WormBase-Caltech Weekly Calls January 2014
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- 1 January 9, 2014
- 2 January 16, 2014
- 3 January 23, 2014
- 4 January 30, 2014
January 9, 2014
- 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 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
- WOBr discussion
- Author-person issues
- Timeline for construct model
- Topic Curation
- 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
- 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
- Biocuration 2014
- Mary Ann's flights are booked.
- Shall we ask for a WormBase booth/helpdesk table?
Biocuration Meeting April 2014, OICR, Toronto, CA
- 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
- 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?
- Tuesday morning 10am, 1-28-2014 deadline
- Models available tomorrow (Friday 1-24-2014)
January 30, 2014
- Models deadline
- Curating pseudogenes
- Part-time help
lin-15 - Creating a page for it
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?
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 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 (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)