out how to incorporate. Start simple.
  • We will make links to pages on their site.