Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
= 2020 Meetings =
+
= 2021 Meetings =
 
 
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
 
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
+
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
+
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
 
  
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
+
== April 1, 2021 ==
  
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
+
=== 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_October_2020|October]]
+
All changes proposed above were approved by the group
  
[[WormBase-Caltech_Weekly_Calls_November_2020|November]]
+
=== 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
  
= 2021 Meetings =
 
== January 14th, 2021 ==
 
 
=== PubMed LinkOut to WormBase (Kimberly) ===
 
* Other databases link out from PubMed to their respective paper pages
 
* For exampel, 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)?
 
  
 +
== April 8, 2021 ==
  
 +
=== Braun server outage ===
 +
* Raymond fixed; now Spica, wobr and wobr2 are back up
  
==Dec 3rd, 2020==
+
=== Textpresso API ===
 +
* Was down yesterday affecting WormiCloud; Michael has fixed
 +
* Valerio will learn how to manage the API for the future
  
=== Hench et al paper ===
+
=== Grant opportunities ===
* Thomas Burglin would like the data from paper 00046864 to be included in WB
+
* Possibilities to apply for supplements
* They want to provide APT profiles (signal intensity along the  anterior-posterior axis over time) as images and movies (time lapse reporter expression)
+
* May 15th deadline
* They have recorded movies for 60 homeobox genes and over 85 genes in total.
+
* Druggable genome project
* 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
+
** Pharos: https://pharos.nih.gov/
 +
** could we contribute?
 +
* Visualization, tools, etc.
 +
* Automated person descriptions?
 +
* Automated descriptions for proteins, ion channels, druggable targets, etc.?
  
=== WormBase Papers and Alliance ABC - What papers to add? ===
+
=== New WS280 ONTOLOGY FTP directory ===
 +
* Changes requested here: https://github.com/WormBase/website/issues/7900
 +
* Here's the FTP URL: ftp://ftp.wormbase.org/pub/wormbase/releases/WS280/ONTOLOGY/
 +
* Known issues (Chris will report):
 +
** 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
  
* PubMed keyword search 'elegans' (Approve, Reject, Remove)
+
=== Odd characters in Postgres ===
* Legacy papers from manual concise descriptions
+
* 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
  
  
{| border=1 cell-padding=5 cell-spacing=10
+
== April 15, 2021 ==
|-
 
! PMID
 
! Paper Editor Action
 
! WBPaper ID
 
! Paper Title
 
! Species (For primary papers, species are those for which experiments are reported; does not include sequence alignments)
 
! 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
 
| No
 
|
 
|
 
|
 
|-
 
| 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
 
| Used in human manual GO curation (Protein2GO)
 
| 492 non-nematode-flagged papers in WB; not systematically associated with species, but we could do that
 
|-
 
| N/A
 
| Entered into curation database via custom script
 
| 57497
 
| The ER chaperone ENPL-1 acts outside the ER to promote insulin secretion in concert with oxidized ASNA-1.
 
| Caenorhabditis elegans
 
| Not designated
 
| Author-Person
 
| N/A
 
| Yes
 
| 2019 International Worm Meeting Abstract
 
|
 
|
 
|-
 
|}
 
  
*/home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids - ~3300 papers
+
=== Special characters in Postgres/OA ===
*/home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids - ~100 papers
+
* Juancarlos working on/proposing a plan to store UTF-8 characters in Postgres and the OA which would then get converted, at dumping, to HTML entities (e.g. α) for the ACE files
 +
* There is still a bit of cleanup needed to fix or remove special characters (not necessarily UTF-8) that apparently got munged upon copy/pasting into the OA in the past
 +
* Note: copy/paste from a PDF often works fine, but sometimes does not work as expected so manual intervention would be needed (e.g. entering Greek characters by hand in UTF-8 format)
 +
* Would copy/pasting from HTML be better than PDF?
 +
* For Person curation it would be good to be able to faithfully store and display appropriate foreign characters (e.g. Chinese characters, Danish characters, etc.)
 +
* Mangolassi script called "get_summary_characters.pl" located here: /home/postgres/work/pgpopulation/grg_generegulation/20200618_summary_characters
 +
** Juancarlos will modify script to take a data type code as an argument on the command line and return all Postgres tables (and their respective PGIDs) that have special characters, e.g.
 +
*** $ ./get_summary_characters.pl exp
 +
*** $ ./get_summary_characters.pl int
 +
*** $ ./get_summary_characters.pl grg
 +
** or could pass just the datatype + field (postgres table). e.g.
 +
*** $ ./get_summary_characters.pl pic_description
 +
** Juancarlos will email everyone once it's ready.  It's ready, email sent.  Script is at /home/postgres/work/pgpopulation/oa_general/20210411_unicode_html/get_summary_characters.pl  Symlink this to your directory and run it from there, it will create files in the directory you are at when running it.
 +
* Action items:
 +
** Juancarlos will update the "get_summary_characters.pl" script as described above
 +
** Curators should use the "get_summary_characters.pl" to look for (potentially) bad characters in their OAs/Postgres tables
 +
** Need to perform bulk (automated) replacement of existing HTML entities into corresponding UTF-8 characters
 +
** Curators will need to work with Juancarlos for each OA to modify the dumper
 +
** Juancarlos will write (or append to existing) Postgres/OA dumping scripts to:
 +
*** 1) Convert UTF-8 characters to HTML entities in ACE files
 +
*** 2) Convert special quote and hyphen characters into simple versions that don't need special handling
  
