Difference between revisions of "WormBase-Caltech Weekly Calls"
From WormBaseWiki
Jump to navigationJump to searchm |
m (→July 13, 2017) |
||
| Line 72: | Line 72: | ||
* It would be good to have a mechanism to curate these attributes to alleles independent of phenotype curation | * It would be good to have a mechanism to curate these attributes to alleles independent of phenotype curation | ||
* As far as modeling goes I (Chris) had intended to do dump these attributes directly into the ?Variation object like this: | * As far as modeling goes I (Chris) had intended to do dump these attributes directly into the ?Variation object like this: | ||
| − | ?Variation Null ?Phenotype_experiment | + | ?Variation |
| + | Null ?Phenotype_experiment | ||
* 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: | * 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: | ||
| − | ?Variation Null ?Paper | + | ?Variation |
| + | Null ?Paper | ||
* 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 | * 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 | ||
Revision as of 17:51, 13 July 2017
Contents
Previous Years
2017 Meetings
July 6, 2017
Noctua
- Use for all literature curation in future?
- We would need to see how it could be used for all data types
- We would also want a full-time developer working on Noctua; maybe bring Juancarlos into the project
SPELL
- SPELL related data - how to deal with?
- Data: recalculated, mapping, results dependent on SPELL
- Analysis (clustering tool): clunky, freezes w/limited resources
- Wen will work with Juancarlos to generate a SimpleMine-like tool for downloading data sets
- Wen has to remove log files to make space on machine
- ~360 data sets
- Current virtual machine has 10G memory; is becoming limiting
- SPELL has lots of dependencies; difficult to account for them all when building SPELL
- 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?
Micropublications
- Poster at Zebrafish meeting pointing to micropublications
- Microarray micropublications? Unpublished results
- Can make links to GEO submissions
- Daniela and Karen can draw up a mock publication to look at as a template
Community Curation
- Considering sending requests to only one person, first author when have info
- This should allow for more emails to be sent out per week, and more submissions, even if we maintain the 16% response rate
- Chris will work with Juancarlos once he's back from vacation
- What's next data type? Interactions? Site of action? Anatomy?
- What's required for site of action? Phenotype, gene, cell/tissue where gene is introduced or removed
- Can send requests to lab heads to fill in phenotype info for alleles from their lab
Linking
- Will human genes link to AGR human gene pages? Gene Cards? HGNC?
July 13, 2017
Allele attribute assignment
- Some attributes of alleles are currently only assigned in the context of a phenotype annotation
- Many times these attributes are reported independently of a phenotype experiment
- It would be good to have a mechanism to curate these attributes to alleles independent of phenotype curation
- As far as modeling goes I (Chris) had intended to do dump these attributes directly into the ?Variation object like this:
?Variation Null ?Phenotype_experiment
- 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:
?Variation Null ?Paper
- 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
Phenotype form submission requests
- Originally we sent email requests independently of Author First Pass pipeline emails
- 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
- I (Chris) am considering returning to original approach of sending requests independently of AFP, to see if we can get response rate up at all
