Difference between revisions of "WormBase-Caltech Weekly Calls"

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= Previous Years =
 +
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
  
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[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
  
2013 Meetings
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[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
 
 
 
 
[[WormBase-Caltech_Weekly_Calls_January_2013|January]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_February_2013|February]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_March_2013|March]]
 
 
 
[[WormBase-Caltech_Weekly_Calls_April_2013|April]]
 
  
[[WormBase-Caltech_Weekly_Calls_May_2013|May]]
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[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_June_2013|June]]
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[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_July_2013|July]]
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[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
= August 1, 2013 =
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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
Quarterly Progress Reports
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[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
*Capturing curation stats from the Curation Status form
 
*What data types do we want to capture curation stats for that we are not currently?
 
*We have frequent database dumps that can be read for stats
 
*We can capture the stats table statically on a regular basis (daily)
 
** form at http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi
 
** cronjob to get data from "Curation Statistics Page" button at
 
** /home/acedb/cron/curation_stats/get_daily_curation_stats.pl
 
** deposits files every day at 5am to :
 
** /home/acedb/cron/curation_stats/files/
 
  
RNA-Seq and Tiling Array data
 
*Data in SPELL
 
*Wen found a lot more non modENCODE data sets
 
*May use SVM for expression cluster data
 
*Gene IDs can be found from original paper or data set
 
*Up-to-date mapping to genes is not currently done
 
  
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= 2021 Meetings =
 +
== January 14th, 2021 ==
  
AMIGO2 (Wormbase Ontology Browser)
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===PubMed LinkOut to WormBase Paper Pages (Kimberly) ===
*Raymond and Juancarlos have taken AMIGO2 infrastructure to make an ontology browser for integration into WormBase
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* Other databases [https://www.ncbi.nlm.nih.gov/projects/linkout/doc/nonbiblinkout.html link out from PubMed] to their respective paper pages
*GO Term [http://mangolassi.caltech.edu/~azurebrd/cgi-bin/testing/amigo/wobr/amigo.cgi focus page demo]
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* For example, https://pubmed.ncbi.nlm.nih.gov/20864032/ links out to GO and MGI paper pages
*Graph view shows path to root (DAG view)
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* Would like to set this up for WormBase and ultimately for the Alliance, but this will require some developer help
*Inferred tree view shows:
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* Work on this next month (after AFP and GO grant submissions)?
**Ancestor terms, no annotation numbers
 
**Main term and children, with annotation numbers (inferred, term and descendant annotations)
 
**Annotation numbers link to list of genes
 
**Will not show "direct" annotations, only inferred
 
*Sibling term displays: list parents with option to expand to see siblings of the main term
 
*Separate [http://mangolassi.caltech.edu/~azurebrd/cgi-bin/testing/amigo/wobr/treeExpand.cgi expandable/collapsible tree] of ontology ("Browse entire ontology")
 
*Widget can be coded to integrate the ontology browser
 
  
 +
===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">
  
Paper Categorization
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There's a script here that repopulates the postgres obo_*_hgnc tables
*Word frequency
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based off of Chris and Wen's data
**We chose papers from the Author First Pass (AFP) list with 'stress'
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/home/postgres/work/pgpopulation/obo_oa_ontologies/populate_obo_hgnc.pl
**About 40 papers in list, varied topics ('stress' is a broad term)
 
**Curation essentially now complete for most data types
 
**Expanding beyond AFP?
 
*Chris will draw up preliminary tree of topics and send around
 
**We can discuss, edit, and expand as a group
 
**We want to 1) Collect positive and negative training papers and 2) Manually generate a list of key words to use for training
 
*Todd proposes for paper pages on WormBase:
 
**Show a table of flagged data types for a paper?
 
**Give users a sense of where paper is in the curation pipeline
 
  
 +
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 ?
  
 +
</pre>
  
= August 8, 2013 =
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===Minutes===
 +
====PubMed LinkOut to WormBase Paper Pages====
  
New Spica now has a closed (private) 'citace' account
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====Update cycle for HGNC data in the OA====
*citpub account is accessible to everyone with password
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*We will update when Alliance updates the data
*People can create their own spica accounts
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*Juancarlos will set it to check the timestamps and if they change will do an update for the OAs
*Personal accounts are encouraged so as to avoid saving changes to citpub database
 
  
 +
====CENGEN====
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*Wen, Daniela, and Raymond will look at the datasets to work out how to incorporate. Start simple.
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*We will make links to pages on their site.
  
Worm Ontology Browser
 
*Raymond has set up a server
 
*Browsing should be faster now
 
*Should be transferable to the Amazon cloud
 
*Raymond will establish a WormBase development environment
 
  
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== January 21, 2021 ==
  
Curation priorities
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=== Neural Network (NN) Paper Classification Results ===
*Paper categorization
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* Linking to Paper Display tool (as opposed to Paper Editor) from Michael's webpage for NN results (Michael will make change)
*Depth vs breadth of topics (number of papers?)
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* NN results will be incorporated into the Curation Status Form
**'Stress' has been a pilot topic, but is a very broad topic
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* 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
**Will work on generating subcategories of 'Stress' on the [http://wiki.wormbase.org/index.php/WormBase_Paper_Categorization Paper Categorization Wiki] page
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* Decision: we will omit blackbox results (at least for now) from curation status form (just add the new NN results separately)
**Curators can analyze the Author First Pass list of 'Stress' papers as well as entire backlog/corpus
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* We have stopped running SVM on new papers
*Goals of 'covering' a topic?
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* Interactions SVM has performed better than new NN results; would be worth attempting a retraining
**'Complete' and vetted process page, Wikipathway
 
**Promote 'featured processes' on WormBase for a given release
 
  
 +
=== 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
  
Curator's should check CGIs
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=== AFP Anatomy Function flagging ===
*Submission forms and other CGIs may have been altered
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* 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

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