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 =
 +
== January 14th, 2021 ==
  
= 2020 Meetings =
+
===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_January_2020|January]]
+
===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">
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
+
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
  
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
+
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-Caltech_Weekly_Calls_April_2020|April]]
+
</pre>
  
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
+
===Minutes===
 +
====PubMed LinkOut to WormBase Paper Pages====
  
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
+
====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
  
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
+
====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.
  
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
 
  
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
+
== January 21, 2021 ==
  
[[WormBase-Caltech_Weekly_Calls_October_2020|October]]
+
=== 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
 +
* [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
  
==Nov 5th, 2020==
+
=== AFP Anatomy Function flagging ===
 
+
* Sometimes it is difficult to assess whether an author flag is correct (often times can be wrong/absent)
===WS279 GAF 2.0 and disease files===
+
* What about giving authors/users feedback on their flagging results?
*Valerio and Ranjana still working with the GAF 2.0 files to generate gene descriptions
+
* 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)
*Valerio and Ranjana will probably have a meeting with Magdalena to sort out the FTP file issues for gene descriptions
+
* 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
*Will let Raymond know if the disease GAFs are okay after they test these for gene descriptions
 
*Raymond needs the GAFs for WoBR
 
 
 
===Experimenting with addeding new citace data to the current WS release ===
 
*Wen will take the newest expression, physical interaction, and paper class from postgres, add them to WS279 to create a "WS279.1" version of ACeDB database. Then compare WS279.1 to WS279 by comparing the SimpleMine results generated from these two versions of ACeDB. The goal is to explore the possibility of notifying users some of the new curation since the data freeze for the WS build.
 
 
 
===MicroPub user webinar on Nov 9th===
 
*Ranjana and Kimberly have conflicts--Alliance call and GO call. Anyway microPub team is running the show and they have other WormBasers to help as well.
 
 
 
===WS280 deadlines===
 
*Caltech files due for citace: Dec 15th, 2020
 
 
 
 
 
==Nov 12th, 2020==
 
=== Cynthia Kenyon tool ===
 
* developed a new tool for the worm, complete with very nice tutorials, for analyzing gene expression data using Gene Module analysis.
 
* tool at http://genemodules.org
 
* add link outs from the gene expression widget or add in general WB tools?
 
 
 
=== Graphical curation tool update===
 
* We will show a live demo on the current state of the graphical curation tool
 
 
 
=== Curating to human genes in ACEDB ===
 
* Karen requested option to curate constructs with human genes
 
* Would we need to change our human genes in ACEDB? For example, migrate from Ensembl IDs to HGNC IDs as primary keys?
 
 
 
=== GAF (and GAF-like) file headers ===
 
* GO GAF files (on FTP, WS279) for WormBase now in 2.2 format with header like
 
!gaf-version: 2.2
 
!generated-by: WormBase
 
!date-generated: 2020-10-30
 
! WB annotations 00015014
 
* For files that can migrate to 2.2 format (e.g. always require column 4 qualifier) we could adopt a similar header
 
* For other files (that cannot always have a qualifier in column 4), we could stick to 2.0 format with a header like:
 
!gaf-version: 2.0
 
!generated-by: WormBase
 
!date-generated: 2020-10-30
 
* Current need is to include information about format specification, possibly in addition to other extra header content.
 

Latest revision as of 17:52, 21 January 2021

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

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