Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
  
= 2019 Meetings =
+
= 2021 Meetings =
 +
== January 14th, 2021 ==
  
[[WormBase-Caltech_Weekly_Calls_January_2019|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_2019|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">
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
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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
  
== April 4, 2019 ==
+
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 ?
  
=== Paul's Biocuration Keynote ===
+
</pre>
* At Biocuration keynote, Paul S. will talk about web forms, including Author First Pass form
 
* Can someone send Paul the latest AFP form location and documentation
 
* Will also discuss the future of micropublications
 
  
=== IWM Swag ===
+
===Minutes===
* Stickers vs. screen cloths
+
====PubMed LinkOut to WormBase Paper Pages====
* Daniela had contacted Jessie to make new graphic; she's interested, but do we still need a new graphic?
 
* Plan was to make ~2,000 screen cloths (4x4 inch or 6x6 inch?)
 
** As for design would be nice to have new design
 
** Gary had made cartoon for community curation (proposal might be offensive to some)
 
* Include water bottles for special contributors? In addition to shot glasses?
 
* Turn around time? ~ 1 month; designs done in April; submit request by mid-May at latest
 
* Worm in apple graphic? Dragon worm cartooon? Maybe some variation on it?
 
** We can ask Jessie if she can draw up a couple quick sketch ideas
 
  
=== Collaborators tool ===
+
====Update cycle for HGNC data in the OA====
* Juancarlos worked on a tool to extract WBPerson collaborators
+
*We will update when Alliance updates the data
* WB staff generally had ~100 collaborators, Paul S has 670
+
*Juancarlos will set it to check the timestamps and if they change will do an update for the OAs
* Distinguish between collaborators and coauthors? Manual (self reported) vs. automatic associations?
 
* Make modification to ACEDB model?
 
* Maybe 'collaborators' should be restricted to the laboratory level?
 
  
 
+
====CENGEN====
== April 11, 2019 ==
+
*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.
=== Canadian C. elegans meeting ===
 
the "Canadian C. elegans meeting” that will follow the 2019 annual conference of the Canadian Society for Molecular Biosciences. The CSMB conference is held at Université de Montréal on June 2-5, 2019 and will focus on Model systems in cancer research (https://www.fourwav.es/view/1174/info/). The C. elegans conference will be held at the CHUM Research Center in downtown Montréal on Thursday June 6, 2019, and will offer opportunities for both oral and poster presentations. The schedule is not finalized yet but it should start around 8:30am and end around 6pm, followed by an apero in a nearby pub. The costs of registrations will depend on the number of participants but will be between 35 and 50 $ per person (it will cover the costs of lunch, coffee break and logistics).
 
* Karen may be able to go; she will contact Kimberly for any pertinent information
 
 
 
=== Feedback from small RNA meeting April 3-5, 2019 ===
 
* Future meeting invitations and summer workshop?
 
* Dustin Updike - in Maine - interested in running a summer workshop for students
 
** Maybe one or two week-long (5-10 days); unconfirmed
 
** Wen followed up with him: WormBase curator could attend and present on JBrowse, scientific writing, micropublications
 
** Hopefully they can cover travel costs of WB curators
 
** Dustin will get back to us about details as they emerge
 
* Julie Claycomb interested in having WB curator at Toronto's worm meeting
 
 
 
=== New SVM approach ===
 
* Michael will send around paper list with new and old results in the same file
 
* Raymond looked at his data types; at first glance thinks there may be quite a few false positives and false negatives
 
* Can represent new SVM scores as histograms, presumably produce Gaussian curves, can we accept the overlap in distribution tails?
 
