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 ==
  
 +
=== 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
  
== October 1, 2020 ==
+
=== 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
  
=== Gene association file formats on FTP ===
+
=== AFP Anatomy Function flagging ===
* For example, current production release ONTOLOGY directory: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/ONTOLOGY/
+
* Sometimes it is difficult to assess whether an author flag is correct (often times can be wrong/absent)
* Our association files have format "*.wb"; is this useful or necessary?
+
* What about giving authors/users feedback on their flagging results?
* Other than referring to GAF in the header, it isn't clear to users what the columns refer to or what the column headers should be
+
* 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 could add a README file and/or convert to the new [https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md GAF 2.2 format] which would have a more expressive file header and possibly column headers(?)
+
* 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
** File headers could possibly link to the format specification page
 
 
 
=== Phenotype association file idiosyncrasy ===
 
* As we've discussed previously, there is an oddity to how the phenotype association file we provide lists, or doesn't, references
 
* According to the GAF spec, column 6 is for reference and is required, whereas column 8 is "With (or) From" and is optional
 
* When we have a reference, the WBPaper ID is provided in column 6 and the WBVar ID or RNAi ID is provided in column 8
 
* However, when we have no reference (personal communication, e.g. from NBP allele submissions), the WBVar ID is instead put in column 6 (because we need something there), and column 8 is blank.
 
** This results in (1) column 6 having a mix of paper/reference IDs (good) and WBVar IDs (not good) and (2) WBVar IDs split between column 6 and 8; thus making it tedious to parse this file
 
* Proposed solution: Can we come up with some type of reference object ID to associate to the personal communications (or any annotations currently lacking a formal reference)?
 
* With the proposed solution, we can always have a reference ID in column 6 (the intended purpose of the column) and WBVar IDs for alleles can always remain consistently in column 8
 
* Proposal is to put WBPerson IDs in column 6 for personal communications. Chris & Karen will check if this will work.
 
 
 
=== Server space in Chen Building ===
 
* It looks like that we will not have a specific space for server computers.
 
 
 
 
 
== October 8, 2020 ==
 
 
 
=== Webinar Announcement ===
 
* Here is the live registration site: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/webinar.cgi
 
* Caltech zoom allows 300 attendees.
 
 
 
=== Descriptions from GO-CAM models ===
 
* One suggestion for the Alliance is to create a description based on a GO-CAM model
 
* Could also micropublish some descriptions (semi-automated?)
 
* Can make curators authors of micropublications for GO-CAM models/pathways
 
 
 
=== Transcription Factors in WormBase ===
 
* WormBase has a ?Transcription_factor class that is currently underutilized
 
* Chris spoke with Gary Williams about the status as he has done much of the work on the class
 
* Because transcription factors can often be complexes, it was decided to create the ?Transcription_factor class rather than simply an extension of tags to the existing ?Gene class
 
* The class seems reasonably complete; it's important to note that some TFs are general transcription factors, not necessarily gene-specific or sequence-specific DNA-binding TFs; it will be good to make that distinction clear to users
 
* Chris has compiled a [https://docs.google.com/spreadsheets/d/1KdmvybWDWHXdlJwZgfleL4xHDoyPoYR13WAUcERF82g/edit?usp=sharing Google sheet] to assess the class before Gary W. leaves WB in the next couple of weeks
 
* The Google sheet has several tabs/worksheets, including one for the ACEDB data model (and notes about usage of tags), a summary table of associated genes, bound sequence features, existence of other protein-DNA binding data, etc.
 
* It would be good to make TF binding info (per gene and globally) more accessibly to our users, maybe via a new widget on gene pages (e.g. list incoming, regulating TFs and, for TF genes themselves, list potential target genes)
 
 
 
== October 15, 2020 ==
 
 
 
=== BioGRID data sharing ===
 
* Rose from BioGRID proposed that BioGRID curate high-throughput C. elegans interaction datasets, capturing confidence scores when available, and making those annotations available to WormBase for regular ingest
 
* Will need to consider a few points:
 
** BioGRID doesn't curate protein-DNA interactions
 
** We don't yet know the turn-around timeline for BioGRID curation of worm datasets; WB may be able to curate them much sooner
 
* Chris and Jae will work with Rose et al. to coordinate HTP curation
 
 
 
=== Enriched genes ===
 
* Some genes are considered "enriched" for an expression cluster data set even if the enrichment was in comparison to another cell or tissue (not whole animal)
 
* We should reconsider the ?Expression_cluster model to make sure we can appropriately model and communicate enrichment or subtypes thereof
 
 
 
 
 
== October 22, 2020 ==
 
 
 
=== CHEBI ===
 
* Karen spoke to CHEBI personnel on Tuesday
 
* CHEBI only has ~2 curators to create new entities
 
* CHEBI had submitted a proposal to establish pipelines to process requests from MODs
 
* Chemical Translation Service (CTS)
 
* OxO = https://www.ebi.ac.uk/spot/oxo/search
 
 
 
=== Training Webinar ===
 
* Scheduled for tomorrow at 1pm Pacific/4pm Eastern
 
 
 
 
 
== October 29, 2020 ==
 
 
 
=== Overview Webinar debriefing ===
 
* What's Good
 
* What needs improvement
 
* Participant requests:
 
  A place to look for Worm methods (a public {moderated} wiki page?)
 
 
 
 
 
=== New alleles extraction pipeline ===
 
* current pipeline (on textpresso-dev) is sending data to Sanger RT system, which is being retired
 
* the plan is to build a new pipeline to send AFP-like alerts with new entities
 
* current pipeline reads alleles data from GSA and gene lists from Sanger, but I (Valerio) would need help from curators to understand how to get these data
 
 
 
==Nov 5th, 2020==
 
===WS279 GAF 2.0 and disease files===
 
*Valerio and Ranjana still working with the GAF 2.0 files to generate gene descriptions
 
*Will let Raymond know if the disease GAFs are okay after they test these for gene descriptions
 
*Raymond needs the GAFs for WoBR
 

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