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
  
 +
=== 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
  
== June 4, 2020 ==
+
=== Braun servers ===
 
+
* 3 servers stored in Braun server room; is there a new contact person for accessing these servers?
=== Citace (tentative) upload ===
+
* Mike Miranda replacement just getting settled; Paul will find out who is managing the server room and let Raymond know
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
 
* Citace upload to Hinxton on Friday, July 10th
 
 
 
=== Caltech reopening ===
 
* Paul looking to get plan approved
 
* People that want to come to campus need to watch training video
 
* Masks available in Paul's lab
 
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
 
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
 
* Need to coordinate, maybe make a Google calendar to do so (also Slack)
 
* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
 
* Also, need to submit who you were in contact with for contact tracing
 
* Form is used all week, and hold on to it until asked to be submitted
 
* If someone goes in to the office, they could print several forms for people to pick up in WB offices
 
 
 
=== Nameserver ===
 
* Nameserver was down
 
* CIT curators would still like to have a single form to interact with
 
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
 
* Still putting genotype and all info for a strain in the reason/why field in the nameserver
 
* We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
 
* Hinxton is pulling in CGC strains, how often?
 
* Caltech could possibly get a block of IDs
 
 
 
=== Alliance SimpleMine ===
 
* Any updates? 3.1 feature freeze is tomorrow
 
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
 
 
 
 
 
== June 11, 2020 ==
 
 
 
=== Name Service ===
 
* Testing site now up; linked to Mangolassi
 
* CGI from Juancarlos not accepting all characters, including double quotes like "
 
* Example submission that fails via CGI
 
WBPaper000XXXX; genotype: blah::' " ` / < > [ ] { } ? , . ( ) * ^ & % $ # @ ! \ | &alpha; &beta; Ω ≈ µ ≤ ≥ ÷ æ … ˚ ∆ ∂ ß œ ∑ † ¥ ¨ ü i î ø π “  ‘ « • – ≠ Å ´ ∏ » ± — ‚ °
 
* Juancarlos will look into and try to fix
 
 
 
=== Alliance Literature group ===
 
* Textpresso vs. OntoMate vs. PubMed
 
* Still some confusion about what the different tasks can be performed in each tool
 
* Working on collecting different use cases on spreadsheet
 
* Sentence-based search is big strength of Textpresso
 
* At latest meeting performed some large searches for OntoMate and Textpresso
 
* Literature acquisition: still needs work
 
** Using SVM vs. Textpresso search to find relevant papers
 
** Species based SVM? Currently use string matching to derive different corpora
 
** Finding genes and determining which species those genes belong to?
 
 
 
=== Alliance priorities? ===
 
* Transcription regulatory networks
 
* Interactions can focus on network viewer eventually
 
** May want different versions/flavors of interaction viewers
 
** May also want to work closely with GO and GO-CAMs
 
* Gene descriptions can focus on information poor genes, protein domains, etc.
 
 
 
=== Sandbox visual cues ===
 
* Juancarlos and Daniela will discuss ways to provide visual cues that a curator is on a sandbox form (on Mangolassi) vs live form (on Tazendra)
 
* AFP and Micropub dev sites have indicators
 
* Could play with changing the background color? Maybe too hard to look at?
 
* Change the color of the title of the form, e.g. the OA?
 
* Will add red text "Development Site" at top of the OA form
 
 
 
=== Evidence Code Ontology ===
 
* Kimberly and Juancarlos have worked on a parser
 
* Will load into ACEDB soon
 
 
 
 
 
== June 18, 2020 ==
 
 
 
=== Undergrad phenotype submissions ===
 
* Chris gave presentation to Lina Dahlberg's class about community phenotype curation
 
* Class took survey about experience with presentation and experience trying to curate worm phenotypes
 