*What about WormBase Parasite papers?
+
=== CeNGEN pictures ===
 +
* Model change went in to accommodate images from the CeNGEN project
 +
* Want gene page images for CeNGEN data; have the specifications for such images been worked out? Maybe not yet
 +
* Raymond and Daniela will work with data producers to acquire images when ready
  
 +
=== Supplement opportunities ===
 +
* Money available for software development to "harden" existing software
 +
* Might be possible to make Eduardo's single cell analysis tools more sustainable
 +
* Could make WormiCloud adapted to Alliance?
 +
* Put Noctua on more stable production footing? (GO cannot apply as they are in final year of existing grant)
  
== December 17, 2020 ==
+
=== Student project for Textpresso ===
* HGNC IDs/names/etc. in OA
+
* Create tool to allow user to submit text and return a list of similar papers
* What shows up in autocomplete? What shows up in term info?
+
* Use cases:
* Juancarlos will need to get curator preferences for autocomplete list and term info list.
+
** curator wants an alert to find papers similar to what they've curated
* Wen will update the Alliance Simplemine to provide updated info to Postgres/OA
+
** look for potential reviewers of a paper based on similar text content
** "AGR Gene ID" and "AGR Gene Name" will be changed to "Gene ID", "Gene Name", "Gene Symbol"
 

Latest revision as of 19:34, 15 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


April 15, 2021

Special characters in Postgres/OA

  • Juancarlos working on/proposing a plan to store UTF-8 characters in Postgres and the OA which would then get converted, at dumping, to HTML entities (e.g. α) for the ACE files
  • There is still a bit of cleanup needed to fix or remove special characters (not necessarily UTF-8) that apparently got munged upon copy/pasting into the OA in the past
  • Note: copy/paste from a PDF often works fine, but sometimes does not work as expected so manual intervention would be needed (e.g. entering Greek characters by hand in UTF-8 format)
  • Would copy/pasting from HTML be better than PDF?
  • For Person curation it would be good to be able to faithfully store and display appropriate foreign characters (e.g. Chinese characters, Danish characters, etc.)
  • Mangolassi script called "get_summary_characters.pl" located here: /home/postgres/work/pgpopulation/grg_generegulation/20200618_summary_characters
    • Juancarlos will modify script to take a data type code as an argument on the command line and return all Postgres tables (and their respective PGIDs) that have special characters, e.g.
      • $ ./get_summary_characters.pl exp
      • $ ./get_summary_characters.pl int
      • $ ./get_summary_characters.pl grg
    • or could pass just the datatype + field (postgres table). e.g.
      • $ ./get_summary_characters.pl pic_description
    • Juancarlos will email everyone once it's ready. It's ready, email sent. Script is at /home/postgres/work/pgpopulation/oa_general/20210411_unicode_html/get_summary_characters.pl Symlink this to your directory and run it from there, it will create files in the directory you are at when running it.
  • Action items:
    • Juancarlos will update the "get_summary_characters.pl" script as described above
    • Curators should use the "get_summary_characters.pl" to look for (potentially) bad characters in their OAs/Postgres tables
    • Need to perform bulk (automated) replacement of existing HTML entities into corresponding UTF-8 characters
    • Curators will need to work with Juancarlos for each OA to modify the dumper
    • Juancarlos will write (or append to existing) Postgres/OA dumping scripts to:
      • 1) Convert UTF-8 characters to HTML entities in ACE files
      • 2) Convert special quote and hyphen characters into simple versions that don't need special handling

CeNGEN pictures

  • Model change went in to accommodate images from the CeNGEN project
  • Want gene page images for CeNGEN data; have the specifications for such images been worked out? Maybe not yet
  • Raymond and Daniela will work with data producers to acquire images when ready

Supplement opportunities

  • Money available for software development to "harden" existing software
  • Might be possible to make Eduardo's single cell analysis tools more sustainable
  • Could make WormiCloud adapted to Alliance?
  • Put Noctua on more stable production footing? (GO cannot apply as they are in final year of existing grant)

Student project for Textpresso

  • Create tool to allow user to submit text and return a list of similar papers
  • Use cases:
    • curator wants an alert to find papers similar to what they've curated
    • look for potential reviewers of a paper based on similar text content