Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
(405 intermediate revisions by 9 users not shown)
Line 18: Line 18:
  
 
[[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
 
GoToMeeting link: https://www.gotomeet.me/wormbase1
 +
 +
= 2020 Meetings =
 +
 +
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
 +
 +
 +
== March 5, 2020 ==
 +
 +
=== WormBase curation ===
 +
* Tim Schedl: WB needs to do more curation for phenotype and variation
 +
* Doing community curation, but not fast enough
 +
* Would like to work on more automation; e.g. having Textpresso return all sentences mentioning an allele in papers that are predicted to have phenotype data
 +
 +
=== Alaksa ===
 +
* Joesph may be able to meet with Raymond
 +
* How can the tool be maintained? If it can't it needs to be pulled
 +
 +
=== Single cell expression tool ===
 +
* Tool is here: http://de.wormcells.com/
 +
* What do we need to consider for pulling into WormBase?
 +
* Where does the data sit and how does the tool access it? Can we integrate the data more into WormBase (e.g. local curation databases)?
 +
** Would want it to be in sync with WormBase releases
 +
** May not need to reprocess with every release with current (small-ish) data set
 +
* Fully integrated tool versus an embedded tool?
 +
 +
=== Name service updates ===
 +
* For now we will stick to the CGIs that Juancarlos has built for variations and strains
 +
* Juancarlos can discuss with Matt R. and Sibyl the possibility of integrating API requests to the Name service into a CGI form for the OA
 +
 +
 +
== March 12, 2020 ==
 +
 +
=== Cancelled meetings ===
 +
* Meetings are being cancelled, including Biocuration 2020. Ranjana will update our Wormbase meeting page with a note to users (done)
 +
* We should start doing online advertisement for micropublications with webinars
 +
 +
=== Storing invalid/avoided WBPersons and email addresses in Postgres ===
 +
* Currently Chris has been maintaining ([https://docs.google.com/spreadsheets/d/1FHhQk_IZIBLYkOUdVf9Kfh5zx66rkHOEVFQQ6wzT2ks/edit?usp=sharing on Google sheets]) a list of papers, people, and email addresses to omit from future WormBase outreach requests
 +
* Valerio would like to add these to Postgres to keep a more central repository of them
 +
* Chris would still like to be able to readily update/edit the content of those lists
 +
 +
* Proposed solutions: Keep the list in a flat file and have a cron job to sync the data to postgres daily or create a simple form to create/modify entries directly in postgres
 +
 +
=== Updates on Alaska ===
 +
 +
Raymond and Eduardo met with Joseph and decided to have the tool running as is for now even though maintaining it can be hard
 +
The future plan is to move the platform to Google colab to reduce maintainance work.
 +
 +
==Nameservice discussion==
 +
*Getting a token has worked for Chris and Ranjana
 +
*Karen and Daniela need to get tokens
 +
 +
==Noctua GO-CAM updates==
 +
*Noctua is a production tool available for annotations right now
 +
*Create as many interconnected models and make available for curators is the ongoing goal
 +
*Reactome models are in the process of being imported
 +
*Real time validation messages as curation is being done, is being worked on
 +
*Kimberly will send out the details for logging into Noctua and make sure all curators are on the login list
  
  
= 2019 Meetings =
+
== March 19, 2020 ==
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
+
=== Citace Upload ===
 +
* Tuesday, March 31st
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
+
=== Latest ACEDB ===
 +
* Getting latest ACEDB build from staging FTP (for descriptions, etc.)
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
+
=== Storing email addresses/persons to omit from requests ===
 +
* Chris and Juancarlos will work on a form to submit email addresses and WBPerson IDs to Postgres
  
== April 4, 2019 ==
+
=== Mailing lists ===
 +
* Let Todd know if you want to keep your caltech.edu account on the mailing lists
  
=== Paul's Biocuration Keynote ===
 
* At Biocuration keynote, Paul S. will talk about web forms, including Author First Pass form
 
