WBConfCall 2020.10.01-Agenda and Minutes
- Current schedule: https://wiki.wormbase.org/index.php/Meetings#2020_-_2021_WormBase_Webinars
- We will promote all webinars together.
- We will ask users to register.
- We will use email@example.com as the webinar contact.
- Wen will use her Caltech Zoom account for the webinar.
Current Production Release on FTP is still WS276
- Can we update this to WS277 data? Or, if WS278 is coming soon skip to that when we go live? (Todd will work on it after the meeting.)
- Kimberly/Paul - Species model additions
> ?Species Evidence #Evidence // Meta data for why the object was created > References ?Paper (optional XREF Species_in_paper) > Remark ?Text #Evidence
new tag "Sequence_comparison"
Adding Caltech designated WBIDs to the nameserver
added by Karen
- Michael Paulini found that some Transgene IDs were missing in acedb from db to db
- Caltech assigned IDs include, transgene, construct, molecule, others....
- MP suggests using a centralized nameserver to keep track of ID history (merges, kills etc)
- KY suggests alternative of added history to .ace files in citace upload
A dump of the merge information to Transgene Summary or Remark will get the info into WS. Karen will decide if a schema change is necessary.
- Emails sent to firstname.lastname@example.org did not generate github tickets.
* "phm-2 has been cloned. It is F32B4.4" help desk email from Jonathan Ewbank Sept 30 GitHub ticket #7905
- "eiF3-L and dhs-6 confusion" help desk email from Mary-Anne Felix Sept 29 -- [PD I will look at this]
* "paper link missing to sax-1?" help desk email from Nathalie Pujol Sept 26
** all gene-paper links for that paper have been added to the paper object; responded to Nathalie (Kimberly)
- Did anyone help Nathalie Pujol with this one: (PD will look at this)
I am working on COL-17 that was recently taken out of the collagen family (see Matrisome data). As it still have a weak homology to Briggsae COL-77 A, I wanted to check the prediction of the Briggsae protein with you. Cbr COL-77 in wormbase has 2 isoforms, A 351 aa and B 304 aa. It seems that the A long form is specific to Briggsae (and contain the very short homology domain with COL-17). The B form is shorter and produced after a frameshift after one or two base splice out, which is strange, but is 100 % identical to all other COL-77 protein in Caenorhabditis.
My question is then the following: Does the Cbr COL-77 A long isoform is real? I couldn’t have access to RNAseq or Est sequences.
New WormBase Tables
- All New WormBase Tables Ready for Testing. Sibyl sent an email to the staff email list.
GAF file headers & column contents
- We need files that are not GAF standard gene association files.
- FTP site is organized is a way that a file can be accessed from different directories via symbolic links.
- Not to make major changes to the file format. Change GAF2.1 file format.
- GAF does not need column headers because there is a format specification. We are adding more headers.
- Hinxton will generate both GAF and GAF-like files.