WormBase-Caltech Weekly Calls
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- 1 Previous Years
- 2 2015 Meetings
- 2.1 November 5, 2015
- 2.1.1 IEA GO Annotations informating descriptions for non-elegans
- 2.1.2 Wen using Textpresso machine to build SPELL
- 2.1.3 Community Curation Tracker CGI
- 2.1.4 SObA Graphs for phenotype
- 2.1.5 Micropublications
- 2.1.6 Status of WormBase User Survey?
- 2.1.7 Sending author updates
- 2.1.8 Objectifying/Itemizing annotations from Postgres
- 2.1 November 5, 2015
November 5, 2015
IEA GO Annotations informating descriptions for non-elegans
- Some non-elegans genes have confident-sounding descriptions, about localization for example; likely not manual
- Will make sure automated descriptions handle IEA's appropriately
Wen using Textpresso machine to build SPELL
- Athena was taking 48 hours to build SPELL (4GB max memory allotted)
- Textpresso machine took 24 hours (8GB memory allotted)
- Maybe we can use Textpresso machine for future builds
- SPELL java program running on Athena (alloted 4GB out of 6GB)
- Can monitor Athena memory usage; check for any memory leaks
Community Curation Tracker CGI
- Purpose: To automate many steps of the e-mailing process to authors requesting community curation and to track those papers for which we've sent e-mails
- There is a "Ready" form and a "Tracker" form; "Ready" for generating list of papers to e-mail about, "Tracker" to track the status of papers that have already been e-mailed about
- Wiki documentation at: http://wiki.wormbase.org/index.php/Contacting_the_Community#Community_Contact_.26_Curation_Tracker_CGI
- Sandbox CGI located at: http://mangolassi.caltech.edu/~postgres/cgi-bin/community_curation_tracker.cgi
- EMAIL FUNCTIONALITY IS LIVE: please note!
- Allele-phentoype("New mutant" datatype) CGI is live on Tazendra
- Concise description version will be cloned from the New Mutant CGI and modified as needed
SObA Graphs for phenotype
- Juancarlos will transfer code tomorrow, if there are no change requests before then
- Existing feature requests will be added to future releases of SObA
- Daniela spoke with Daniel about having web pages in WormBook style to house micropublications
Status of WormBase User Survey?
- Paul sent around paper this morning: http://www.nature.com/nature/journal/v527/n7576_supp/full/527S16a.html
- What aspects of databases really get used by users?
- How can we be more efficient with existing curation pipelines?
- Question of the month on WormBase?
- We could get user feedback when visiting labs
- Would be nice to have a mechanism to update authors on what has been curated for their paper
- Could give paper data summaries as well as recent updates to curation for a paper
Objectifying/Itemizing annotations from Postgres
- What if we objectified itemized Postgres entries for easier display of all annotations per paper, for example?
- May require addition of a text field tag to the ?Paper class, for example, that would capture each annotation item for a paper
- This would be in lieu of actually objectifying all annotations