Difference between revisions of "WormBase-Caltech Weekly Calls"

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= 2014 Meetings =  
= 2014 Meetings =  
== January 9, 2014 ==
=== AGENDA ===
* Apologies from Mary Ann - in Strasboug. Might try and Skype in. - Mary Ann joined in at the end of the call.
* 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
**M. Tuli, X. Wang interested in attending.
== January 16, 2014 ==
=== AGENDA ===
* WOBr discussion
* Author-person issues
* Timeline for construct model
* Topic Curation
=== Author/Person issues ===
*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)
=== Timeline for ?Construct model ===
*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
=== Topic Curation ===
*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 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 ===
*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
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.
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).
* 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 ===
* Models deadline first conference call of the (upload) month?
* 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
** 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 28th (Friday), 2014 (Caltech curators submit ace files to Wen before Tues. March 25)
*** 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 30th (Friday), 2014 (Caltech curators submit ace files to Wen before Tues. May 27)
=== Curating Pseudogenes (Kimberly) ===
*Two cases have come up recently wrt functional annotation of pseudogenes.
*drh-2 - a Dicer-related helicase for which there is apparently protein evidence and some functional studies (although it is part of an operon)
***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 ===
* Part-time help (undergrads, etc.); Paul was wondering if we thought we could use any
* Mary Ann: allele curation, check through papers for true positives (appropriate for undergrads)
** 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)

Revision as of 18:15, 5 February 2014