Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
  
= 2020 Meetings =
+
= 2021 Meetings =
 +
== January 14th, 2021 ==
  
== January 9, 2020 ==
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===PubMed LinkOut to WormBase Paper Pages (Kimberly) ===
 +
* Other databases [https://www.ncbi.nlm.nih.gov/projects/linkout/doc/nonbiblinkout.html link out from PubMed] to their respective paper pages
 +
* For example, https://pubmed.ncbi.nlm.nih.gov/20864032/ links out to GO and MGI paper pages
 +
* Would like to set this up for WormBase and ultimately for the Alliance, but this will require some developer help
 +
* Work on this next month (after AFP and GO grant submissions)?
  
=== Phenotype Curation Requests ===
+
===Update cycle for HGNC data in the OA (Ranjana) ===
* 1,229 emails sent Dec 3-6, 2019
+
*Juancarlos had these questions for us:
* Received 194 annotations from 40 papers and from 37 distinct community curators
+
<pre style="white-space: pre-wrap;
** 37 papers requested, 3 additional papers annotated
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white-space: -moz-pre-wrap;
** 104 Phenotype OA annotations (from 27 papers; 25 distinct curators)
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white-space: -pre-wrap;
** 90 RNAi OA annotations (from 20 papers; 19 distinct curators)
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white-space: -o-pre-wrap;  
* 43 bounced emails
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word-wrap: break-word">
** 2 resent to new addresses
 
** 5 have backup email addresses (also sent)
 
  
=== Worm Area Meetings ===
+
There's a script here that repopulates the postgres obo_*_hgnc tables
* Chris has (re)requested slots for WormBase for the Worcester Area Worm Meeting and the Boston Area Worm Meeting
+
based off of Chris and Wen's data
* Will update group if/when a slot is assigned (probably not until Fall 2020 at the earliest)
+
/home/postgres/work/pgpopulation/obo_oa_ontologies/populate_obo_hgnc.pl
  
=== Reference widget Textpresso linkouts ===
+
It's not on a cronjob, because I think the files are not updated that
* Now live on WormBase, WS274
+
often. Do we want to run this every night, or run it manually when
* [https://github.com/WormBase/website/issues/7347 GitHub ticket]
+
the files get re-generated ?  Or run every night, and check if the
* Applies to the following classes: genes, strains, variations, transgenes, constructs, anatomy terms, clones, life stages, rearrangements, molecules, processes
+
files's timestamps have changed, then repopulate postgres ?
* Gene example: https://wormbase.org/species/c_elegans/gene/WBGene00022861#0d--10
 
* Strain example: https://wormbase.org/species/c_elegans/strain/WBStrain00004309#05--10
 
* Variation example: https://wormbase.org/species/c_elegans/variation/WBVar00248884#08--10
 
* Transgene example: https://wormbase.org/species/all/transgene/WBTransgene00004654#04--10
 
** Known issue: searching on synonyms in addition to public name; Sibyl will fix
 
* Construct example: https://wormbase.org/species/all/construct/WBCnstr00023113#03--10
 
** Known issue: not working now; need to only search on public name when available, not on summary; Sibyl will fix
 
* Anatomy term example: https://wormbase.org/species/all/anatomy_term/WBbt:0005772#05--10
 
** Known challenge: "Psub1" will essentially never match the intended target and "P1" may find the embryonic cell or the postembryonic cell
 
* Clone example: https://wormbase.org/species/c_elegans/clone/W02C12#03--10
 
* Life stage example: https://wormbase.org/species/all/life_stage/WBls:0000038#03--10
 
** Known challenge: "L4 larva Ce" will never match; "L4 larva" maybe; but "L4" alone will not unless a synonym
 
* Rearrangement example: https://wormbase.org/species/all/rearrangement/sDp3#03--10
 
* Molecule example: https://wormbase.org/resources/molecule/WBMol:00003650#03--10
 
* Process examples:
 