* Can someone send Paul the latest AFP form location and documentation
 
* Will also discuss the future of micropublications
 
  
=== IWM Swag ===
+
==March 26th==
* Stickers vs. screen cloths
+
===Community curation===
* Daniela had contacted Jessie to make new graphic; she's interested, but do we still need a new graphic?
+
*Do we need to publicize any data form and urge Users to contribute? The AFP and phenotype forms already send targeted e-mail
* Plan was to make ~2,000 screen cloths (4x4 inch or 6x6 inch?)
+
* Paul S. is getting people from the lab to do phenotype curation; Chris G will run a tutorial for interested people
** As for design would be nice to have new design
+
* Blog about phenotype form to make people generally aware
** Gary had made cartoon for community curation (proposal might be offensive to some)
+
* Could the phenotype form be adapted for other species? Possibly but depends on:
* Include water bottles for special contributors? In addition to shot glasses?
+
** Whether genotypes could be loaded and recognized
* 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 ===
+
=== AFP for older papers ===
* Juancarlos worked on a tool to extract WBPerson collaborators
+
* Discussed recently
* WB staff generally had ~100 collaborators, Paul S has 670
+
* Many (all?) Old papers have already gone through the old AFP pipeline
* Distinguish between collaborators and coauthors? Manual (self reported) vs. automatic associations?
+
* Need to check what has already been curated
* Make modification to ACEDB model?
 
* Maybe 'collaborators' should be restricted to the laboratory level?
 
  
== April 11, 2019 ==
+
=== Omit form ===
 +
* http://tazendra.caltech.edu/~postgres/cgi-bin/omit_form.cgi
 +
* Can view, add, or edit persons, email addresses, and IP addresses to omit from email requests (and IP addresses to block)
  
=== Canadian C. elegans meeting ===
+
=== Problems accessing Textpresso Central ===
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).
+
* Ranjana had noticed that the server was acting slow
 +
* Unknown problem; hard to pin down
 +
* Definitely a Caltech network system
 +
* Issue for past couple of weeks
 +
* May be able to ask Caltech IMSS for a diagnostic analysis
 +
* Bad switch? Maybe; there is an unused switch that could be used to test
 +
** Maybe should dedicate an ethernet socket to the server(s) (avoiding switch altogether)
 +
* Tazendra is good, mangolassi seems to have had some trouble recently as well
 +
* All on subnet 52; Raymond has been monitoring and seems to be working well; could suggest a local (e.g. computer-specific, switch-specific) issue
  
 +
=== Automated concise pathway descriptions? ===
 +
* Could we generate pathway descriptions based on, for example, GO-CAM models?
 +
* Might be straightforward if clear guidelines can be documented (important players/genes, important/central functions/processes)
  
=== Feedback from small RNA meeting Apilr 3-5, 2019 ===
+
=== Genotype OA on Sandbox ===
 +
* http://mangolassi.caltech.edu/~postgres/cgi-bin/oa/ontology_annotator.cgi
 +
* Take a look and send feedback to Juancarlos and Chris
  
Future meeting invitations and summer workshop?
+
=== Name Service temp submission for strain and variation to Postgres ===
 +
* Sandbox: http://mangolassi.caltech.edu/~postgres/cgi-bin/temp_objects.cgi
 +
* Adding strains or variations will create the object in the Name Service as well as add it to Postgres
 +
* Test it and make sure it works; NOTE: Creating objects on both Mangolassi AND Tazendra will create real object entries in the Name Service; if testing on the Sandbox, make sure to tell Paul Davis and Matt Russell to remove test submissions from the Name Service

Latest revision as of 00:44, 27 March 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings


GoToMeeting link: https://www.gotomeet.me/wormbase1

2020 Meetings

January

February


March 5, 2020

WormBase curation

  • Tim Schedl: WB needs to do more curation for phenotype and variation
  • Doing community curation, but not fast enough
  • Would like to work on more automation; e.g. having Textpresso return all sentences mentioning an allele in papers that are predicted to have phenotype data

Alaksa

  • Joesph may be able to meet with Raymond
  • How can the tool be maintained? If it can't it needs to be pulled

Single cell expression tool

  • Tool is here: http://de.wormcells.com/
  • What do we need to consider for pulling into WormBase?
  • Where does the data sit and how does the tool access it? Can we integrate the data more into WormBase (e.g. local curation databases)?
    • Would want it to be in sync with WormBase releases
    • May not need to reprocess with every release with current (small-ish) data set
  • Fully integrated tool versus an embedded tool?

