Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
(294 intermediate revisions by 8 users not shown)
Line 21: Line 21:
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
 +
= 2021 Meetings =
  
 +
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
= 2020 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
+
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
+
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
+
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
+
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
  
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
+
[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
  
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
+
[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
  
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
 
  
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
+
== September 2, 2021 ==
  
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
+
1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking<br>
 +
Needed for
 +
*AFP community curation
 +
*microPublication author tracking for all species
 +
*stub of person Alliance model already exists made by Adam http://dev.alliancegenome.org:11223/redoc#tag/Person
  
[[WormBase-Caltech_Weekly_Calls_October_2020|October]]
+
Problems:
 +
*this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
 +
*need to do this outside of Alliance
  
[[WormBase-Caltech_Weekly_Calls_November_2020|November]]
+
Action
 +
*Paul talks to zfin about interest in person pages
 +
*Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
 +
*Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite
  
 +
Will do
 +
*create biolink model based on current WB postgres/Caltech model
 +
*Adam will add tables when we have them
  
==Dec 3rd, 2020==
+
2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.
  
=== Hench et al paper ===
+
== September 16, 2021 ==
* Thomas Burglin would like the data from paper 00046864 to be included in WB
 
* They want to provide APT profiles (signal intensity along the  anterior-posterior axis over time) as images and movies (time lapse reporter expression)
 
* They have recorded movies for 60 homeobox genes and over 85 genes in total.
 
* If we decide to import the collection, movies, images, and description could be displayed as the collection from Murray: https://wormbase.org/species/all/expr_pattern/Expr10431#012--10
 
  
=== WormBase Papers and Alliance ABC - What papers to add? ===
+
1. CeNGEN enriched genes per cell type data targeted for WS283.
  
* PubMed keyword search 'elegans' (Approve, Reject, Remove)
+
2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump.  Juancarlos changed the OA population script script to exclude those.
* Legacy papers from manual concise descriptions
 
  
 +
== September 23, 2021 ==
  
{| border=1 cell-padding=5 cell-spacing=10
+
1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?
|-
+
* Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
! PMID
+
* Update the WB page on citing WormBase
! Paper Editor Action
 
! WBPaper ID
 
! Paper Title
 
! Species
 
! Primary/Not Primary
 
! Other Paper Editor Flags
 
! Any SVM Positives
 
! Add to ABC
 
! Comments (1)
 
! Comments (2)
 
! Comments (3)
 
|-
 
| 31761535
 
| Approve
 
| 58971
 
| The Hyaluronidase, TMEM2, Promotes ER Homeostasis and Longevity Independent of the UPR ER
 
| Homo sapiens, Caenorhabditis elegans
 
| Primary
 
| Author-Person
 
| Catalytic Activity; Genetic Interactions; Gene Regulation; New Mutant Phenotype; Overexpression Phenotype; RNAi Phenotype
 
| Yes
 
|
 
|
 
|
 
|-
 
| 31868179
 
| Approve
 
| 58999
 
| Measuring the Effects of Bacteria and Chemicals on the Intestinal Permeability of Caenorhabditis elegans
 
| Caenorhabditis elegans
 
| Primary
 
| Author-Person
 
| None
 
| Yes
 
|
 
|
 
|
 
|-
 
| 16919905
 
| Approve
 
| 28426
 
| The trifecta of aging in Caenorhabditis elegans.
 
| Caenorhabditis elegans
 
| Not-primary
 
| Author-Person
 
| N/A
 
| Yes
 
|
 
|
 
|
 
|-
 
| 28744338
 
| Approve
 
| 51561
 
| Role of Kallistatin Treatment in Aging and Cancer by Modulating miR-34a and miR-21 Expression.
 
| Caenorhabditis elegans, Homo sapiens (human, humans), Mus musculus (mice, mouse), Rattus norvegicus (rats)
 
| Not-primary
 
| Author-Person
 
| N/A
 
| Yes
 
|
 
|
 
|
 
|-
 
| 31875562
 
| Reject
 
| None
 
| Intracellular Vesicle Fusion Requires a Membrane-Destabilizing Peptide Located at the Juxtamembrane Region of the v-SNARE
 
| Mus musculus (mouse), Rattus norvegicus (rat)
 
| Primary
 
| N/A
 
| N/A
 
| Not from WormBase, but if added from another group we'd want to indicate that it doesn't have C. elegans experimental data?
 
| Paper shows partial sequence alignment including C. elegans snb-1 in Figure 1A; other species in alignment include M. musculus, H. sapiens, X. leavis, and D. melanogaster
 
| PubMed indexes proteins and their respective species shown in sequence alignments
 
|
 
|-
 
| 31569547
 
| Reject
 
| None
 
| Mapping the Biotransformation of Coumarins through Filamentous Fungi
 
| Cunninghamella elegans, Aspergillus brasiliensis
 
| Primary
 
| N/A
 
| N/A
 
|
 
|
 
|
 
|
 
|-
 
| 10625658
 
| Entry into WB pre-dated current paper editor
 
| 12789
 
| Both PCE-1/RX and OTX/CRX interactions are necessary for photoreceptor-specific gene expression
 
| Homo sapiens (human), Mus musculus (mouse, mice, murine), Rattus norvegicus (rat, rats), Bos taurus(bovine)
 
| Primary
 
| non-nematode; Author-Person (pre-dated current Author-Person curation criteria)
 
| N/A
 
| Yes??
 
| Used in legacy manual ceh-8 gene description (how many of these papers were used)
 
| Used in human manual GO curation (Protein2GO)
 
| 492 non-nematode papers; not systematically associated with species
 
|-
 
|}
 
  
*/home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids - ~3300 papers
+
2. CeNGEN data on Gene page for WS282. A short blog to highlight.
*/home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids - ~100 papers
 
  
*What about WormBase Parasite papers?
+
3. Server room in Braun power down for no apparent reason. Reset.

Latest revision as of 18:17, 23 September 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

February

March

April

May

June

July

August


September 2, 2021

1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking
Needed for

Problems:

  • this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
  • need to do this outside of Alliance

Action

  • Paul talks to zfin about interest in person pages
  • Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
  • Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite

Will do

  • create biolink model based on current WB postgres/Caltech model
  • Adam will add tables when we have them

2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.

September 16, 2021

1. CeNGEN enriched genes per cell type data targeted for WS283.

2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump. Juancarlos changed the OA population script script to exclude those.

September 23, 2021

1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?

  • Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
  • Update the WB page on citing WormBase

2. CeNGEN data on Gene page for WS282. A short blog to highlight.

3. Server room in Braun power down for no apparent reason. Reset.