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| = 2014 Meetings = | | = 2014 Meetings = |
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− | == January 9, 2014 ==
| + | [[WormBase-Caltech_Weekly_Calls_January_2014|January]] |
− | | |
− | === AGENDA ===
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− | | |
− | * Apologies from Mary Ann - in Strasboug. Might try and Skype in. - Mary Ann joined in at the end of the call.
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− | * Curation of protein complexes - will wait until Chris can join in.
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− | * 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]
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− | * Raymond gave an update on WObr. Juancarlos has learned enough Catalyst to create a workable ontology browser on the caltech wormbase sandbox.
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− | **The browser can accommodate all ontologies used by Caltech curators (all GO, Phenotype, Anatomy, Life Stage, Disease)
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− | **A browser will be on each respective ontology page;
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− | ***direct and indirect gene connections will be displayed in a list format
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− | ***there was a request that the gene connections to ontology terms display the indirect annotations with direct annotations in parenths
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− | **various ontology browsers can be in their own widgets where desired.
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− | **still need to set up the search function from the main wb search
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− | * Caltech Models due Thursday 16 January 2014
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− | * Caltech WS242 data due into Citace by Tuesday Jan 28.
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− | * Biocuration 2014
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− | **http://biocuration2014.events.oicr.on.ca/biocuration
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− | **M. Tuli, X. Wang interested in attending.
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− | | |
− | | |
− | == January 16, 2014 ==
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− | | |
− | === AGENDA ===
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− | * WOBr discussion
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− | * Author-person issues
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− | * Timeline for construct model
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− | * Topic Curation
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− | | |
− | | |
− | === Author/Person issues ===
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− | *User was looking for papers for a specific person
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− | *Person was an author, but did not have a WBPerson object
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− | *Cecilia will contact user
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− | *Make author names searchable? ~32,000 authors without a person object
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− | *How many authors (without a WBPerson) have multiple (5+?) papers?
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− | *Proposal 1: make WBPersons for authors with 5 or more articles, and/or sort results of a search by number of publications
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− | *Proposal 2: Search for WBPerson (no autocomplete function); if no WBPerson, look up authors (prioritized search)
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− | | |
− | | |
− | === Timeline for ?Construct model ===
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− | *For WS243?
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− | *Mapping primers used for expression constructs or reporters
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− | *Integration of sequence features
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− | *Examples of the new Crispr/CAS (genome editing) alleles (curated with flanking sequences)
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− | *AddGene plasmids etc.
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− | *Karen will move ahead with the ?Construct model just for the context of genome-editing alleles
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− | *Other contexts can be added later
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− | | |
− | | |
− | === Topic Curation ===
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− | *Is there a way to update curators if a new paper is added to the current focus topic?
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− | *No, but curators can just send around an e-mail and/or query through the topic OA and curation status form
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− | | |
− | | |
− | === WormBase Ontology Browser (WOBr) ===
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− | *Juancarlos can now modify WormBase widgets, but would need to learn how ACEDB is handled, if required
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− | *We want to workout a pipeline for widget/website modifications, proposals etc.
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− | *WOBr is not working off of ACEDB
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− | *Note: WOBr is going to be a widget on the Ontology Term page (all other ACEDB-based info will be present on page)
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− | *General structure:
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− | **Testing site: http://juancarlos.wormbase.org/tools/ontology_browser
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− | **Two entry points: 1. Homepage "Tools" menu (tree-like view from root terms), 2. Specific ontology term page (WOBr widget)
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− | **Data present: ontology term objects, associated genes
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− | *Association files needed: Disease, Life stage
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− | *Curators are now testing and commenting on WOBr
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− | *Difficult to implement: display of evidence codes, sorting by species
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− | **Will consider for second generation WOBr
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− | *Do we want species-specific WOBr? C. elegans WOBr? Yes, probably; not clear how to implement
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− | **WormBase ontologies are currently species-agnostic
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− | **Maybe we should have species-specific ontology terms/pages
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− | *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)
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− | *Direct vs. indirect/inferred annotations, how to display at different points? Ignore numbers for ancestor terms? Speed is an issue
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− | *The new Solr update may allow for precalculated/precached number calculations, which should improve speed
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− | | |
− | | |
− | == January 23, 2014 ==
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− | | |
− | === AGENDA ===
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− | | |
− | * Biocuration 2014
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− | ** Mary Ann's flights are booked.
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− | ** Shall we ask for a WormBase booth/helpdesk table?
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− | | |
− | === Biocuration Meeting April 2014, OICR, Toronto, CA ===
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− | | |
− | * http://biocuration2014.events.oicr.on.ca/biocuration
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− | * Mary Ann going
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− | * Xiaodong may go, present info presented at IWM
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− | * Wen considering, may want to see what's up for RNAseq etc.
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− | * February 10, 2014 is abstract deadline, March registration deadline
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− | * More WormBase curators?
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− | * Registration discount for "International Society for Biocuration" members
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− | | |
− | === Topic Curation ===
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− | | |
− | * Considerations for WS243
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− | * Innate immunity, response to pathogens?
