Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
 +
= 2021 Meetings =
  
= 2019 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
+
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
 
  
== April 4, 2019 ==
+
== April 1, 2021 ==
  
=== Paul's Biocuration Keynote ===
+
=== Antibodies ===
* At Biocuration keynote, Paul S. will talk about web forms, including Author First Pass form
+
* Alignment of the antibody class to Alliance:
* Can someone send Paul the latest AFP form location and documentation
+
** Propose to move possible_pseudonym (192) and Other_animal (37) to remarks. Those tags are not currently used for curation.
* Will also discuss the future of micropublications
+
*** 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.
  
=== IWM Swag ===
+
All changes proposed above were approved by the group
* Stickers vs. screen cloths
 
* Daniela had contacted Jessie to make new graphic; she's interested, but do we still need a new graphic?
 
* Plan was to make ~2,000 screen cloths (4x4 inch or 6x6 inch?)
 
** As for design would be nice to have new design
 
** Gary had made cartoon for community curation (proposal might be offensive to some)
 
* Include water bottles for special contributors? In addition to shot glasses?
 
* Turn around time? ~ 1 month; designs done in April; submit request by mid-May at latest
 
* Worm in apple graphic? Dragon worm cartooon? Maybe some variation on it?
 
** We can ask Jessie if she can draw up a couple quick sketch ideas
 
  
=== Collaborators tool ===
+
=== textpress-dev clean up ===
* Juancarlos worked on a tool to extract WBPerson collaborators
+
* Michael has asked curators to assess what they have on textpresso-dev as it will not be around forever :-(
* WB staff generally had ~100 collaborators, Paul S has 670
+
* is it okay to transfer data and files we want to keep to tazendra? and then to our own individual machines?
* Distinguish between collaborators and coauthors? Manual (self reported) vs. automatic associations?
+
* Direct access may be possible via Caltech VPN
* Make modification to ACEDB model?
+
* Do we want to move content to AWS? May be complicated; it is still easy and cheap to maintain local file systems/machines
* Maybe 'collaborators' should be restricted to the laboratory level?
 
  
 +
=== 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
  
== April 11, 2019 ==
+
=== Citace upload ===
 +
* Next Friday, April 9th, by end of the day
 +
* Wen will contact Paul Davis for the frozen WS280 models file
  
=== Canadian C. elegans meeting ===
 
the "Canadian C. elegans meeting” that will follow the 2019 annual conference of the Canadian Society for Molecular Biosciences. The CSMB conference is held at Université de Montréal on June 2-5, 2019 and will focus on Model systems in cancer research (https://www.fourwav.es/view/1174/info/). The C. elegans conference will be held at the CHUM Research Center in downtown Montréal on Thursday June 6, 2019, and will offer opportunities for both oral and poster presentations. The schedule is not finalized yet but it should start around 8:30am and end around 6pm, followed by an apero in a nearby pub. The costs of registrations will depend on the number of participants but will be between 35 and 50 $ per person (it will cover the costs of lunch, coffee break and logistics).
 
* Karen may be able to go; she will contact Kimberly for any pertinent information
 
  
=== Feedback from small RNA meeting April 3-5, 2019 ===
+
== April 8, 2021 ==
* Future meeting invitations and summer workshop?
 
* Dustin Updike - in Maine - interested in running a summer workshop for students
 
** Maybe one or two week-long (5-10 days); unconfirmed
 
** Wen followed up with him: WormBase curator could attend and present on JBrowse, scientific writing, micropublications
 
** Hopefully they can cover travel costs of WB curators
 
** Dustin will get back to us about details as they emerge
 
* Julie Claycomb interested in having WB curator at Toronto's worm meeting
 
  
=== New SVM approach ===
+
=== Braun server outage ===
* Michael will send around paper list with new and old results in the same file
+
* Raymond fixed; now Spica, wobr and wobr2 are back up
* Raymond looked at his data types; at first glance thinks there may be quite a few false positives and false negatives
 
* Can represent new SVM scores as histograms, presumably produce Gaussian curves, can we accept the overlap in distribution tails?
 
