Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
= 2016 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2016|January]]
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_February_2016|February]]
 
  
  
  
== March 3, 2016 ==
+
= 2020 Meetings =
  
=== Sentence-level indexing ===
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
* Chris playing around with flagging sentences as positive/negative for phenotype and flagging keywords as true or false positives
 
* It may be helpful to objectify sentences and generate unambiguous, unique IDs for sentences
 
* There will likely be difficulty in unambiguously pulling out sentences from re-processed papers
 
* Best identifier would be the sentence itself
 
* Sentence 'objects' could be connected to annotations in WB
 
  
=== Proteomic datasets ===
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
* Wen wants to systematically collect proteomic datasets
 
* Many are scattered across different resources
 
* Would also help ParaSite to index similar datasets for parasites
 
* MESH terms may help identify proteomic papers
 
  
=== MOD-human disease collaboration ===
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
* FlyBase working on a shared template for curating human disease
 
* SGD, ZFIN, MGI, FlyBase, and WormBase meeting at Caltech to discuss
 
* One priority is minimizing redundancy of effort
 
* There is a common portal for human diseases in progress
 
* Should consider Monarch initiative approach
 
  
=== AddGene & WB constructs ===
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
* Karen working with AddGene to pull in worm reagents (plasmids/constructs)
 
* AddGene does want to have better linking to WormBase
 
  
=== Metabolomic data ===
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
* Can we show chemical structures for metabolites?
 
* User (M. Witting) says metabolism people will want monoisotopic masses - these masses aren't available through ChEBI at the moment and it will be a while for them to provide them.  Will find a formula and sources files for Juancarlos to implement a calculator in the OA.
 
* We already use, sync and collaborate with ChEBI
 
  
== March 10, 2016 ==
+
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
=== Adding WormBase-Parasite Paper to the Curation Pipeline (Kimberly) ===
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
*Developing new paper editor for Jane and Michael P. to approve parasite papers
+
 
*Adding species information to ALL papers; can be one or more species per paper
+
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
*Would like to then incorporate parasite papers into downstream SVM flagging pipeline and curation status form
+
 
*Species information could be used to keep curation stats clear
+
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
* We should discuss the curation and tracking of non-elegans species on the next site-wide call
+
 
* Might be best to have a separate ParaSite-specific curation status form
+
[[WormBase-Caltech_Weekly_Calls_October_2020|October]]
* We may be able to just add new columns to the curation status form, Caltech vs EBI
+
 
* Michael and Jane want to curate gene function, e.g. GO; not sure what else
+
 
 +
==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.
 +
* are they maintaining it?
 +
* there's no RNAseq, can be outdated
 +
* 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
 +
 
 +
 
 +
== Nov 19, 2020 ==
 +
 
 +
=== Webinars ===
 +
* JBrowse webinar tomorrow (Friday)
 +
** Ranjana will host; Wen will provide tech support; Daniela will collect user questions from chat in Google Doc; Chris will write staff answers to questions in Google Doc
 +
* Background slides put together for when audience is waiting
 +
* Wen will start the meeting at 9:30am Pacific; can run a test poll
 +
* Questions will be collected in Google Doc; answers can be written into the Google Doc in real time; we can use the Google Doc as a reference to assemble FAQs later
 +
 
 +
=== Alaska ===
 +
* Is Eduardo still working on it?
 +
* He replied to a user asking about Alaska
 +
* Is it still running? Maintained?
 +
* Can we tell what usage it gets?
 +
* Is it useful for the Alliance? Maybe can write it into grant?
 +
* Is it commercially viable? Maybe someone can write an SBIR grant proposal?
 +
 
 +
=== Server space ===
 +
* No new space in Chen building
 +
* Many servers will stay in a server room where they are currently
 +
* Other servers we will need to see if they can be moved to Chen
 +
* Paul may have some space for servers in his lab designated space (or his own office)
 +
* It may be possible to move some machines over to the WB space in Chen as soon as we can get a key, but may have to wait until the official move in late January

Latest revision as of 17:52, 19 November 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings



2020 Meetings

January

February

March

April

May

June

July

August

September

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.
  • are they maintaining it?
  • there's no RNAseq, can be outdated
  • 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


Nov 19, 2020

Webinars

  • JBrowse webinar tomorrow (Friday)
    • Ranjana will host; Wen will provide tech support; Daniela will collect user questions from chat in Google Doc; Chris will write staff answers to questions in Google Doc
  • Background slides put together for when audience is waiting
  • Wen will start the meeting at 9:30am Pacific; can run a test poll
  • Questions will be collected in Google Doc; answers can be written into the Google Doc in real time; we can use the Google Doc as a reference to assemble FAQs later

Alaska

  • Is Eduardo still working on it?
  • He replied to a user asking about Alaska
  • Is it still running? Maintained?
  • Can we tell what usage it gets?
  • Is it useful for the Alliance? Maybe can write it into grant?
  • Is it commercially viable? Maybe someone can write an SBIR grant proposal?

Server space

  • No new space in Chen building
  • Many servers will stay in a server room where they are currently
  • Other servers we will need to see if they can be moved to Chen
  • Paul may have some space for servers in his lab designated space (or his own office)
  • It may be possible to move some machines over to the WB space in Chen as soon as we can get a key, but may have to wait until the official move in late January