Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
(14 intermediate revisions by 2 users not shown)
Line 46: Line 46:
 
[[WormBase-Caltech_Weekly_Calls_October_2020|October]]
 
[[WormBase-Caltech_Weekly_Calls_October_2020|October]]
  
 +
[[WormBase-Caltech_Weekly_Calls_November_2020|November]]
  
−
==Nov 5th, 2020==
 
  
−
===WS279 GAF 2.0 and disease files===
+
==Dec 3rd, 2020==
−
*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 ===
+
=== Hench et al paper ===
−
*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.
+
* 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
  
−
===MicroPub user webinar on Nov 9th===
+
=== WormBase Papers and Alliance ABC - What papers to add? ===
−
*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===
+
* PubMed keyword search 'elegans' (Approve, Reject, Remove)
−
*Caltech files due for citace: Dec 15th, 2020
+
* Legacy papers from manual concise descriptions
  
  
−
==Nov 12th, 2020==
+
{| border=1 cell-padding=5 cell-spacing=10
−
=== Cynthia Kenyon tool ===
+
|-
−
* developed a new tool for the worm, complete with tutorials, for analyzing gene expression data using Gene Module analysis.
+
! PMID
−
* tool at http://genemodules.org
+
! Paper Editor Action
−
* add link outs from the gene expression widget or add in general WB tools?
+
! WBPaper ID
−
* if we want to incorporate we need to have it updated.
+
! Paper Title
−
* are they maintaining it?
+
! Species
−
* there's no RNAseq, can be outdated
+
! Primary/Not Primary
−
* maybe good to add a blog post
+
! 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
 +
| Yes
 +
| 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
 +
|-
 +
|}
  
−
=== Graphical curation tool update===
+
*/home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids - ~3300 papers
−
* We will show a live demo on the current state of the graphical curation tool
+
*/home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids - ~100 papers
  
−
=== Curating to human genes in ACEDB ===
+
*What about WormBase Parasite papers?
−
* 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
 

Revision as of 16:23, 3 December 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

November


Dec 3rd, 2020

Hench et al paper

  • 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?

  • PubMed keyword search 'elegans' (Approve, Reject, Remove)
  • Legacy papers from manual concise descriptions


PMID 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 Yes 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
  • /home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids - ~100 papers
  • What about WormBase Parasite papers?
Retrieved from "https://wiki.wormbase.org/index.php?title=WormBase-Caltech_Weekly_Calls&oldid=36098"