Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
  
= 2018 Meetings =
 
  
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
 
  
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
+
= 2020 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
 +
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
== May 3, 2018 ==
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
=== SimpleMine output ===
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
* Wen was working on simplification of SimpleMine output
 
* Considering removing general terms in an ontology when more specific terms exist
 
* Concern that we would be removing information; will keep terms
 
  
=== SPELL topics ===
 
* Topics in SPELL need some organization, possibly trimming
 
* We could create a graph (SObA) display of topics (based on GO process)
 
  
=== SPELL problem with WS265 ===
+
== June 4, 2020 ==
* Wen had to debug; SPELL has limit of how many genes can be processed per data set (46,340)
 
* Wen trying to accommodate, deleting some genes from data set that had no expression (kludge)
 
* Wen will write to Matt Hibbs to ask how to deal with
 
* Will Alliance work together on a system to analyze large scale expression data?
 
  
=== Curator candidate ===
+
=== Citace (tentative) upload ===
* Will arrive at 10am
+
* CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
* Skype calls with remote curators
+
* Citace upload to Hinxton on Friday, July 10th
* Curators will send group Skype handle and requested time to talk
 
  
 +
=== Caltech reopening ===
 +
* Paul looking to get plan approved
 +
* People that want to come to campus need to watch training video
 +
* Masks available in Paul's lab
 +
* Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
 +
** Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
 +
* Need to coordinate, maybe make a Google calendar to do so (also Slack)
 +
* Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
 +
* Also, need to submit who you were in contact with for contact tracing
 +
* Form is used all week, and hold on to it until asked to be submitted
 +
* If someone goes in to the office, they could print several forms for people to pick up in WB offices
  
== May 10, 2018 ==
+
=== Nameserver ===
 +
* Nameserver was down
 +
* CIT curators would still like to have a single form to interact with
 +
* Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
 +
* Still putting genotype and all info for a strain in the reason/why field in the nameserver
 +
* We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
 +
* Hinxton is pulling in CGC strains, how often?
 +
* Caltech could possibly get a block of IDs
  
=== ECO terms for genome editing ===
+
=== Alliance SimpleMine ===
* Asking group's feedback on ECO terms for genome editing (Daniela)
+
* Any updates? 3.1 feature freeze is tomorrow
* What would be used for fly-enhancer trap experiment?
+
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
* Genomically encoded GFP, for example
 
* ECO: GFP localization
 
* ECO term, example: Fluorescent protein transcript localization evidence
 
* Single copy transgene? Endogenous locus?
 
* Whether it is CRISPR or not may not be relevant
 
* May request ECO terms that capture distinct types of transgenes evidence
 
* Will use generic term for now
 
* Do other MODs use ECO?
 
* May want to capture endogenous/non-endogenous, multi-copy/single-copy distinctions
 
* Many of these features are captured in the transgene and construct objects already; specific ECO code redundant?
 
  
=== ZFIN SAB ===
 
* Significant involvement in Alliance
 
* Interest in micropublications; will push a pilot
 
* June 19, moving from older DB to Postgres
 
* Investigating automation for some curation processes
 
* Students review which papers to include; acquire PDF
 
* Curate paper-by-paper
 
  
=== Alliance ===
+
== June 11, 2020 ==
* Supplement request for year 3, due soon (May 15)
 
* Formal report from NHGRI, 18-month plan looks good
 
* Further future plans (from NHGRI perspective) aren't quite clear
 
* Software infrastructure?
 
* Central- vs. MOD-control of resources questions
 
* Likely will have to write a NIH proposal in Fall or Winter
 
* How much is Alliance going to handle human variants?
 
* NHGRI interested in metabolomics; Alliance plans?
 
  
=== Genome-wide screens ===
+
=== Name Service ===
* Had help desk question about phenotypic screens in organisms other than worms, flies, yeast, bacteria
+
* Testing site now up; linked to Mangolassi
* There have been human cell line phenotypic screens (e.g. siRNA/shRNA); who curates these, if anyone?
+
* CGI from Juancarlos not accepting all characters, including double quotes like "
* Also, induced pluripotent stem cell experiments
+
* Example submission that fails via CGI
 +
WBPaper000XXXX; genotype: blah::' " ` / < > [ ] { } ? , . ( ) * ^ & % $ # @ ! \ | &alpha; &beta; Ω ≈ µ ≤ ≥ ÷ æ … ˚ ∆ ∂ ß œ ∑ † ¥ ¨ ü i î ø π “  ‘ « • – ≠ Å ´ ∏ » ± — ‚ °
 +
* Juancarlos will look into and try to fix
  