** Survey results: https://www.dropbox.com/s/00cit5aitv8yu27/Dahlberg_class_survey_results.xlsx?dl=0
 
** Some students didn't benefit, but most did; nice feedback!
 
** Lina intends to publish/micropublish the survey results so please don't share
 
* Since April 24, the class has submitted 171 annotations from 23 papers (some redundant and some still under review)
 
 
 
=== Special characters in OA/Postgres ===
 
* There are many special characters in free text entries in the OA; probably all from copy-pasting directly from PDF
 
* In some cases it seems the special characters cause problems for downstream scripts (e.g. FTP interactions file generator)
 
* It would probably be good to script the replacement of special characters with their appropriate simple characters or encoded characters
 
* Juancarlos wrote Perl script on Mangolassi at:
 
** /home/postgres/work/pgpopulation/grg_generegulation/20200618_summary_characters/get_summary_characters.pl
 
** Will find bad characters and their pgids for a given Postgres table
 
** Will find bad data and their pgids for the same table
 
** People can query their data tables for these characters
 
* Chris & Wen will work on compiling a list of bad characters that tend to come up
 
  
 
=== Citace upload ===
 
=== Citace upload ===
* July 10th citace-to-Hinxton upload
+
* Next Friday, April 9th, by end of the day
* July 7th citace upload, but Wen will be on vacation so will upload to Wen on Tuesday, June 30th
+
* Wen will contact Paul Davis for the frozen WS280 models file
  
  
== June 25, 2020 ==
+
== April 8, 2021 ==
  
=== Caltech Summer Student ===
+
=== Braun server outage ===
* Paul has new summer student
+
* Raymond fixed; now Spica, wobr and wobr2 are back up
** Molecular lesion curation, maybe
 
** Are early stops more or less likely to be null mutations?
 
** Alleles are flagged as null in WB in the context of phenotypes
 
** Would be good to query Postgres for null alleles and work from there
 
* Fernando
 
** Anatomy function
 
** GO curation? Curating transcription factors?
 
*** Checking for consistent curation
 
  
=== Worm Community Diversity Meeting ===
+
=== Textpresso API ===
* Organized by Ahna Skop and Dana Miller
+
* Was down yesterday affecting WormiCloud; Michael has fixed
* Invite posted on Facebook "C. elegans Researchers" group
+
* Valerio will learn how to manage the API for the future
* Two meetings held: one Thursday (June 18th), one Friday (June 19th)
 
* Chris attended last Friday (June 19th)
 
* Worm Board looking to take input and ideas from this meeting and incorporate into meetings and events
 
* One idea was to document and track outreach efforts and what people have learned from them and organize them in a central location, maybe WormBase or Worm Community Forum
 
* Also, there was a suggestion to have a tool that could inform potential students of worm labs in their respective local area
 
** Ask Todd; he used to have a map of researchers; Todd had asked Cecilia to curate lab location and institution
 
* Person and Laboratory addresses in ACEDB have a different format, so looking to reconcile
 
* Do we know how many labs are still viable? Check for a paper verified in the last 5 years, or requested strains from the CGC recently
 
** Most labs were real
 
  
=== C_elegans Slack group ===
+
=== Grant opportunities ===
* Called "C_elegans"
+
* Possibilities to apply for supplements
* Chris made a "WormBase" channel for people to post questions, comments
+
* May 15th deadline
* Chris will look into inviting everyone and possibly integrating with help@wormbase.org email list
+
* 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.?
  
=== WormBase Outreach Webinars ===
+
=== New WS280 ONTOLOGY FTP directory ===
* While travel is still restricted, we should consider WormBase webinars
+
* Changes requested here: https://github.com/WormBase/website/issues/7900
* Scott working on a JBrowse webinar
+
* Here's the FTP URL: ftp://ftp.wormbase.org/pub/wormbase/releases/WS280/ONTOLOGY/
* Could have a different topic each month
+
* Known issues (Chris will report):
* Should collect topics to cover and assign speakers (maybe multiple speakers per topic; keep it lively)
+
** Ontology files are provided as ".gaf" in addition to ".obo"; we need to remove the ".gaf" OBO files
* Should set up a schedule
+
** Some files are duplicated and/or have inappropriate file extensions
* How should we advertise? Can post on blog, twitter, etc.
 
