Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
= 2017 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2017|January]]
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_February_2017|February]]
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
== March 2, 2017 ==
+
GoToMeeting link: https://www.gotomeet.me/wormbase1
  
=== Expression Cluster SVM ===
+
= 2020 Meetings =
* Started curating expression clusters in 2007
 
* Had been using text pattern match to identify expression cluster papers
 
* Now with more papers for positive and negative training set, shifting to SVM identification
 
* 540 positive papers, 900 negative papers for training
 
* Wen received first batch, roughly ~70% precision, possibly ~80-90% recall
 
* Wen reviewed papers from WormEXP (http://wormexp.zoologie.uni-kiel.de/wormexp/)
 
  
=== Karen's SBIR grant ===
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
* Looks like it will get funded
 
* Karen will need to become part time at WormBase (needs to be more than half time on SBIR)
 
* Paul put in a request for posting another curator position
 
** If anyone has ideas about a potential (part-time or full-time) curator, let Paul know
 
* Will need to consider re-allocation of curation responsibilities
 
* Molecule curation in maintenance mode, may require updating of mapping terms with our internal IDs
 
** Ranjana: want to incorporate molecules in disease curation for WB/AGR, can offer to take over maintenance
 
** Do other AGR members curate molecules? In some cases yes; don't capture metabolites
 
* Transgene curation could be distributed
 
** Karen will be working on more automated curation of transgenes from papers; maybe also for molecules
 
  
=== Metabolomics ===
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
* What would we like to see in WB for metabolomics?
 
* Marian Walhout lab created the WormFlux database (http://wormflux.umassmed.edu/)
 
* WB enzyme gene pages link out to respective gene pages on WormFlux
 
* How are enzymatic pathways represented in GO, or by phenotype info? What's the cross-talk?
 
  
=== Pathway representation ===
 
* What are the best ways to capture empirical evidence as support for pathway models?
 
* Want clear, granular evidence for each assertion in a model, but need to accommodate probabilistic statements
 
* How can micropublications be used to fill in the gaps?
 
  
=== SObA GO on human data ===
+
== March 5, 2020 ==
* What would be a good set of genes to test?
 
* If we omit IEAs (most from mouse), are we left with substantial data for human genes?
 
  
 +
=== 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
  
== March 9, 2017 ==
+
=== Alaksa ===
 +
* Joesph may be able to meet with Raymond
 +
* How can the tool be maintained? If it can't it needs to be pulled
  
=== Expression widget via Datomic ===
+
=== Single cell expression tool ===
* Sibyl is working on delivering the Expression widget from Datomic
+
* Tool is here: http://de.wormcells.com/
* Issue with gene expression "mountain" data
+
* What do we need to consider for pulling into WormBase?
* AcePerl script/query underlying the data, may be incorrect and needs an update
+
* 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?
  
=== Human GO SObA graph ===
+
=== Name service updates ===
* Working SObA graph for human gene ontology data:
+
* For now we will stick to the CGIs that Juancarlos has built for variations and strains
** http://131.215.12.204/~raymond/cgi-bin/soba_go_hs.cgi?action=annotSummaryCytoscape&focusTermId=UniProtKB:O94905
+
* 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
* Running off GOLR server for now
 
* Would be great to have a SObA widget on AGR portal
 
* Will need to get widgets working on AGR portal
 
* Will be good to have, for now, a stand alone version
 
  
=== AGR update ===
 
* SAB meeting on Tuesday (two days ago)
 
* Positive feedback
 
  
=== AGR database ===
+
== March 12, 2020 ==
* Although official database has not been chosen, most portal processes are running just on memory, need to start storing things in a database
 
* The database used may be the stepping stone for eventual database migration for AGR
 
  
=== AGR Curator calls ===
+
=== Cancelled meetings ===
* Karen asking about purpose of curator calls going forward
+
* Meetings are being cancelled, including Biocuration 2020. Ranjana will update our Wormbase meeting page with a note to users (done)
* Have covered a good number of topics, a few still yet to be covered: synteny browser, person curation
+
* We should start doing online advertisement for micropublications with webinars
* Possibly have discussions about the functions of different (and possibly new) working groups
 
