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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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
+
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 ?
  
== April 2, 2020 ==
+
</pre>
  
=== Community phenotype requests ===
+
===Minutes===
* March 9-28
+
====PubMed LinkOut to WormBase Paper Pages====
* 2,548 emails went out; 89 bounced; 6 resent; 13 backup; 2,478 successful emails
 
* 361 annotations overall
 
* 48 papers requested received curation (2% response rate)
 
* 53 distinct papers overall (5 papers without request)
 
* 53 distinct persons overall
 
  
=== Community curation volunteers ===
+
====Update cycle for HGNC data in the OA====
* Tracking volunteers [https://docs.google.com/spreadsheets/d/1ldECC44PXMilcDO6ctz-8AkRZntfDoV0Wtc4F-T_Zvg/edit?usp=sharing here]
+
*We will update when Alliance updates the data
* 14 volunteers so far, all have been assigned a WBPerson ID
+
*Juancarlos will set it to check the timestamps and if they change will do an update for the OAs
* Chris will set up a webinar tutorial in the coming week or two
 
  
=== AFP pipeline ===
+
====CENGEN====
* Will resend email requests to authors that haven't already responded
+
*Wen, Daniela, and Raymond will look at the datasets to work out how to incorporate. Start simple.
* May also send out for older papers
+
*We will make links to pages on their site.
* May work with people to help
 
* Does the old AFP form still work? It should
 
* If someone has a link to the old form, they won't get one for the new form
 
* Maybe could set up an automatic redirect from the old form to the new form
 
* Received many submissions recently (>20% response rate)
 
 
 
=== Ontology Annotator ===
 
* Need to work on Genotype OA dumper
 
* Turns out semicolons are problematic (currently in genotypes and transgenes) for object names (ontology fields)
 
* Ampersands (&) are also problematic for object names in the OA
 
** 20237  | Is[Pgcy-5::daf-2a::venus; Punc-122::mCherry]                          | 2014-10-08 10:32:45.874519-07
 
** 20239  | Ex[Pgcy-5::casy-1::venus; Pgcy-5::aman-2::mCherry; Punc-122::mCherry] | 2014-10-08 10:45:23.202362-07
 
** 20238  | Is[Pgcy-5::daf-2c::venus; Punc-122::mCherry]                          | 2014-10-08 10:38:19.859078-07
 
** 25249  | Ex[Prheb-1::rheb-1::GFP; unc-119(+]                                  | 2018-06-29 10:16:40.784295-07
 
** 16283  | [hlh-13::GFP;unc-119(+)]                                              | 2013-02-07 17:43:22.384819-08
 
** 26131  | Ex[pedc-3EDC-3::DsRed;pRF4]                                          | 2019-08-14 08:44:49.91063-07
 
 
 
=== Use Slack More ===
 
* Slack is a good tool for quick communication among team members; would be good for all curators to join Slack to enable efficient communication
 
 
 
 
 
== April 9, 2020 ==
 
 
 
=== Volunteer curators ===
 
* Have sent out emails to schedule tutorials
 
* Chris had one tutorial with Michael Davies (Alyson Ashe's lab) yesterday
 
* One already scheduled for next Monday with Wilber and Stephanie from Paul's lab
 
* Two others already scheduled for next Tuesday with Lina Dahlberg and Colin Dolphin
 
 
 
===TAGC is virtual (4.22-25.2020)===
 
FYI in case you missed it
 
*You still have to register (it's free), if you hadn't before
 
https://genetics-gsa.org/tagc-2020/registration/
 
 
 
===summer students===
 
* Caltech SURF students (and other summer students worldwide) now are looking for projects
 
* Maybe they could curate for WormBase
 
* In addition to phenotype, they could curate:
 
** Allele/lesion sequence curation (using Allele Sequence form); maybe Paul Davis could make a tutorial video?
 
** Anatomy function, looking for novel info; opportunity to program/code
 
 
 
=== OA semicolon issue ===
 
* Juancarlos has fixed the issues on sandbox
 
* Curators should test on Mangolassi
 
 
 
=== Textmining/automation ===
 
* Daniela will discuss with Christina Zorn from Xenbase
 
* Will discuss SVM, AFP, Textpresso, etc.
 