* Old thresholds were not necessarily gold standards, probably somewhat arbitrarily chosen initially; we can use the old metrics to roughly choose a new set of corresponding thresholds for the new SVM scores
 
  
=== IWM workshop ===
+
=== Textpresso API ===
* On Saturday of meeting
+
* Was down yesterday affecting WormiCloud; Michael has fixed
 +
* Valerio will learn how to manage the API for the future
  
=== NIH workshop on Trustworthiness ===
+
=== Grant opportunities ===
* Chris attended on Monday and Tuesday
+
* Possibilities to apply for supplements
* Not quite clear that there is or will be any mandate from funders; just encouragement
+
* May 15th deadline
* FAIR data and TRUST-worthy repositories
+
* Druggable genome project
** FAIR = Findable, Accessible, Interoperable, Reusable
+
** Pharos: https://pharos.nih.gov/
** TRUST = Transparency, Responsibility, User community, Sustainability, Technology
+
** could we contribute?
* Chris will review briefly at next site-wide call
+
* Visualization, tools, etc.
* Karen: This is something the data commons really wants
+
* Automated person descriptions?
** Maybe just need to make sure that the Alliance meets these requirements going forward, not so much for WormBase (?)
+
* Automated descriptions for proteins, ion channels, druggable targets, etc.?
  
 +
=== 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
  
== April 18, 2019 ==
+
=== 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
  
=== IWM swag ===
 
* Stickers, screen cloths?
 
* Jessie's design(s)?
 
* Daniel reaching out to Caltech security who has nice screen cloths
 
* Print list of WormBase tools or user guide on cloth (one side; logo on the other?)?
 
* Will get quote (maybe ≤$1 per cloth?)
 
  
=== Life stage and anatomy ontologies ===
+
== April 15, 2021 ==
* Each ontology now has an ODK GitHub repository (thanks Nico!):
 
** Anatomy ontology: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology
 
** Life stage ontology: https://github.com/obophenotype/c-elegans-development-ontology
 
* We will perform a round of comparisons between the original OBO files and the ODK-generated OBO files
 
* Will follow up with quality control fixes (e.g. duplicate or missing definitions)
 
  
=== Biocurator meeting ===
+
=== Special characters in Postgres/OA ===
* EuroPMC - have access to 80-90% full text of open access 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
** Would be good for WormBase & Textpresso to work with them
+
* 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
* Lots of groups working together on pathways
+
* 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)
** SwissProt, GO, Reactome
+
* Would copy/pasting from HTML be better than PDF?
* SwissLipids
+
* 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.)
** Metabolomics database pilot
+
* Mangolassi script called "get_summary_characters.pl" located here: /home/postgres/work/pgpopulation/grg_generegulation/20200618_summary_characters
** https://www.swisslipids.org/#/
+
** 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.
* RHEA to replace KEGG (which is well curated but not (no longer) open)
+
*** $ ./get_summary_characters.pl exp
** https://www.rhea-db.org/home
+
*** $ ./get_summary_characters.pl int
* Author First Pass poster presented (won 3rd place out of ~200 posters!)
+
*** $ ./get_summary_characters.pl grg
** Analogous to FlyBase's 'Fast Track Your Paper' (FTYP)
+
** or could pass just the datatype + field (postgres table). e.g.
** FTYP does not extract entities
+
*** $ ./get_summary_characters.pl pic_description
** Should evolve into an Alliance pipeline
+
** 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.
* Data visualization talk (Sean O'Donoghue)
+
* Action items:
** Don't use rainbow heatmaps
+
** Juancarlos will update the "get_summary_characters.pl" script as described above
** Oval representation of time course
+
** Curators should use the "get_summary_characters.pl" to look for (potentially) bad characters in their OAs/Postgres tables
** Valerio spoke to him; D3 is now a standard library for data visualization
+
** 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
  
=== GO CAM ===
+
=== CeNGEN pictures ===
* Could try to generate automated descriptions using GO CAM models
+
* Model change went in to accommodate images from the CeNGEN project
* Group is trying to come up with model naming scheme
+
* 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
  
=== Gene Expression Omnibus (GEO) ===
+
=== Supplement opportunities ===
* GEO data has user submission forms that refer to life stages, anatomy but don't map to WB unique IDs
+
* Money available for software development to "harden" existing software
* Maybe we can ask GEO to update their data submission forms to use standard IDs
+
* Might be possible to make Eduardo's single cell analysis tools more sustainable
* Would help reduce amount of effort required by WB to curate the entries after submission to GEO
+
* Could make WormiCloud adapted to Alliance?
* GEO forms apply to all species; controlled vocabularies/ontologies could be submitted to GEO for incorporation into their forms
+
* Put Noctua on more stable production footing? (GO cannot apply as they are in final year of existing grant)
  
=== RNA-Seq data processing pipeline (Alaska) ===
+
=== Student project for Textpresso ===
* Raymond, Juancarlos, David Angeles and Joseph developed automated data processing pipeline
+
* Create tool to allow user to submit text and return a list of similar papers
* http://alaska.caltech.edu/
+
* Use cases:
* Maps reads to the genome; will it return FPKM values for each gene?
+
** 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
 
 
== April 25, 2019 ==
 
 
 