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− | * Good to work on something for which a WormBook chapter exists
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− | * Jonathan Ewbank, "Signaling in the immune response" 2006 WormBook chapter
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− | * Creg Darby, "Interactions with microbial pathogens" 2005 WormBook chapter
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− | * Action items: Look over two WormBook chapters, collect relevant genes and send to EBI/Hinxton, collect relevant papers
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− | * 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?
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− | | |
− | === Upload ===
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− | | |
− | * Tuesday morning 10am, 1-28-2014 deadline
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− | * Models available tomorrow (Friday 1-24-2014)
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− | | |
− | | |
− | == January 30, 2014 ==
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− | | |
− | === AGENDA ===
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− | * lin-15
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− | * Models deadline
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− | * Curating pseudogenes
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− | * Part-time help
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− | | |
− | === lin-15 - Creating a page for it ===
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− | <pre>
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− | Karen:
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− | *Should it be considered a gene or can we fix up it up better as an operon?
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− | It has been assigned to operon CEOPX140, but searching for
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− | lin-15 in the operon class does not work, is there an other_name tag in the operon
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− | class to store 'lin-15'.
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− | *'lin-15' is frequently published object. Although many people in the field know
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− | that it is a complex locus comprised of two separate genes, lin-15A and lin-15B,
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− | many people do not.
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− | *There are many lin-15AB alleles, e.g., n765. Where in WB can we see that one
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− | allele affects more than one gene, is this something a lin-15 operon page can
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− | display?
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− | | |
− | </pre>
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− | <pre>
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− | Mary Ann:
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− | *There are no plans to kill the lin-15 gene object at this time.
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− | *I agree that the operon object is rather vague. That it is the lin-15 operon
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− | could currently only be curated in the Description tag, which is not ideal.
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− | Should we propose a Name (or similar) tag for the ?Operon model?
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− | *The operon object is linked from lin-15A and lin-15B and is visible in the
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− | Overview on their respective Gene Summary pages.
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− | </pre>
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− | | |
− | <pre>
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− | Tim Schedl:
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− | I think there should be a lin-15 page that explains the original allele/
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− | why it was called lin-15 and then refers the user to the lin-15A and lin-15B
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− | pages. The lin-15 page need not have any/much other information, although
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− | a description of the define allele would be useful.
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− | Just killing the lin-15 page might lead to confusion for someone who
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− | does not know the history (which is the majority of current worm researchers).
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− | </pre>
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− | | |
− | * Mary Ann would like to attribute as many strains as possible to lin-15A or lin-15B
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− | * lin-15 is the only gene/locus with ONLY a "Public_name"
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− | * Can lin-15 be the CGC name? What about synonyms/"Other_names"
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− | * Should the operon of lin-15 be called "lin-15"? Can we apply descriptions to operons?
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− | * Proposal: create a "Name" tag for operons?
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− | * Important: We need a page for the "lin-15" entity, for historical reasons at least, either as a gene or an operon (something else?)
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− | * Allele attribution, e.g. n765? others?
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− | | |
− | === Models deadline ===
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− | * Models deadline first conference call of the (upload) month?
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− | * Proposal to EBI
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− | ** First conference call of the "Upload" month (3rd conference call of the cycle, usually), finalize models
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− | ** Paul Davis has 1 week to finish the models.wrm file and tag it for the official release
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− | ** Once tagged, the "final" models.wrm file can be tested by curators for ~1 week before data upload for citace build by Wen
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− | ** So, for example, on the current calendar we are on, we would have the following dates:
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− | *** WS243 model submission deadline : March 6th, 2014
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− | *** Paul finishes tagging WS243 models.wrm: March 13th, 2014
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− | *** Curators can test official WS243 models.wrm file: March 14th, 2014 - March 24th, 2014
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− | *** CITace data upload for WS243: March 28th (Friday), 2014 (Caltech curators submit ace files to Wen before Tues. March 25)
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− | *** WS244 model submission deadline: May 1st, 2014
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− | *** Paul finishes tagging WS244 models.wrm: May 8th, 2014
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− | *** Curators can test official WS244 models.wrm file: May 9th, 2014 - May 26th, 2014
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− | *** CITace data upload for WS244: May 30th (Friday), 2014 (Caltech curators submit ace files to Wen before Tues. May 27)
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− | | |
− | === Curating Pseudogenes (Kimberly) ===
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− | *Two cases have come up recently wrt functional annotation of pseudogenes.
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− | *drh-2 - a Dicer-related helicase for which there is apparently protein evidence and some functional studies (although it is part of an operon)
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− | ***klp-10 - a kinesin-related protein that lacks a critical motif was recently converted to a pseudogene
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− | *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).
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− | *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.
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− | *How best to reconcile all this data? Should we contact authors of the papers? What should we do with experimental data attached to pseudogenes?
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− | *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
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− | | |
− | === Part-time help ===
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− | * Part-time help (undergrads, etc.); Paul was wondering if we thought we could use any
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− | * Mary Ann: allele curation, check through papers for true positives (appropriate for undergrads)
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− | ** Could undergrads at Caltech use the Hinxton curation tools? Would they need a "sponsored" account or something?
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− | ** Or, more simply, papers could be scanned for data and results sent to Mary Ann
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− | * Karen: downloading papers and supplemental information (high school students could do this)
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