** https://wormbase.org/resources/wbprocess/WBbiopr:00000001#09--10
 
** https://wormbase.org/resources/wbprocess/WBbiopr:00000079#09--10
 
* Michael has improved phrase search and combined supplemental documents with main paper documents; should roll out soon
 
  
=== WS276 Citace upload ===
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</pre>
* Hinxton upload Jan 31, 2020
 
* Citace upload on Tuesday, Jan 28, 2020
 
  
=== Author First Pass paper ===
+
===Minutes===
* AFP resent to Database
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====PubMed LinkOut to WormBase Paper Pages====
* Automated descriptions about to be sent
 
* SObA, write for micropub? One micropub on SObA and another on comparative SObA
 
  
=== Noctua/GO-CAM ===
+
====Update cycle for HGNC data in the OA====
* New version of the Noctua form released next week
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*We will update when Alliance updates the data
* Imports from WormBase?
+
*Juancarlos will set it to check the timestamps and if they change will do an update for the OAs
** Big push in coming months will be to pull in all manual annotations from WB into Noctua (on track)
 
** Need to work on annotation history on back end
 
** May have face-to-face meeting in Pasadena
 
  
=== Variation curation ===
+
====CENGEN====
* Have a backlog; Paul D is assigned but has been overwhelmed
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*Wen, Daniela, and Raymond will look at the datasets to work out how to incorporate. Start simple.
* Have asserted this as a priority
+
*We will make links to pages on their site.
* We have the allele-sequence form; where does it go? Hinxton
 
* Need to get allele/variation data in an Alliance-submission friendly form and pull it into the Alliance
 
* Need to integrate curation with the Variant Effect Predictor (VEP) pipeline
 
 
 
=== Topic meetings ===
 
* Asia (Taipei) meeting, Paul S going
 
* Aging meeting, Wen could go? (Wen: I can ask if they provide a timeslot for oral presentation.)
 
* TAGC in April, Chris going
 
 
 
 
 
== January 16, 2020 ==
 
 
 
=== Variation names ===
 
* Daniela entered a new allele name (tkTi1) in the temporary allele form CGI but it prompted an error: tkTi1 does not match 1 or 2 sets of 1-3 letters and 1-6 digits
.
 
* Daniela asked Juancarlos to modify the temporary variation ID form to allow up to 4 letters instead of 3.
 
* Form here: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo
 
* Paul D  will talk with Tim about this as, while the Nomenclature has an example of this 'Ti' nomenclature being used in genotype description, it is not covered in the variation nomenclature guide.
 
 
 
=== Webinars ===
 
* During an AFP call we discussed the possibility to have webinars for authors to guide them through the form.
 
* Is having a webinar series something WB is interested in doing?
 

Latest revision as of 20:03, 14 January 2021

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings


2021 Meetings

January 14th, 2021

PubMed LinkOut to WormBase Paper Pages (Kimberly)

  • Other databases link out from PubMed to their respective paper pages
  • For example, https://pubmed.ncbi.nlm.nih.gov/20864032/ links out to GO and MGI paper pages
  • Would like to set this up for WormBase and ultimately for the Alliance, but this will require some developer help
  • Work on this next month (after AFP and GO grant submissions)?

Update cycle for HGNC data in the OA (Ranjana)

  • Juancarlos had these questions for us:

There's a script here that repopulates the postgres obo_*_hgnc tables
based off of Chris and Wen's data
/home/postgres/work/pgpopulation/obo_oa_ontologies/populate_obo_hgnc.pl 

It's not on a cronjob, because I think the files are not updated that
often.  Do we want to run this every night, or run it manually when
the files get re-generated ?  Or run every night, and check if the
files's timestamps have changed, then repopulate postgres ?

Minutes

PubMed LinkOut to WormBase Paper Pages

Update cycle for HGNC data in the OA

  • We will update when Alliance updates the data
  • Juancarlos will set it to check the timestamps and if they change will do an update for the OAs

CENGEN

  • Wen, Daniela, and Raymond will look at the datasets to work out how to incorporate. Start simple.
  • We will make links to pages on their site.