Name service updates

  • For now we will stick to the CGIs that Juancarlos has built for variations and strains
  • Juancarlos can discuss with Matt R. and Sibyl the possibility of integrating API requests to the Name service into a CGI form for the OA


March 12, 2020

Cancelled meetings

  • Meetings are being cancelled, including Biocuration 2020. Ranjana will update our Wormbase meeting page with a note to users (done)
  • We should start doing online advertisement for micropublications with webinars

Storing invalid/avoided WBPersons and email addresses in Postgres

  • Currently Chris has been maintaining (on Google sheets) a list of papers, people, and email addresses to omit from future WormBase outreach requests
  • Valerio would like to add these to Postgres to keep a more central repository of them
  • Chris would still like to be able to readily update/edit the content of those lists
  • Proposed solutions: Keep the list in a flat file and have a cron job to sync the data to postgres daily or create a simple form to create/modify entries directly in postgres

Updates on Alaska

Raymond and Eduardo met with Joseph and decided to have the tool running as is for now even though maintaining it can be hard The future plan is to move the platform to Google colab to reduce maintainance work.

Nameservice discussion

  • Getting a token has worked for Chris and Ranjana
  • Karen and Daniela need to get tokens

Noctua GO-CAM updates

  • Noctua is a production tool available for annotations right now
  • Create as many interconnected models and make available for curators is the ongoing goal
  • Reactome models are in the process of being imported
  • Real time validation messages as curation is being done, is being worked on
  • Kimberly will send out the details for logging into Noctua and make sure all curators are on the login list


March 19, 2020

Citace Upload

  • Tuesday, March 31st

Latest ACEDB

  • Getting latest ACEDB build from staging FTP (for descriptions, etc.)

Storing email addresses/persons to omit from requests

  • Chris and Juancarlos will work on a form to submit email addresses and WBPerson IDs to Postgres

Mailing lists

  • Let Todd know if you want to keep your caltech.edu account on the mailing lists


March 26th

Community curation

  • Do we need to publicize any data form and urge Users to contribute? The AFP and phenotype forms already send targeted e-mail
  • Paul S. is getting people from the lab to do phenotype curation; Chris G will run a tutorial for interested people
  • Blog about phenotype form to make people generally aware
  • Could the phenotype form be adapted for other species? Possibly but depends on:
    • Whether genotypes could be loaded and recognized

AFP for older papers

  • Discussed recently
  • Many (all?) Old papers have already gone through the old AFP pipeline
  • Need to check what has already been curated

Omit form

Problems accessing Textpresso Central

  • Ranjana had noticed that the server was acting slow
  • Unknown problem; hard to pin down
  • Definitely a Caltech network system
  • Issue for past couple of weeks
  • May be able to ask Caltech IMSS for a diagnostic analysis
  • Bad switch? Maybe; there is an unused switch that could be used to test
    • Maybe should dedicate an ethernet socket to the server(s) (avoiding switch altogether)
  • Tazendra is good, mangolassi seems to have had some trouble recently as well
  • All on subnet 52; Raymond has been monitoring and seems to be working well; could suggest a local (e.g. computer-specific, switch-specific) issue

Automated concise pathway descriptions?

  • Could we generate pathway descriptions based on, for example, GO-CAM models?
  • Might be straightforward if clear guidelines can be documented (important players/genes, important/central functions/processes)

Genotype OA on Sandbox

Name Service temp submission for strain and variation to Postgres

  • Sandbox: http://mangolassi.caltech.edu/~postgres/cgi-bin/temp_objects.cgi
  • Adding strains or variations will create the object in the Name Service as well as add it to Postgres
  • Test it and make sure it works; NOTE: Creating objects on both Mangolassi AND Tazendra will create real object entries in the Name Service; if testing on the Sandbox, make sure to tell Paul Davis and Matt Russell to remove test submissions from the Name Service