=== Nameserver issues ===
+
=== Alliance Literature group ===
* Issue came up about assigning unique WBStrain IDs
+
* Textpresso vs. OntoMate vs. PubMed
* Can use a nightly nameserver dump from Hinxton to populate Postgres/OA
+
* Still some confusion about what the different tasks can be performed in each tool
* Will need to clean up existing strains in Postgres
+
* Working on collecting different use cases on spreadsheet
* Also, considering unique IDs for genotypes
+
* Sentence-based search is big strength of Textpresso
* Mechanics of naming and managing naming of objects
+
* At latest meeting performed some large searches for OntoMate and Textpresso
** Nightly syncing (cronjob) to nameserver
+
* Literature acquisition: still needs work
** Ideally, we would have instant updates; Hinxton firewall prevents direct access; Matt working on establishing a separate nameserver location to gain direct access
+
** Using SVM vs. Textpresso search to find relevant papers
** Strain names (at least historically) have been updated quarterly from CGC file
+
** Species based SVM? Currently use string matching to derive different corpora
** Curators need mechanism to create and use strain (and variation) names right away
+
** Finding genes and determining which species those genes belong to?
** Current system requires manual denormalization step; has worked so far
 
  
 +
=== Alliance priorities? ===
 +
* Transcription regulatory networks
 +
* Interactions can focus on network viewer eventually
 +
** May want different versions/flavors of interaction viewers
 +
** May also want to work closely with GO and GO-CAMs
 +
* Gene descriptions can focus on information poor genes, protein domains, etc.
  
== May 17, 2018 ==
+
=== Sandbox visual cues ===
 +
* Juancarlos and Daniela will discuss ways to provide visual cues that a curator is on a sandbox form (on Mangolassi) vs live form (on Tazendra)
 +
* AFP and Micropub dev sites have indicators
 +
* Could play with changing the background color? Maybe too hard to look at?
 +
* Change the color of the title of the form, e.g. the OA?
 +
* Will add red text "Development Site" at top of the OA form
  
=== Strains ===
+
=== Evidence Code Ontology ===
* Create a strain OA? Central curation tool for strain data?
+
* Kimberly and Juancarlos have worked on a parser
* Would need to maintain synchrony with CGC and Hinxton
+
* Will load into ACEDB soon
* Postgres/Tazendra variation adding CGI: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo
 
* Will add similar link for Strains, adding info to obo_name_strain and obo_data_strain as well as a tempfile, which will those objects in postgres when the nightly_geneace.pl updates the OA strain info
 
  
=== SAB 2018 ===
 
* Who will present? Present what?
 
* We can generate a central document with stats to give to SAB
 
* Ask SAB for opinions and guidance?
 
* Would be good to assess current efforts and priorities, ask if we should stay the course or make modifications to our approach
 
  
 +
== June 18, 2020 ==
  
== May 24th, 2018 ==
+
=== Undergrad phenotype submissions ===
 +
* Chris gave presentation to Lina Dahlberg's class about community phenotype curation
 +
* Class took survey about experience with presentation and experience trying to curate worm phenotypes
 +
** Survey results: https://www.dropbox.com/s/00cit5aitv8yu27/Dahlberg_class_survey_results.xlsx?dl=0
 +
** Some students didn't benefit, but most did; nice feedback!
 +
** Lina intends to publish/micropublish the survey results so please don't share
 +
* Since April 24, the class has submitted 171 annotations from 23 papers (some redundant and some still under review)
  
=== Helpdesk ===
+
=== Special characters in OA/Postgres ===
*[https://github.com/WormBase/website/issues/6423 Not sure if this falls under content....]
+
* There are many special characters in free text entries in the OA; probably all from copy-pasting directly from PDF
* User asked about phenotype information being incorporated into the gene description
+
* In some cases it seems the special characters cause problems for downstream scripts (e.g. FTP interactions file generator)
* Chris directed him to phenotype submission form; he has since submitted the phenotypes
+
* It would probably be good to script the replacement of special characters with their appropriate simple characters or encoded characters
* Phenotype data hasn't yet been incorporated into the automated descriptions pipeline
+
* Juancarlos wrote Perl script on Mangolassi at:
* We can direct him to the gene description submission form
+
** /home/postgres/work/pgpopulation/grg_generegulation/20200618_summary_characters/get_summary_characters.pl
* Ranjana will respond to user email
+
** Will find bad characters and their pgids for a given Postgres table
* Will likely swap out older WB automated description pipeline with newer Alliance automated description pipeline
+
** Will find bad data and their pgids for the same table
 +
** People can query their data tables for these characters
 +
* Chris & Wen will work on compiling a list of bad characters that tend to come up
  
