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]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
  
= 2020 Meetings =
+
= 2021 Meetings =
 +
== January 14th, 2021 ==
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
+
===PubMed LinkOut to WormBase Paper Pages (Kimberly) ===
 +
* Other databases [https://www.ncbi.nlm.nih.gov/projects/linkout/doc/nonbiblinkout.html link out from PubMed] to their respective paper pages
 +
* For example, 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)?
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
+
===Update cycle for HGNC data in the OA (Ranjana) ===
 +
*Juancarlos had these questions for us:
 +
<pre style="white-space: pre-wrap;
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white-space: -moz-pre-wrap;
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white-space: -pre-wrap;
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white-space: -o-pre-wrap;
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word-wrap: break-word">
  
 +
There's a script here that repopulates the postgres obo_*_hgnc tables
 +
based off of Chris and Wen's data
 +
/home/postgres/work/pgpopulation/obo_oa_ontologies/populate_obo_hgnc.pl
  
== March 5, 2020 ==
+
It's not on a cronjob, because I think the files are not updated that
 +
often.  Do we want to run this every night, or run it manually when
 +
the files get re-generated ?  Or run every night, and check if the
 +
files's timestamps have changed, then repopulate postgres ?
  
=== WormBase curation ===
+
</pre>
* 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 ===
+
===Minutes===
* Joesph may be able to meet with Raymond
+
====PubMed LinkOut to WormBase Paper Pages====
* How can the tool be maintained? If it can't it needs to be pulled
 
  
=== Single cell expression tool ===
+
====Update cycle for HGNC data in the OA====
* Tool is here: http://de.wormcells.com/
+
*We will update when Alliance updates the data
* What do we need to consider for pulling into WormBase?
+
*Juancarlos will set it to check the timestamps and if they change will do an update for the OAs
* 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 ===
+
====CENGEN====
* For now we will stick to the CGIs that Juancarlos has built for variations and strains
+
*Wen, Daniela, and Raymond will look at the datasets to work out how to incorporate. Start simple.
* 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
+
*We will make links to pages on their site.
  
  
== March 12, 2020 ==
+
== January 21, 2021 ==
  
=== Cancelled meetings ===
+
=== Neural Network (NN) Paper Classification Results ===
* Meetings are being cancelled, including Biocuration 2020. Ranjana will update our Wormbase meeting page with a note to users (done)
+
* Linking to Paper Display tool (as opposed to Paper Editor) from Michael's webpage for NN results (Michael will make change)
* We should start doing online advertisement for micropublications with webinars
+
* NN results will be incorporated into the Curation Status Form
 +
* For AFP and VFP, there is now a table with mixed SVM and NN results ("blackbox" results); for a given paper, if NN results exist, they take priority over any SVM results
 +
* Decision: we will omit blackbox results (at least for now) from curation status form (just add the new NN results separately)
 +
* We have stopped running SVM on new papers
 +
* Interactions SVM has performed better than new NN results; would be worth attempting a retraining
  
=== Storing invalid/avoided WBPersons and email addresses in Postgres ===
+
=== Community Phenotype Curation ===
* 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
+
* On hold for a few months to commit time to updating the phenotype annotation model to accommodate, e.g. double mutant phenotypes, multiple RNAi targets (intended or otherwise), mutant transgene products causing phenotypes, expressed human genes causing phenotypes, etc.
* Valerio would like to add these to Postgres to keep a more central repository of them
+
* Changes made for WB phenotypes may carry over to Alliance phenotype work
* Chris would still like to be able to readily update/edit the content of those lists
+
* [https://www.preprints.org/manuscript/202101.0169/v1 Paper out now] on undergrad community phenotype curation project with Lina Dahlberg; we may get more requests for trying this with other undergrad classes
  
* 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
+
=== AFP Anatomy Function flagging ===
 
+
* Sometimes it is difficult to assess whether an author flag is correct (often times can be wrong/absent)
=== Updates on Alaska ===
+
* What about giving authors/users feedback on their flagging results?
 
+
* Would be good to provide content from paper where this data is said to exist (automatically from a Textpresso pipeline or manually from author identified data)
Raymond and Eduardo met with Joseph and decided to have the tool running as is for now even though maintaining it can be hard
+
* We want to be careful about how we provide feedback; we should be proactive to make improvements/modifications on our end and bring those back to users for feedback to us
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==
 
*Do we need to publicize any data form, the AFP and phenotype forms already send targeted e-mails (from Paul D's email)
 

Latest revision as of 17:52, 21 January 2021

Previous Years

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2011 Meetings

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2015 Meetings

2016 Meetings

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2018 Meetings

2019 Meetings

2020 Meetings


2021 Meetings

January 14th, 2021

PubMed LinkOut to WormBase Paper Pages (Kimberly)

  • Other databases link out from PubMed to their respective paper pages
  • For example, 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)?

Update cycle for HGNC data in the OA (Ranjana)

  • Juancarlos had these questions for us:

There's a script here that repopulates the postgres obo_*_hgnc tables
based off of Chris and Wen's data
/home/postgres/work/pgpopulation/obo_oa_ontologies/populate_obo_hgnc.pl 

It's not on a cronjob, because I think the files are not updated that
often.  Do we want to run this every night, or run it manually when
the files get re-generated ?  Or run every night, and check if the
files's timestamps have changed, then repopulate postgres ?

Minutes

PubMed LinkOut to WormBase Paper Pages

Update cycle for HGNC data in the OA

  • We will update when Alliance updates the data
  • Juancarlos will set it to check the timestamps and if they change will do an update for the OAs

CENGEN

  • Wen, Daniela, and Raymond will look at the datasets to work out how to incorporate. Start simple.
  • We will make links to pages on their site.


January 21, 2021

Neural Network (NN) Paper Classification Results

  • Linking to Paper Display tool (as opposed to Paper Editor) from Michael's webpage for NN results (Michael will make change)
  • NN results will be incorporated into the Curation Status Form
  • For AFP and VFP, there is now a table with mixed SVM and NN results ("blackbox" results); for a given paper, if NN results exist, they take priority over any SVM results
  • Decision: we will omit blackbox results (at least for now) from curation status form (just add the new NN results separately)
  • We have stopped running SVM on new papers
  • Interactions SVM has performed better than new NN results; would be worth attempting a retraining

Community Phenotype Curation

  • On hold for a few months to commit time to updating the phenotype annotation model to accommodate, e.g. double mutant phenotypes, multiple RNAi targets (intended or otherwise), mutant transgene products causing phenotypes, expressed human genes causing phenotypes, etc.
  • Changes made for WB phenotypes may carry over to Alliance phenotype work
  • Paper out now on undergrad community phenotype curation project with Lina Dahlberg; we may get more requests for trying this with other undergrad classes

AFP Anatomy Function flagging

  • Sometimes it is difficult to assess whether an author flag is correct (often times can be wrong/absent)
  • What about giving authors/users feedback on their flagging results?
  • Would be good to provide content from paper where this data is said to exist (automatically from a Textpresso pipeline or manually from author identified data)
  • We want to be careful about how we provide feedback; we should be proactive to make improvements/modifications on our end and bring those back to users for feedback to us