=== WormBase plans for coming year ===
 
* Jae
 
** help develop better usability of data and tools for expression and regulation
 
** Venn diagrams
 
** Get more up to date on protein-DNA and protein-RNA interactions, may distinguish small scale from large scale
 
** GO CAM curation, once there are defined best practices for editing with Noctua
 
* Kimberly
 
** Migration of all manual GO annotations to Noctua as GO CAM models; Jae may want to wait until the migration is done (aiming for mid-summer)
 
*** Will write rules for converting individual simple annotations and complex annotations (with LEGO extensions) into GO-CAM models
 
** Will continue to develop GO CAM models and tools to help/expedite GO CAM model development
 
*** Will work with developers to create next generation of annotation forms; some more table-based input forms
 
*** Annotation review tool: Once annotations are in, this will allow for efficient annotation search and editing
 
*** Will continue to work on defining best practices for Noctua usage
 
** Will keep working on developing the gene ontology
 
* Ranjana
 
** Gene descriptions: need to bring in pathway data; processes alone are insufficient; will try to use GO CAM models (proof of concept)
 
*** Paul S: would be good to identify low information genes for curation priorities
 
*** Can include information about relevant chemicals
 
** Human disease curation: WB disease data into the Alliance
 
*** Improved text-mining approach to identify disease model papers
 
*** Paul S: May want to work on pathways/GO-CAM models for disease genes
 
* Wen
 
** Proteomics curation, tool development
 
*** Work with Hinxton to curate proteomics data at Caltech
 
*** 50 existing datasets
 
*** Common follow up to RNA Seq experiments
 
*** Jae: will we handle single-cell proteomics? Wen: Can consider part of sample condition, and include with all other proteomics data
 
** Expression clusters - will focus on 'high quality' papers, i.e. useful to community; some have poor metadata and authors don't respond to emails
 
** Outreach - will explore possibility of having local institutes invite WormBase staff to give talks (pay travel costs?); coincide with meetings?
 
*** Northwest worm meeting in Seattle? Chicago worm meeting?
 
*** Bar Harbor tutorial this summer; good precedent/model for future visits to other institutes?
 
** RNA Seq, don't want to step on Hinxton's toes WRT RNA-seq curation
 
* Raymond
 
** Focused cell function curation; want to use Noctua, but not sure we can use all relevant (WB-specific) ontologies in Noctua
 
** Are supported relations in Noctua good enough for this purpose? May need development
 
** Re-working the anatomy ontology; work on logical definitions; e.g. how do we define a single cell type?
 
* Marie Claire
 
** Finishing a micropublication on a GO CAM model; continuing to work with Noctua and improve usage
 
* Daniela
 
** Gene expression - want to attempt to automate expression curation; using AFP-like pipelines and other automation
 
*** ~150 expression pattern papers coming in every two months; many are reassessing expression using CRISPR constructs
 
*** Wen: focus on genes whose expression have never been studied?
 
*** Will still do manual steps of curation pipeline, but would begin to automate certain steps of curation pipeline
 
*** Complex patterns are difficult to automate
 
** Micropublication, Wen: is there anything else we can do to help?
 
*** Daniela: Trial attempts to submit a paper to test and provide feedback on submission pipeline
 
*** Will continue to develop methods to calculate metrics and citation indices, etc.
 
* Chris
 
** Will continue with mass email and community curation pipeline
 
*** Want to evaluate existing issues and how to improve efficiency and minimize technical and submission errors
 
** Will continue working on relevant sentence detection for phenotype, maybe expand to genetic interactions
 
** Will continue to develop phenotype ontology and alignment with other phenotype ontologies; patternization and logical definitions
 
** Will also work on life stage and anatomy ontologies with Raymond
 
** Paul S: maybe we can present authors with predicted genetic interactions and ask for confirmation of binary interactions which can then feed into GO-CAM models and pathway curation; can stick to simple binary associations for now, forgoing details like interaction type and alleles etc.
 
* Gary
 
** Continue working on phenotype ontology
 
** Prioritizing genes that don't have phenotype info; working with Juancarlos to identify papers that may have high value, novel annotations
 
* Juancarlos
 
** General tool maintenance and development
 
** Working with Ranjana and Valerio to work on automated gene description tools: React forms for curators to do QC check, using filters and search options
 
 
 
=== Screen cloths for IWM swag ===
 
* Daniel got quotes
 
* Give feedback on style
 
* Maybe use the cartoon (Dick & Jane) for community curators and tool menu for general meeting participants
 
* Will try to order next week
 

Latest revision as of 19:34, 15 April 2021

Previous Years

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2011 Meetings

2012 Meetings

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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