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]]
  
  
 +
= 2021 Meetings =
 +
== January 14th, 2021 ==
  
= 2020 Meetings =
+
===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)?
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
+
===Update cycle for HGNC data in the OA (Ranjana) ===
 +
*Juancarlos had these questions for us:
 +
<pre style="white-space: pre-wrap;
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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
+
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
  
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
+
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 ?
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
+
</pre>
  
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
+
===Minutes===
 +
====PubMed LinkOut to WormBase Paper Pages====
  
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
+
====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
  
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
+
====CENGEN====
 
+
*Wen, Daniela, and Raymond will look at the datasets to work out how to incorporate. Start simple.
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
+
*We will make links to pages on their site.
 
 
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_October_2020|October]]
 
 
 
 
 
==Nov 5th, 2020==
 
 
 
===WS279 GAF 2.0 and disease files===
 
*Valerio and Ranjana still working with the GAF 2.0 files to generate gene descriptions
 
*Valerio and Ranjana will probably have a meeting with Magdalena to sort out the FTP file issues for gene descriptions
 
*Will let Raymond know if the disease GAFs are okay after they test these for gene descriptions
 
*Raymond needs the GAFs for WoBR
 
 
 
===Experimenting with addeding new citace data to the current WS release ===
 
*Wen will take the newest expression, physical interaction, and paper class from postgres, add them to WS279 to create a "WS279.1" version of ACeDB database. Then compare WS279.1 to WS279 by comparing the SimpleMine results generated from these two versions of ACeDB. The goal is to explore the possibility of notifying users some of the new curation since the data freeze for the WS build.
 
 
 
===MicroPub user webinar on Nov 9th===
 
*Ranjana and Kimberly have conflicts--Alliance call and GO call. Anyway microPub team is running the show and they have other WormBasers to help as well.
 
 
 
===WS280 deadlines===
 
*Caltech files due for citace: Dec 15th, 2020
 
 
 
 
 
==Nov 12th, 2020==
 
=== Cynthia Kenyon tool ===
 
* developed a new tool for the worm, complete with tutorials, for analyzing gene expression data using Gene Module analysis.
 
* tool at http://genemodules.org
 
* add link outs from the gene expression widget or add in general WB tools?
 
* if we want to incorporate we need to have it updated.
 
* maybe good to add a blog post
 
 
 
=== Graphical curation tool update===
 
* We will show a live demo on the current state of the graphical curation tool
 
 
 
=== Curating to human genes in ACEDB ===
 
* Karen requested option to curate constructs with human genes
 
* Would we need to change our human genes in ACEDB? For example, migrate from Ensembl IDs to HGNC IDs as primary keys?
 
* Will discuss on next site-wide call
 
 
 
=== GAF (and GAF-like) file headers ===
 
* GO GAF files (on FTP, WS279) for WormBase now in 2.2 format with header like
 
!gaf-version: 2.2
 
!generated-by: WormBase
 
!date-generated: 2020-10-30
 
! WB annotations 00015014
 
* For files that can migrate to 2.2 format (e.g. always require column 4 qualifier) we could adopt a similar header
 
* For other files (that cannot always have a qualifier in column 4), we could stick to 2.0 format with a header like:
 
!gaf-version: 2.0
 
!generated-by: WormBase
 
!date-generated: 2020-10-30
 
* Current need is to include information about format specification, possibly in addition to other extra header content.
 
* New proposed headers:
 
!project-URL: https://wormbase.org
 
!specification-URL: https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md
 
OR
 
!specification-URL: https://wiki.wormbase.org/index.php/WormBase_gene_association_file
 
!project-release: WS279
 
* Could repurpose the Wiki page: https://wiki.wormbase.org/index.php/WormBase_gene_association_file from internal docs only to include user guide info, including how our GAF-like files deviate in format from standard GAF
 

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.