Difference between revisions of "WormBase-Caltech Weekly Calls"

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== April 2, 2020 ==
=== Community phenotype requests ===
* March 9-28
* 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 ===
* Tracking volunteers [https://docs.google.com/spreadsheets/d/1ldECC44PXMilcDO6ctz-8AkRZntfDoV0Wtc4F-T_Zvg/edit?usp=sharing here]
* 14 volunteers so far, all have been assigned a WBPerson ID
* Chris will set up a webinar tutorial in the coming week or two
=== AFP pipeline ===
* Will resend email requests to authors that haven't already responded
* May also send out for older papers
* 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
===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 OA 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 approval of proposed models, will need dumper changes as well; hopefully we have enough time to get all this done for WS278
===ZOOM for tutorial===
* High Definition (1440p)
* Caltech account works well
===New AFP version===
* Planned to be released in June
* We need to improve datatype definitions. Please take a look at the current form here: http://textpressocentral.org:5000
* Frequency of automated alerts on new submissions for specific datatypes will change monthly to weekly

Revision as of 15:33, 7 May 2020