=== Relations Ontology ===
+
=== Citace upload ===
*Working on new model for importing RO terms into WormBase
+
* July 10th citace-to-Hinxton upload
*Question: Do we need to import all of RO?
+
* July 7th citace upload, but Wen will be on vacation so will upload to Wen on Tuesday, June 30th
**For example, RO also has terms from other ontologies:
 
    [Term]
 
    id: GO:0003674
 
    name: molecular_function
 
    is_a: BFO:0000015 ! process
 
    property_value: IAO:0000589 "molecular process" xsd:string
 
*Question: How much term information do we want and/or need?
 
**For example:
 
    [Typedef]
 
    id: BFO:0000050
 
    name: part of
 
    def: "a core relation that holds between a part and its whole" []
 
    property_value: IAO:0000111 "is part of" xsd:string
 
    property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string
 
    property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string
 
    property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string
 
    property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string
 
    property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at
 
    certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string
 
    property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an
 
    independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically
 
    dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A
 
    material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent
 
    continuant: use 'bearer of'." xsd:string
 
    property_value: IAO:0000118 "part_of" xsd:string
 
    property_value: RO:0001900 RO:0001901
 
    property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections
 
    property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf
 
    property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string
 
    is_transitive: true
 
    is_a: RO:0002131 ! overlaps
 
    inverse_of: BFO:0000051 ! has part
 
  
*For curation, we could import only the BFO and RO ID spaces of RO, but include all of the tag-value pairs (the usage examples might be helpful)
 
*For WB, though, we could injest only the BFO and RO ID spaces of RO, and only include in the model: id, name, def, is_a, domain, range, and inverse_of tags
 
**We can always link out from WB to pages with more detail on RO terms
 
  
*Will use RO ids in ?GO_annotation model in the Annotation_relation part (model will need an update)
+
== June 25, 2020 ==
**The ?GO_annotation model also refers to relations used in annotation extensions.  Unfortunately, though, not all annotation extension relations are in RO, so we can't yet use RO in this part of the model.
 
**We can either import these other GO relations as a separate class, or import them if/when they get included in RO (there is a PRO/RO meeting scheduled for late October with some preliminary phone conferences prior).
 
**The Alliance Gene Expression group is also dealing with this issue.
 
*Where can we use RO terms in other curation models?
 
* Kimberly will add to the agenda for the next WB site-wide conference call
 
  
=== Methods in Molecular Biology book ===
+
=== Caltech Summer Student ===
* Eukaryotic Genome Databases, has WormBase chapter
+
* Paul has new summer student
* Book arrived at Caltech
+
** Molecular lesion curation, maybe
* Chris will ask publishers about getting PDFs without watermarks
+
** Are early stops more or less likely to be null mutations?
 +
** Alleles are flagged as null in WB in the context of phenotypes
 +
** Would be good to query Postgres for null alleles and work from there
 +
* Fernando
 +
** Anatomy function
 +
** GO curation? Curating transcription factors?
 +
*** Checking for consistent curation
  
=== ICBO 2018 meeting ===
+
=== Worm Community Diversity Meeting ===
* International Conference on Biological Ontology (2018)
+
* Organized by Ahna Skop and Dana Miller
* Raymond considering submitting abstract
+
* Invite posted on Facebook "C. elegans Researchers" group
* Not clear if it needs to be a full paper; can we resubmit Biocuration meeting abstract?
+
* Two meetings held: one Thursday (June 18th), one Friday (June 19th)
* Can the content be published elsewhere once submitted to the meeting?
+
* Chris attended last Friday (June 19th)
 +
* Worm Board looking to take input and ideas from this meeting and incorporate into meetings and events
 +
* One idea was to document and track outreach efforts and what people have learned from them and organize them in a central location, maybe WormBase or Worm Community Forum
 +
* Also, there was a suggestion to have a tool that could inform potential students of worm labs in their respective local area
 +
** Ask Todd; he used to have a map of researchers; Todd had asked Cecilia to curate lab location and institution
 +
* Person and Laboratory addresses in ACEDB have a different format, so looking to reconcile
 +
* Do we know how many labs are still viable? Check for a paper verified in the last 5 years, or requested strains from the CGC recently
 +
** Most labs were real
  