 
 
=== Retracted WBPapers ===
 
* Jae & Kimberly put in GitHub ticket to make retractions clear on WormBase site
 
* https://github.com/WormBase/website/issues/7637
 
* Can we systematically detect retractions? Yes
 
* What about finding papers that cite retractions? Maybe, but likely tricky
 
 
 
 
 
== April 16, 2020 ==
 
 
 
=== Community Phenotype Curation Tutorials ===
 
* Chris has run 6 tutorials, recorded 4
 
* MPG files saved on DropBox; ask Chris for access
 
* Plan to edit videos to make tutorial video to post on WB YouTube channel
 
 
 
=== Author First Pass ===
 
* May run a webinar and use Zoom to record
 
* May make a short tutorial video
 
* Jae: Is there documentation for terminology used in the form?
 
 
 
=== Zoom accounts ===
 
* People can try to use Caltech Zoom account
 
 
 
 
 
== April 23, 2020 ==
 
 
 
=== Community Phenotype Curation Tutorials ===
 
* Chris has finished first round of tutorials; 8 tutorials, 6 video recordings
 
* There are ~8 new volunteers; will setup tutorials for them soon
 
 
 
=== ECO code implementation ===
 
* ?ECO_term to replace ?GO_code in ACEDB models
 
* GAF files with three-letter codes can still be generated by mapping
 
 
 
=== Simplemine for Alliance ===
 
* Wen has presented proposal to Search group
 
* Plan is to have a link to the Alliance Simplemine prototype from the Alliance web page
 
 
 
=== Venn diagram tool ===
 
* Conceived by Jae, implemented by Sibyl
 
* Currently used for interactions data
 
* Could use for other data types like phenotype (e.g. comparing RNAi vs. allele phenotype)
 
* Could also use for Expression data, e.g. comparing results from different methods
 
* Could maybe use for disease data
 
 
 
=== AFP tutorial ===
 
* Daniela, Kimberly, Valerio will run through the AFP form with Nikita from Gupta lab tomorrow
 
* May record in the future to make a tutorial video
 
* Daniela may (re-)start curating markers for relevant expression patterns
 
* Wen noticed that many tissue markers are artificial (not necessarily endogenous sequence)
 
 
 
=== Expression markers ===
 
* SURF student projects: Identifying good expression markers? Maybe, but may require more curation experience
 
* Wen looked at expression cluster data; hard to find good, very specific (i.e. neuron) markers
 
* Daniela may (re-)start curating markers for relevant expression patterns
 
* Wen noticed that many tissue markers are artificial (not necessarily endogenous sequence)
 
* Already have an "Expression markers" widget on anatomy term pages
 
* Could combinations of genes (e.g. cGal) act as markers?
 
 
 
== April 30, 2020 ==
 
 
 
=== Adding ?ECO_term class for WS278 ===
 
* Proposed[https://wiki.wormbase.org/index.php/Evidence_Code_Ontology#.3FECO_term_Model ?ECO_term model]
 
** How are the Parent/Child and Ancestor/Descendant tags used in WB for ontology classes?  Do we still need them in .ace files?
 
*Confirm proposed changes to class models that will use this tag:
 
** ?GO_annotation
 
** ?Phenotype
 
** ?Disease_model_annotation
 
 
 
=== Ontology term models in WB ===
 
* Discuss using ?RO_term values in our WB ontology term models
 
* Currently relations between ontology terms are captured with text that is sometimes inconsistent for the same concept, e.g. is_a
 
* Where possible, should be use ?RO_term to express the relations between ontology terms in our WB models?
 
* Impact on web display?
 
 
 
===Entries in the new Genotype OA===
 
*21 genotype entries created in the Genotype required for disease curation
 
*Few more to come, and at some point need to work on the dumper, in order to submit for WS278
 
*The use of the Genotype class across disease related classes waiting on Paul D. for approval, will need dumper changes as well; hopefully we have enough time to get all this done for WS278
 

Latest revision as of 20:03, 14 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.