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| | [[WormBase-Caltech_Weekly_Calls_March_2020|March]] | | [[WormBase-Caltech_Weekly_Calls_March_2020|March]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_April_2020|April]] |
| − | == April 2, 2020 ==
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| − | | |
| − | === Community phenotype requests ===
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| − | * March 9-28
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| − | * 2,548 emails went out; 89 bounced; 6 resent; 13 backup; 2,478 successful emails
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| − | * 361 annotations overall
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| − | * 48 papers requested received curation (2% response rate)
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| − | * 53 distinct papers overall (5 papers without request)
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| − | * 53 distinct persons overall
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| − | | |
| − | === Community curation volunteers ===
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| − | * Tracking volunteers [https://docs.google.com/spreadsheets/d/1ldECC44PXMilcDO6ctz-8AkRZntfDoV0Wtc4F-T_Zvg/edit?usp=sharing here]
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| − | * 14 volunteers so far, all have been assigned a WBPerson ID
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| − | * Chris will set up a webinar tutorial in the coming week or two
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| − | | |
| − | === AFP pipeline ===
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| − | * Will resend email requests to authors that haven't already responded
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| − | * May also send out for older papers
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| − | * May work with people to help
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| − | * Does the old AFP form still work? It should
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| − | * If someone has a link to the old form, they won't get one for the new form
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| − | * Maybe could set up an automatic redirect from the old form to the new form
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| − | * Received many submissions recently (>20% response rate)
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| − | | |
| − | === Ontology Annotator ===
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| − | * Need to work on Genotype OA dumper
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| − | * Turns out semicolons are problematic (currently in genotypes and transgenes) for object names (ontology fields)
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| − | * Ampersands (&) are also problematic for object names in the OA
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| − | ** 20237 | Is[Pgcy-5::daf-2a::venus; Punc-122::mCherry] | 2014-10-08 10:32:45.874519-07
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| − | ** 20239 | Ex[Pgcy-5::casy-1::venus; Pgcy-5::aman-2::mCherry; Punc-122::mCherry] | 2014-10-08 10:45:23.202362-07
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| − | ** 20238 | Is[Pgcy-5::daf-2c::venus; Punc-122::mCherry] | 2014-10-08 10:38:19.859078-07
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| − | ** 25249 | Ex[Prheb-1::rheb-1::GFP; unc-119(+] | 2018-06-29 10:16:40.784295-07
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| − | ** 16283 | [hlh-13::GFP;unc-119(+)] | 2013-02-07 17:43:22.384819-08
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| − | ** 26131 | Ex[pedc-3EDC-3::DsRed;pRF4] | 2019-08-14 08:44:49.91063-07
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| − | | |
| − | === Use Slack More ===
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| − | * Slack is a good tool for quick communication among team members; would be good for all curators to join Slack to enable efficient communication
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| − | | |
| − | | |
| − | == April 9, 2020 ==
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| − | | |
| − | === Volunteer curators ===
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| − | * Have sent out emails to schedule tutorials
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| − | * Chris had one tutorial with Michael Davies (Alyson Ashe's lab) yesterday
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| − | * One already scheduled for next Monday with Wilber and Stephanie from Paul's lab
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| − | * Two others already scheduled for next Tuesday with Lina Dahlberg and Colin Dolphin
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| − | | |
| − | ===TAGC is virtual (4.22-25.2020)===
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| − | FYI in case you missed it
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| − | *You still have to register (it's free), if you hadn't before
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| − | https://genetics-gsa.org/tagc-2020/registration/
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| − | | |
| − | ===summer students===
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| − | * Caltech SURF students (and other summer students worldwide) now are looking for projects
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| − | * Maybe they could curate for WormBase
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| − | * In addition to phenotype, they could curate:
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| − | ** Allele/lesion sequence curation (using Allele Sequence form); maybe Paul Davis could make a tutorial video?
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| − | ** Anatomy function, looking for novel info; opportunity to program/code
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| − | | |
| − | === OA semicolon issue ===
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| − | * Juancarlos has fixed the issues on sandbox
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| − | * Curators should test on Mangolassi
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| − | | |
| − | === Textmining/automation ===
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| − | * Daniela will discuss with Christina Zorn from Xenbase
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| − | * Will discuss SVM, AFP, Textpresso, etc.
