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| [[WormBase-Caltech_Weekly_Calls_June_2017|June]] | | [[WormBase-Caltech_Weekly_Calls_June_2017|June]] |
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− | == July 6, 2017 ==
| + | [[WormBase-Caltech_Weekly_Calls_July_2017|July]] |
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− | === Noctua ===
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− | * Use for all literature curation in future?
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− | * We would need to see how it could be used for all data types
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− | * We would also want a full-time developer working on Noctua; maybe bring Juancarlos into the project
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− | | |
− | === SPELL ===
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− | * SPELL related data - how to deal with?
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− | ** Data: recalculated, mapping, results dependent on SPELL
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− | ** Analysis (clustering tool): clunky, freezes w/limited resources
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− | * Wen will work with Juancarlos to generate a SimpleMine-like tool for downloading data sets
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− | * Wen has to remove log files to make space on machine
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− | * ~360 data sets
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− | * Current virtual machine has 10G memory; is becoming limiting
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− | * SPELL has lots of dependencies; difficult to account for them all when building SPELL
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− | * Would be good if we could setup a new (larger) virtual machine to run SPELL; how much time/resources do we want to spend on it?
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− | | |
− | === Micropublications ===
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− | * Poster at Zebrafish meeting pointing to micropublications
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− | * Microarray micropublications? Unpublished results
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− | * Can make links to GEO submissions
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− | * Daniela and Karen can draw up a mock publication to look at as a template
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− | | |
− | === Community Curation ===
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− | * Considering sending requests to only one person, first author when have info
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− | * This should allow for more emails to be sent out per week, and more submissions, even if we maintain the 16% response rate
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− | * Chris will work with Juancarlos once he's back from vacation
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− | * What's next data type? Interactions? Site of action? Anatomy?
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− | * What's required for site of action? Phenotype, gene, cell/tissue where gene is introduced or removed
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− | * Can send requests to lab heads to fill in phenotype info for alleles from their lab
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− | | |
− | === Linking ===
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− | * Will human genes link to AGR human gene pages? Gene Cards? HGNC?
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− | | |
− | | |
− | == July 13, 2017 ==
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− | | |
− | === Allele attribute assignment ===
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− | * Some attributes of alleles are currently only assigned in the context of a phenotype annotation
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− | * Many times these attributes are reported independently of a phenotype experiment
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− | * It would be good to have a mechanism to curate these attributes to alleles independent of phenotype curation
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− | * As far as modeling goes I (Chris) had intended to do dump these attributes directly into the ?Variation object like this:
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− | ?Variation
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− | Null ?Phenotype_experiment
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− | * This would allow us to always point to a ?Phenotype_experiment object as a container of evidence, but if we don't always have a ?Phenotype_experiment object to point to then maybe a better approach is just to reference the paper like this:
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− | ?Variation
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− | Null ?Paper
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− | * This would require a separate curation pipeline from phenotype to capture these attributes; will discuss more with Mary Ann when she's back from vacation
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− | * We discussed and came up with a couple of potential solutions:
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− | * First:
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− | ?Variation
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− | Variation_effect Null ?Text #Evidence
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− | * Second:
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− | ?Variation
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− | Variation_effect Null ?Paper #Evidence
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− | * The first solution allows to put in a free text remark, potentially referencing a phenotype or some detail, with the #Evidence hash allowing reference to a paper or a person_evidence
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− | * The second solution requires reference to a ?Paper object, which would require a reworking of all person evidence/personal communication to become ?Paper objects, with an #Evidence hash to capture remarks
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− | | |
− | === Phenotype form submission requests ===
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− | * Originally we sent email requests independently of Author First Pass pipeline emails
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− | * Now a link to phenotype form is being included in Author First Pass emails, and we're putting a hold on all new email requests to corresponding author for one month
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− | * I (Chris) am considering returning to original approach of sending requests independently of AFP (and focusing on first authors), to see if we can get response rate up at all
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− | | |
− | === New WormBase Caltech server ===
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− | * We're getting a new server, to consolidate different computers and their services
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− | * Let Raymond know if you have an idea for another (extra) use of the server
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− | * Will likely re-use altair.caltech.edu
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− | * 96 GB memory, ~6 TB hard drive
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− | | |
− | === SPELL ===
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− | * SPELL could go on new server
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− | * Moved from current virtual machine to KVM
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− | * Could expand memory and CPU
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− | | |
− | | |
− | == July 20, 2017 ==
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− | | |
− | === Variation effect assignment ===
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− | * We had discussed last week having either of two models in the ?Variation class
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− | * First:
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− | ?Variation Variation_effect Null ?Text #Evidence
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− | * Second:
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− | ?Variation Variation_effect Null ?Paper #Evidence
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− | * The first option can keep things as they are and can allow a remark in the ?Text entry, with paper or person evidence coming from the #Evidence hash
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− | * The second option likely requires that we consider person evidence/communication as ?Paper objects
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− | * Many entries in the Phenotype OA coming from Jonathan Hodgkin are from the C. elegans I and II books
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− | ** Would be good to create ?Paper objects for C. elegans I and II and reference them accordingly
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− | *** Already exist:
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− | **** C. elegans II WBPaper00004071
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− | **** C. elegans I WBPaper00004052
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− | * Probably best to go with
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− | ?Variation Variation_effect Null ?Text #Evidence
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− | * Going forward we can encourage people to micropublish if they want to submit personal communication
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− | | |
− | === Blog posts for WormMine ===
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− | * Not quite ready; Chris will contact Ranjana about it when ready
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− | | |
− | === WormMine templates ===
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− | * Todd had encouraged development of template queries
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− | * Older templates are still difficult to access and edit, but new queries going forward are OK
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− | | |
− | === New Server ===
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− | * New WormBase server (@ Catlech) is online
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− | * Let Raymond know if anyone has uses for the server
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− | * Anything that needs to be running 24-7 (e.g. services) can be considered
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− | | |
− | === Supplement for AGR ===
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− | * Proposing tuning up of orthology calls
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− | * Paul S. wants to get Gene Orienteer back up, and have RNASeq analysis pipeline
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− | * Pull in WormNet data (predicted interactions)
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− | | |
− | | |
− | == July 27, 2017 ==
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− | | |
− | === AGR GO Slim ===
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− | *Discussion of new AGR GO slim and representation of C. elegans genes
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− | *[https://github.com/geneontology/go-ontology/issues/13791 Modification to AGR slim]
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− | *Key to graphs
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− | **Red = AGR slim
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− | **Orange = C. elegans orphans
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− | **Multi-colors = Other organism orphans, as well
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