* Old thresholds were not necessarily gold standards, probably somewhat arbitrarily chosen initially; we can use the old metrics to roughly choose a new set of corresponding thresholds for the new SVM scores
 
 
 
=== IWM workshop ===
 
* On Saturday of meeting
 
 
 
=== NIH workshop on Trustworthiness ===
 
* Chris attended on Monday and Tuesday
 
* Not quite clear that there is or will be any mandate from funders; just encouragement
 
* FAIR data and TRUST-worthy repositories
 
** FAIR = Findable, Accessible, Interoperable, Reusable
 
** TRUST = Transparency, Responsibility, User community, Sustainability, Technology
 
* Chris will review briefly at next site-wide call
 
* Karen: This is something the data commons really wants
 
** Maybe just need to make sure that the Alliance meets these requirements going forward, not so much for WormBase (?)
 
 
 
 
 
== April 18, 2019 ==
 
 
 
=== IWM swag ===
 
* Stickers, screen cloths?
 
* Jessie's design(s)?
 
* Daniel reaching out to Caltech security who has nice screen cloths
 
* Print list of WormBase tools or user guide on cloth (one side; logo on the other?)?
 
* Will get quote (maybe ≤$1 per cloth?)
 
 
 
=== Life stage and anatomy ontologies ===
 
* Each ontology now has an ODK GitHub repository (thanks Nico!):
 
** Anatomy ontology: https://github.com/obophenotype/c-elegans-gross-anatomy-ontology
 
** Life stage ontology: https://github.com/obophenotype/c-elegans-development-ontology
 
* We will perform a round of comparisons between the original OBO files and the ODK-generated OBO files
 
* Will follow up with quality control fixes (e.g. duplicate or missing definitions)
 
 
 
=== Biocurator meeting ===
 
* EuroPMC - have access to 80-90% full text of open access papers
 
** Would be good for WormBase & Textpresso to work with them
 
* Lots of groups working together on pathways
 
** SwissProt, GO, Reactome
 
* SwissLipids
 
** Metabolomics database pilot
 
** https://www.swisslipids.org/#/
 
* RHEA to replace KEGG (which is well curated but not (no longer) open)
 
** https://www.rhea-db.org/home
 
* Author First Pass poster presented (won 3rd place out of ~200 posters!)
 
** Analogous to FlyBase's 'Fast Track Your Paper' (FTYP)
 
** FTYP does not extract entities
 
** Should evolve into an Alliance pipeline
 
* Data visualization talk (Sean O'Donoghue)
 
** Don't use rainbow heatmaps
 
** Oval representation of time course
 
** Valerio spoke to him; D3 is now a standard library for data visualization
 
 
 
=== GO CAM ===
 
* Could try to generate automated descriptions using GO CAM models
 
* Group is trying to come up with model naming scheme
 
 
 
=== Gene Expression Omnibus (GEO) ===
 
* GEO data has user submission forms that refer to life stages, anatomy but don't map to WB unique IDs
 
* Maybe we can ask GEO to update their data submission forms to use standard IDs
 
* Would help reduce amount of effort required by WB to curate the entries after submission to GEO
 
* GEO forms apply to all species; controlled vocabularies/ontologies could be submitted to GEO for incorporation into their forms
 
 
 
=== RNA-Seq data processing pipeline (Alaska) ===
 
* Raymond, Juancarlos, David Angeles and Joseph developed automated data processing pipeline
 
* http://alaska.caltech.edu/
 
* Maps reads to the genome; will it return FPKM values for each gene?
 
 
 
 
 
== April 25, 2019 ==
 
 
 
=== WormBase plans for coming year ===
 
* Jae
 
** help develop better usability of data and tools for expression and regulation
 
** Venn diagrams
 
** Get more up to date on protein-DNA and protein-RNA interactions, may distinguish small scale from large scale
 
** GO CAM curation, once there are defined best practices for editing with Noctua
 
* Kimberly
 
** Migration of all manual GO annotations to Noctua as GO CAM models; Jae may want to wait until the migration is done (aiming for mid-summer)
 
*** Will write rules for converting individual simple annotations and complex annotations (with LEGO extensions) into GO-CAM models
 