 +
=== C_elegans Slack group ===
 +
* Called "C_elegans"
 +
* Chris made a "WormBase" channel for people to post questions, comments
 +
* Chris will look into inviting everyone and possibly integrating with help@wormbase.org email list
  
 +
=== WormBase Outreach Webinars ===
 +
* While travel is still restricted, we should consider WormBase webinars
 +
* Scott working on a JBrowse webinar
 +
* Could have a different topic each month
 +
* Should collect topics to cover and assign speakers (maybe multiple speakers per topic; keep it lively)
 +
* Should set up a schedule
 +
* How should we advertise? Can post on blog, twitter, etc.
  
== May 31th, 2018 ==
+
=== New transcripts expanding gene range ===
 +
* Will bring up at next week's site-wide call
 +
* Possibly due to incorporation of newer nanopore reads
 +
* Many genes coming in WS277 have expanded well beyond the gene limits as seen in WS276
 +
** Example genes: pes-2.2, pck-2, herc-1, atic-1
 +
* Has several repercussions:
 +
** WormBase does not submit alleles affecting more than one gene; with these gene expansions suddenly alleles once only affecting a single gene are now affecting two genes, and so are now omitted from loading into the Alliance (including any phenotype and/or disease annotations)
 +
** Some expanded genes are now being attributed with thousands of alleles/variants
  
=== Feedbacks from Front Range Worm Meeting ===
+
=== Citace upload ===
* Is it possible to collect old theses online and load them into Textpresso?
+
* Upload files to Spica/Wen by Tuesday (June 30th) 10am
* Shall we suggest authors put "elegans" in titles and abstracts? Min Han said some of his papers do not have this keyword.
+
* Wen will clean up folders in Spica (older files from WS277 not cleared out for some reason)
* Community curation. Erin Osborne Nishimura mentioned camps and courses for undergraduate research. Can they do allele and phenotype curation for WormBase? Who will follow up with her?
 
* Shall we send the AFP form to some users for feedback?
 
  
=== Updates about SPELL ===
+
==July 9th, 2020==
* SGD moved their SPELL to AWS. WormBase needs to set up our own AWS and SGD can give us their code. Will Raymond be able to help set up the AWS? Once installing the AWS SPELL following SGD's code, Wen can load WormBase SPELL data to it.
+
===Gene names issue in SimpleMine and other mining tools===
 +
*Wen: Last week, Jonathan Ewbank raised the issue of gene names that may refer to multiple objects.
 +
*this can be an issue for multiple data mining tools including WormMine, BioMart, and Gene Set Enrichment.
 +
*Perhaps have a standalone approach to check if any gene name among a list may refer to multiple objects (users check their name lists before submitting them to any data mining tool).
 +
*Jae: The public name issue has heterogeneous natures. That means there may be no single solution to solve all those problems.
 +
*Gene list curation from high-throughput studies, confusing usage of public names probably less than 2% (still cannot be ignored). See examples below--
 +
**single public name is assigned to multiple WBgene ID, Wen has a list of these genes
 +
**overlapped or dicistronic genes, ex. mrpl-44 and F02A9.10
 +
**overlapped or dicistronic, but has a single sequence name, examples:
 +
    exos-4.1 and tin-9.2 (B0564.1)
 +
    eat-18 and lev-10 (Y105E8A.7)
 +
    cha-1 and unc-17 (ZC416.8)
 +
 
 +
**simple confusion from authors, ex. mdh-1 and mdh-2
 +
*One of the most significant problems is a propagation to other DB and papers of  these gene name issues.
 +
*We can make a special note for each gene page, but the people using batch analysis could not catch that easily.
 +
*Conclusion: Jae and Wen will work on a tool that lets Users "sanitize" their gene lists before submission to data mining tools. They will also write a microPub explaining this issue to the community.
 +
 