* Can revisit curation procedures
 
* Should curator calls happen independently of AGR to share thoughts and methods about curation
 
  
=== Methods in Molecular Biology chapter update ===
+
=== Storing invalid/avoided WBPersons and email addresses in Postgres ===
* Have received drafts for most sections
+
* 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
* Working on making them consistent and making figures legible
+
* 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
  
== March 16, 2017 ==
+
=== Updates on Alaska ===
  
=== Funding opportunities ===
+
Raymond and Eduardo met with Joseph and decided to have the tool running as is for now even though maintaining it can be hard
* Could we focus on curation for disease genes and work with other groups?
+
The future plan is to move the platform to Google colab to reduce maintainance work.
* Maybe work with GO
 
* What diseases would rely more on worm research than others?
 
* Lots of disease models on neurodegeneration diseases testing herbal treatments and compounds to treat
 
* Parasitic nematode research? May not work out
 
* Really want to focus on what worm research informs about human disease
 
* What are the studies that focus on orthology to human disease genes?
 
* If some funding is cut, there will likely be refunding in a targeted manner (e.g. Alzheimer's research)
 
* Can we do Textpresso search for funding agencies?
 
* Much more funding is going to military research; could look at what could apply (Tropical diseases, responses to pathogen, etc.)
 
  
=== IWM swag ===
+
==Nameservice discussion==
* Still have tattoos from last years TAGC meeting
+
*Getting a token has worked for Chris and Ranjana
* WormBase piggy bank?
+
*Karen and Daniela need to get tokens
  
=== Human GO SObA ===
+
==Noctua GO-CAM updates==
* Server that Raymond used originally is not appropriate
+
*Noctua is a production tool available for annotations right now
* Will require some reworking of the backend code
+
*Create as many interconnected models and make available for curators is the ongoing goal
* Might be ready after the Biocuration meeting
+
*Reactome models are in the process of being imported
* Could use in AGR disease pages, showing enriched GO terms (from genes implicated in the disease)
+
*Real time validation messages as curation is being done, is being worked on
* Could have (instead of enriched terms) a graph of all gene annotations merged
+
*Kimberly will send out the details for logging into Noctua and make sure all curators are on the login list
* What is a reasonably sized list of items to manage in the human mind? 7 +/- 3? 20?
 
** Can define a cutoff at which point using SObA is helpful
 
  
=== Micropublications ===
 
* Deadline for grant rebuttal?
 
* Organization name at IWM will be: Micropublication biology
 
* Each micropublication is intended as a curatable unit
 
* Shohei Mitani wants, for example, to submit 100 knockout phenotypes; should be 100 micropublications
 
** Tim concerned that 100 micropubs is too much, but that is probably OK
 
* Want to generate a "narrative" from multiple individual micropubs
 
* Can DOI's be part of another DOI? Are relationships between DOI's allowed?
 
  
=== AGR communication and data pipeline ===
+
== March 19, 2020 ==
* Discussion about number of calls and modes of communication
+
 
* There was concern about data pipeline demands becoming overwhelming, e.g. loading data for Intermine as well as AGR portal
+
=== Citace Upload ===
* There are questions about which database will be used as an interim database, which could possibly become the standard database
+
* Tuesday, March 31st
* AGR members like the Datomic techonology, but are concerned about the non-open-source aspect
+
 
* Should we have an all-hands call once a month (or every two weeks) where working groups could present and discuss issues? Yes, Kimberly will email Stacia about this idea
+
=== Latest ACEDB ===
* AGR PI's were in favor of having a technical meeting face-to-face; disease working group face-to-face meeting worked well
+
* Getting latest ACEDB build from staging FTP (for descriptions, etc.)
* There may be AGR working group meetings at Biocuration meeting
+
 
 +
=== 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 ===
 +
* 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)
 +
 
 +
=== 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 ===
 +
* http://mangolassi.caltech.edu/~postgres/cgi-bin/oa/ontology_annotator.cgi
 +
* Take a look and send feedback to Juancarlos and Chris
 +
 
 +
=== 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