** Will continue to develop GO CAM models and tools to help/expedite GO CAM model development
 
*** Will work with developers to create next generation of annotation forms; some more table-based input forms
 
*** Annotation review tool: Once annotations are in, this will allow for efficient annotation search and editing
 
*** Will continue to work on defining best practices for Noctua usage
 
** Will keep working on developing the gene ontology
 
* Ranjana
 
** Gene descriptions: need to bring in pathway data; processes alone are insufficient; will try to use GO CAM models (proof of concept)
 
*** Paul S: would be good to identify low information genes for curation priorities
 
*** Can include information about relevant chemicals
 
** Human disease curation: WB disease data into the Alliance
 
*** Improved text-mining approach to identify disease model papers
 
*** Paul S: May want to work on pathways/GO-CAM models for disease genes
 
* Wen
 
** Proteomics curation, tool development
 
*** Work with Hinxton to curate proteomics data at Caltech
 
*** 57 existing datasets in ProteomExchange
 
*** Common follow up to RNA Seq experiments
 
*** Jae: will we handle single-cell proteomics? Wen: Can consider part of sample condition, and include with all other proteomics data
 
** Expression clusters - will focus on 'high quality' papers, i.e. useful to community; some have poor metadata and authors don't respond to emails
 
** Outreach - will explore the possibility of having local institutes invite WormBase staff to give talks (pay travel costs?); coincide with meetings?
 
*** Northwest worm meeting in Seattle? Chicago worm meeting?
 
*** Bar Harbor tutorial this summer; a good precedent/model for future visits to other institutes?
 
** RNA Seq, don't want to step on Hinxton's toes WRT RNA-seq curation
 
* Raymond
 
** Focused cell function curation; want to use Noctua, but not sure we can use all relevant (WB-specific) ontologies in Noctua
 
** Are supported relations in Noctua good enough for this purpose? May need development
 
** Re-working the anatomy ontology; work on logical definitions; e.g. how do we define a single cell type?
 
* Marie Claire
 
** Finishing a micropublication on a GO CAM model; continuing to work with Noctua and improve usage
 
* Daniela
 
** Gene expression - want to attempt to automate expression curation; using AFP-like pipelines and other automation
 
*** ~150 expression pattern papers coming in every two months; many are reassessing expression using CRISPR constructs
 
*** Wen: focus on genes whose expression have never been studied?
 
*** Will still do manual steps of curation pipeline, but would begin to automate certain steps of curation pipeline
 
*** Complex patterns are difficult to automate
 
** Micropublication, Wen: is there anything else we can do to help?
 
*** Daniela: Trial attempts to submit a paper to test and provide feedback on submission pipeline
 
*** Will continue to develop methods to calculate metrics and citation indices, etc.
 
* Chris
 
** Will continue with mass email and community curation pipeline
 
*** Want to evaluate existing issues and how to improve efficiency and minimize technical and submission errors
 
** Will continue working on relevant sentence detection for phenotype, maybe expand to genetic interactions
 
** Will continue to develop phenotype ontology and alignment with other phenotype ontologies; patternization and logical definitions
 
** Will also work on life stage and anatomy ontologies with Raymond
 
** Paul S: maybe we can present authors with predicted genetic interactions and ask for confirmation of binary interactions which can then feed into GO-CAM models and pathway curation; can stick to simple binary associations for now, forgoing details like interaction type and alleles etc.
 
* Gary
 
** Continue working on phenotype ontology
 
** Prioritizing genes that don't have phenotype info; working with Juancarlos to identify papers that may have high value, novel annotations
 
* Juancarlos
 
** General tool maintenance and development
 
** Working with Ranjana and Valerio to work on automated gene description tools: React forms for curators to do QC check, using filters and search options
 
 
 
=== Screen cloths for IWM swag ===
 
* Daniel got quotes
 
* Give feedback on style
 
* Maybe use the cartoon (Dick & Jane) for community curators and tool menu for general meeting participants
 
* Will try to order next week
 

Latest revision as of 20:03, 14 January 2021

Previous Years

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2019 Meetings

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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.