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 =
  
 +
[[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_March_2020|March]]
+
== April 1, 2021 ==
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
+
=== Antibodies ===
 +
* Alignment of the antibody class to Alliance:
 +
** Propose to move possible_pseudonym (192) and Other_animal (37) to remarks. Those tags are not currently used for curation.
 +
*** Other animal is sometimes used for older annotations, e.g. authors say that the antibodies were raised both  in rats and rabbits. Standard practice would create 2 records, one for the rat antibody and one for the rabbit.
 +
*** Possible pseudonym was used when  a curator was not able to unambiguously assign a previous antibody to a record. (we have a Other name -synonym- tag to capture unambiguous ones). When moving to remarks we can keep a controlled vocabulary for easy future parsing, e.g. “possible_pseudonym:”
 +
** Antigen field: currently separated into Protein, peptide, and other_antigen (e.g.: homogenate of early C.elegans embryos, sperm). Propose to use just one antigen field to capture antigen info.
  
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
+
All changes proposed above were approved by the group
  
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
+
=== textpress-dev clean up ===
 +
* Michael has asked curators to assess what they have on textpresso-dev as it will not be around forever :-(
 +
* is it okay to transfer data and files we want to keep to tazendra? and then to our own individual machines?
 +
* Direct access may be possible via Caltech VPN
 +
* Do we want to move content to AWS? May be complicated; it is still easy and cheap to maintain local file systems/machines
  
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
+
=== Braun servers ===
 +
* 3 servers stored in Braun server room; is there a new contact person for accessing these servers?
 +
* Mike Miranda replacement just getting settled; Paul will find out who is managing the server room and let Raymond know
  
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
+
=== Citace upload ===
 +
* Next Friday, April 9th, by end of the day
 +
* Wen will contact Paul Davis for the frozen WS280 models file
  
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
 
  
[[WormBase-Caltech_Weekly_Calls_October_2020|October]]
+
== April 8, 2021 ==
  
[[WormBase-Caltech_Weekly_Calls_November_2020|November]]
+
=== Braun server outage ===
 +
* Raymond fixed; now Spica, wobr and wobr2 are back up
  
 +
=== Textpresso API ===
 +
* Was down yesterday affecting WormiCloud; Michael has fixed
 +
* Valerio will learn how to manage the API for the future
  
==Dec 3rd, 2020==
+
=== Grant opportunities ===
 +
* Possibilities to apply for supplements
 +
* May 15th deadline
 +
* Druggable genome project
 +
** Pharos: https://pharos.nih.gov/
 +
** could we contribute?
 +
* Visualization, tools, etc.
 +
* Automated person descriptions?
 +
* Automated descriptions for proteins, ion channels, druggable targets, etc.?
  
=== Hench et al paper ===
+
=== New WS280 ONTOLOGY FTP directory ===
* Thomas Burglin would like the data from paper 00046864 to be included in WB
+
* Changes requested here: https://github.com/WormBase/website/issues/7900
* They want to provide APT profiles (signal intensity along the  anterior-posterior axis over time) as images and movies (time lapse reporter expression)
+
* Here's the FTP URL: ftp://ftp.wormbase.org/pub/wormbase/releases/WS280/ONTOLOGY/
* They have recorded movies for 60 homeobox genes and over 85 genes in total.  
+
* Known issues (Chris will report):
* 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
+
** Ontology files are provided as ".gaf" in addition to ".obo"; we need to remove the ".gaf" OBO files
 +
** Some files are duplicated and/or have inappropriate file extensions
  
=== WormBase Papers and Alliance ABC - What papers to add? ===
+
=== Odd characters in Postgres ===
 
+
* Daniela and Juancarlos discovered some errors with respect to special characters pasted into the OA
* PubMed keyword search 'elegans' (Approve, Reject, Remove)
+
* Daniela would like to automatically pull in micropublication text (e.g. figure captions) into Postgres
* Legacy papers from manual concise descriptions
+
* We would need an automated way to convert special characters, like degree symbols ° into html unicode \&deg\;
 
+
* Juancarlos and Valerio will look into possibly switching from a Perl module to a Python module to handle special characters
 
 
{| border=1 cell-padding=5 cell-spacing=10
 
|-
 
! 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
 
| 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
 
*/home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids - ~100 papers
 
 
 
*What about WormBase Parasite papers?
 

Latest revision as of 19:05, 8 April 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 1, 2021

Antibodies

  • Alignment of the antibody class to Alliance:
    • Propose to move possible_pseudonym (192) and Other_animal (37) to remarks. Those tags are not currently used for curation.
      • Other animal is sometimes used for older annotations, e.g. authors say that the antibodies were raised both in rats and rabbits. Standard practice would create 2 records, one for the rat antibody and one for the rabbit.
      • Possible pseudonym was used when a curator was not able to unambiguously assign a previous antibody to a record. (we have a Other name -synonym- tag to capture unambiguous ones). When moving to remarks we can keep a controlled vocabulary for easy future parsing, e.g. “possible_pseudonym:”
    • Antigen field: currently separated into Protein, peptide, and other_antigen (e.g.: homogenate of early C.elegans embryos, sperm). Propose to use just one antigen field to capture antigen info.

All changes proposed above were approved by the group

textpress-dev clean up

  • Michael has asked curators to assess what they have on textpresso-dev as it will not be around forever :-(
  • is it okay to transfer data and files we want to keep to tazendra? and then to our own individual machines?
  • Direct access may be possible via Caltech VPN
  • Do we want to move content to AWS? May be complicated; it is still easy and cheap to maintain local file systems/machines

Braun servers

  • 3 servers stored in Braun server room; is there a new contact person for accessing these servers?
  • Mike Miranda replacement just getting settled; Paul will find out who is managing the server room and let Raymond know

Citace upload

  • Next Friday, April 9th, by end of the day
  • Wen will contact Paul Davis for the frozen WS280 models file


April 8, 2021

Braun server outage

  • Raymond fixed; now Spica, wobr and wobr2 are back up

Textpresso API

  • Was down yesterday affecting WormiCloud; Michael has fixed
  • Valerio will learn how to manage the API for the future

Grant opportunities

  • Possibilities to apply for supplements
  • May 15th deadline
  • Druggable genome project
  • Visualization, tools, etc.
  • Automated person descriptions?
  • Automated descriptions for proteins, ion channels, druggable targets, etc.?

New WS280 ONTOLOGY FTP directory

Odd characters in Postgres

  • Daniela and Juancarlos discovered some errors with respect to special characters pasted into the OA
  • Daniela would like to automatically pull in micropublication text (e.g. figure captions) into Postgres
  • We would need an automated way to convert special characters, like degree symbols ° into html unicode \&deg\;
  • Juancarlos and Valerio will look into possibly switching from a Perl module to a Python module to handle special characters