Difference between revisions of "WormBase-Caltech Weekly Calls"
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=== Phenotype request mass emails === | === Phenotype request mass emails === | ||
− | * 2,777 emails gone out ( | + | * 2,777 emails gone out (last week) for 2,777 papers |
* Have received 421 direct annotations for 88 papers (81 requested papers; ~3% response rate) from 84 distinct community curators | * Have received 421 direct annotations for 88 papers (81 requested papers; ~3% response rate) from 84 distinct community curators | ||
** 313 to Phenotype OA | ** 313 to Phenotype OA |
Revision as of 18:53, 28 February 2019
Contents
Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2019 Meetings
February 7, 2019
Automation of curation
- For paper-by-paper curators (vs. datatype-by-datatype) it's difficult to parse papers into data types
- MGI and WB curate by datatype, so may have an easier time
- All MODS still need paper triage
IWM workshop
- Ranjana replied to Julie about a consolidated WormBase workshop; hasn't heard back
Site-specific outreach
- Wen has been invited to small RNA meeting in Mexico in April; may go if they offer to pay (waiting to hear back)
SObA
- Raymond and Juancarlos have worked out a way to display top-slicing of the ontology (trimming to higher level nodes)
- Needs a bit more clean up; will send around a URL when ready
February 21, 2019
SObA
- SObA GO graph, with top slicing function. You can try it here <http://wobr2.caltech.edu/~raymond/cgi-bin/soba_biggo.cgi> by entering the name of your favorite gene.
- specific genes, from simple to complex
- Looks good
- Some confusion with filled circle legend (half red and half blue) for slim terms; maybe make two separate circles, one red, one blue and possibly indicate each as direct/indirect, respectively
- May be good to make graph depth options more obvious; we can move it up to the top of the legend, maybe also display all graph depths by default so a user can see them and select one
- Would it be possible to force display of any AGR/Alliance slim terms on the path from an annotation node to root (not all pertinent slim terms are currently displaying due to the trimming algorithms in place); might be possible but would probably significantly interfere with the current trimming and display algorithm
Moving away from dependency on OBO format files
- Nico, an ontology developer with the Monarch group, has some suggestions for how we can move away from dependency on OBO files
- Planning to have a meeting on Monday (Feb 25) at 9am Pacific, 12pm Eastern, 5pm UK to discuss
- How are we handling OBO for GO? GO OBO is parsed into ACE format
- This should be a group-wide discussion as we have many OBO dependencies
- There are several OBO-to-ACE conversion scripts we use
- What is the trend in the ontology field? Seems to be that OBO will become deprecated and OWL will supersede it
- We will try to reschedule to Tuesday (same time) to include more people
Phenotype request mass emails
- 1,820 emails gone out this week (since Monday) for 1,820 papers (957 still in queue; need to wait for Google limit to expire)
- Have received 217 direct annotations for 49 papers (45 requested papers) from 47 distinct community curators
- 158 to Phenotype OA
- 59 to RNAi OA
- Have received 5 submissions via email (4 worksheets)
- 1 of these is just strain/transgene submissions (no phenotypes; 79 strains)
- 4 phenotype submissions, 4 curators, 93 phenotype annotations
- 57 papers flagged as not having phenotypes
- Total: 310 phenotype annotations from 51 community curators for 53 papers
February 28, 2019
Phenotype request mass emails
- 2,777 emails gone out (last week) for 2,777 papers
- Have received 421 direct annotations for 88 papers (81 requested papers; ~3% response rate) from 84 distinct community curators
- 313 to Phenotype OA
- 108 to RNAi OA
- Have received 5 submissions via email (4 worksheets)
- 1 of these is just strain/transgene submissions (no phenotypes; 79 strains)
- 4 phenotype submissions, 4 curators, 93 phenotype annotations
- 83 papers flagged as not having phenotypes
- Total: 514 phenotype annotations from 88 community curators for 92 papers