  
=== New transcripts expanding gene range ===
+
=== Odd characters in Postgres ===
* Will bring up at next week's site-wide call
+
* Daniela and Juancarlos discovered some errors with respect to special characters pasted into the OA
* Possibly due to incorporation of newer nanopore reads
+
* Daniela would like to automatically pull in micropublication text (e.g. figure captions) into Postgres
* Many genes coming in WS277 have expanded well beyond the gene limits as seen in WS276
+
* We would need an automated way to convert special characters, like degree symbols ° into html unicode \&deg\;
** Example genes: pes-2.2, pck-2, herc-1, atic-1
+
* Juancarlos and Valerio will look into possibly switching from a Perl module to a Python module to handle special characters
* Has several repercussions:
 
** WormBase does not submit alleles affecting more than one gene; with these gene expansions suddenly alleles once only affecting a single gene are now affecting two genes, and so are now omitted from loading into the Alliance (including any phenotype and/or disease annotations)
 
** Some expanded genes are now being attributed with thousands of alleles/variants
 
  
=== Citace upload ===
 
* Upload files to Spica/Wen by Tuesday (June 30th) 10am
 
* Wen will clean up folders in Spica (older files from WS277 not cleared out for some reason)
 
  
==July 9th, 2020==
+
== April 15, 2021 ==
===Gene names issue in SimpleMine and other mining tools===
 
*Wen:Last week, Jonathan Ewbank raised the issue of gene names that may refer to multiple objects. I feel this can be an issue for multiple data mining tools including WormMine, BioMart, and Gene Set Enrichment. So I wonder if we should solve it at SimpleMine output (give multiple outputs when a name matches multiple objects)  or have a standalone approach to check if any gene name among a list may refer to multiple objects (users check their name lists before submitting them to any data mining tool).
 
*Jae:Probably, the public name issue has heterogeneous natures. That means there may be no single solution to solve all those problems. In my experience of gene list curation from high-throughput studies, confusing usage of public names are less than 2% (still cannot be ignored). Please see some situations for the examples.
 
**single public name is assigned to multiple WBgene ID.(you listed up these cases in the word file you attached)
 
**overlapped or dicistronic genes, ex. mrpl-44 and F02A9.10
 
**overlapped or dicistronic, but has a single sequence name, examples:
 
    exos-4.1 and tin-9.2 (B0564.1)
 
    eat-18 and lev-10 (Y105E8A.7)
 
    cha-1 and unc-17 (ZC416.8)
 
**simple confusion from authors, ex. mdh-1 and mdh-2
 
  
One of the most significant problems is a propagation to other DB and papers of  these gene name issues.
+
=== Special characters in Postgres/OA ===
We can make a special note for each gene page, but the people using batch analysis could not catch that easily.
+
* 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. &alpha;) 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
  
*Conclusion: Jae and Wen will work on a tool that lets Users "sanitize" their gene lists before submission to data minign tools.  They will also write a microPub explaining this issue to the community.
+
=== 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
  
===Wormicloud===
+
=== Supplement opportunities ===
*Valerio and Jae have worked on a tool that uses data in Textpresso; given a keyword, eg. "transposon", the tool generates a word cloud
+
* Money available for software development to "harden" existing software
*With a pair of keywords can generate a graph that plots trends of occurence across the years in publication abstracts
+
* 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)
  
===Noctua 2.0 form ready to use===
+
=== Student project for Textpresso ===
*Caltech summer student will try using Noctua initially for duaer (neuronal signaling) pathways
+
* 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

Latest revision as of 19:34, 15 April 2021

Previous Years

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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