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| − | | |
| − | === Retracted WBPapers ===
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| − | * Jae & Kimberly put in GitHub ticket to make retractions clear on WormBase site
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| − | * https://github.com/WormBase/website/issues/7637
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| − | * Can we systematically detect retractions? Yes
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| − | * What about finding papers that cite retractions? Maybe, but likely tricky
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| − | | |
| − | | |
| − | == April 16, 2020 ==
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| − | | |
| − | === Community Phenotype Curation Tutorials ===
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| − | * Chris has run 6 tutorials, recorded 4
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| − | * MPG files saved on DropBox; ask Chris for access
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| − | * Plan to edit videos to make tutorial video to post on WB YouTube channel
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| − | | |
| − | === Author First Pass ===
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| − | * May run a webinar and use Zoom to record
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| − | * May make a short tutorial video
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| − | * Jae: Is there documentation for terminology used in the form?
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| − | | |
| − | === Zoom accounts ===
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| − | * People can try to use Caltech Zoom account
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| − | | |
| − | | |
| − | == April 23, 2020 ==
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| − | | |
| − | === Community Phenotype Curation Tutorials ===
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| − | * Chris has finished first round of tutorials; 8 tutorials, 6 video recordings
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| − | * There are ~8 new volunteers; will setup tutorials for them soon
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| − | | |
| − | === ECO code implementation ===
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| − | * ?ECO_term to replace ?GO_code in ACEDB models
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| − | * GAF files with three-letter codes can still be generated by mapping
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| − | | |
| − | === Simplemine for Alliance ===
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| − | * Wen has presented proposal to Search group
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| − | * Plan is to have a link to the Alliance Simplemine prototype from the Alliance web page
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| − | | |
| − | === Venn diagram tool ===
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| − | * Conceived by Jae, implemented by Sibyl
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| − | * Currently used for interactions data
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| − | * Could use for other data types like phenotype (e.g. comparing RNAi vs. allele phenotype)
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| − | * Could also use for Expression data, e.g. comparing results from different methods
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| − | * Could maybe use for disease data
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| − | | |
| − | === AFP tutorial ===
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| − | * Daniela, Kimberly, Valerio will run through the AFP form with Nikita from Gupta lab tomorrow
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| − | * May record in the future to make a tutorial video
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| − | * Daniela may (re-)start curating markers for relevant expression patterns
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| − | * Wen noticed that many tissue markers are artificial (not necessarily endogenous sequence)
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| − | | |
| − | === Expression markers ===
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| − | * SURF student projects: Identifying good expression markers? Maybe, but may require more curation experience
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| − | * Wen looked at expression cluster data; hard to find good, very specific (i.e. neuron) markers
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| − | * Daniela may (re-)start curating markers for relevant expression patterns
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| − | * Wen noticed that many tissue markers are artificial (not necessarily endogenous sequence)
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| − | * Already have an "Expression markers" widget on anatomy term pages
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| − | * Could combinations of genes (e.g. cGal) act as markers?
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| − | | |
| − | == April 30, 2020 ==
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| − | | |
| − | === Adding ?ECO_term class for WS278 ===
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| − | * Proposed[https://wiki.wormbase.org/index.php/Evidence_Code_Ontology#.3FECO_term_Model ?ECO_term model]
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| − | ** How are the Parent/Child and Ancestor/Descendant tags used in WB for ontology classes? Do we still need them in .ace files?
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| − | *Confirm proposed changes to class models that will use this tag:
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| − | ** ?GO_annotation
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| − | ** ?Phenotype
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| − | ** ?Disease_model_annotation
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| − | | |
| − | === Ontology term models in WB ===
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| − | * Discuss using ?RO_term values in our WB ontology term models
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| − | * Currently relations between ontology terms are captured with text that is sometimes inconsistent for the same concept, e.g. is_a
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| − | * Where possible, should be use ?RO_term to express the relations between ontology terms in our WB models?
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| − | * Impact on web display?
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| − | | |
| − | ===Entries in the new Genotype OA===
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| − | *21 genotype entries created in the Genotype OA required for disease curation
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| − | *Few more to come, and at some point need to work on the dumper, in order to submit for WS278
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| − | *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
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| − | | |
| − | ===ZOOM for tutorial===
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| − | | |
| − | * High Definition (1440p)
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| − | * Caltech account works well
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| − | | |
| − | ===New AFP version===
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| − | * Planned to be released in June
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| − | * We need to improve datatype definitions. Please take a look at the current form here: http://textpressocentral.org:5000
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| − | * Frequency of automated alerts on new submissions for specific datatypes will change monthly to weekly
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