 +
===Wormicloud===
 +
*Please test and leave any feedback on the word cloud tool (Wormicloud), https://wormicloud.textpressolab.com/
 +
*Valerio and Jae have worked on a tool that uses data in Textpresso; given a keyword, eg. "transposon", the tool generates a word cloud and word trend.
 +
*Any keyword can generate a graph that plots trends of occurence across the years in publication abstracts.
 +
 
 +
===Noctua 2.0 form ready to use===
 +
*Caltech summer student will try using Noctua initially for dauer (neuronal signaling) pathways
 +
 
 +
===Nightly names service updates to postgres===
 +
*Nightly using Matt's wb-names-export.jar to get full output of genes from datomic/names service, and updating postgres based on that.

Latest revision as of 22:11, 9 July 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings



2020 Meetings

January

February

March

April

May


June 4, 2020

Citace (tentative) upload

  • CIT curators upload to citace on Tuesday, July 7th, 10am Pacific
  • Citace upload to Hinxton on Friday, July 10th

Caltech reopening

  • Paul looking to get plan approved
  • People that want to come to campus need to watch training video
  • Masks available in Paul's lab
  • Can have maximum of 3 people in WormBase rooms at a time; probably best to only allow one person per WB room
    • Could possibly have 2 people in big room (Church 64) as long as they stay at least 10 feet apart
  • Need to coordinate, maybe make a Google calendar to do so (also Slack)
  • Before and after you go to campus, you need to take your temperature and assess your symptoms (if any) and submit info on form
  • Also, need to submit who you were in contact with for contact tracing
  • Form is used all week, and hold on to it until asked to be submitted
  • If someone goes in to the office, they could print several forms for people to pick up in WB offices

Nameserver

  • Nameserver was down
  • CIT curators would still like to have a single form to interact with
  • Is it possible to create objects at Caltech and let a cronjob assign IDs via the nameserver? May not be a good idea
  • Still putting genotype and all info for a strain in the reason/why field in the nameserver
  • We plan to eventually connect strains to genotypes, but need model changes and curation effort to sort out
  • Hinxton is pulling in CGC strains, how often?
  • Caltech could possibly get a block of IDs

Alliance SimpleMine

  • Any updates? 3.1 feature freeze is tomorrow
  • Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call


June 11, 2020

Name Service

  • Testing site now up; linked to Mangolassi
  • CGI from Juancarlos not accepting all characters, including double quotes like "
  • Example submission that fails via CGI
WBPaper000XXXX; genotype: blah::' " ` / < > [ ] { } ? , . ( ) * ^ & % $ # @ ! \ | α β Ω ≈ µ ≤ ≥ ÷ æ … ˚ ∆ ∂ ß œ ∑ † ¥ ¨ ü i î ø π “   ‘ « • – ≠ Å ´ ∏ » ± — ‚ °
  • Juancarlos will look into and try to fix

Alliance Literature group

  • Textpresso vs. OntoMate vs. PubMed
  • Still some confusion about what the different tasks can be performed in each tool
  • Working on collecting different use cases on spreadsheet
  • Sentence-based search is big strength of Textpresso
  • At latest meeting performed some large searches for OntoMate and Textpresso
  • Literature acquisition: still needs work
    • Using SVM vs. Textpresso search to find relevant papers
    • Species based SVM? Currently use string matching to derive different corpora
    • Finding genes and determining which species those genes belong to?

Alliance priorities?

  • Transcription regulatory networks
  • Interactions can focus on network viewer eventually
    • May want different versions/flavors of interaction viewers
    • May also want to work closely with GO and GO-CAMs
  • Gene descriptions can focus on information poor genes, protein domains, etc.

Sandbox visual cues

  • Juancarlos and Daniela will discuss ways to provide visual cues that a curator is on a sandbox form (on Mangolassi) vs live form (on Tazendra)
  • AFP and Micropub dev sites have indicators
  • Could play with changing the background color? Maybe too hard to look at?
  • Change the color of the title of the form, e.g. the OA?
  • Will add red text "Development Site" at top of the OA form

Evidence Code Ontology

  • Kimberly and Juancarlos have worked on a parser
  • Will load into ACEDB soon


June 18, 2020

Undergrad phenotype submissions

  • Chris gave presentation to Lina Dahlberg's class about community phenotype curation
  • Class took survey about experience with presentation and experience trying to curate worm phenotypes
  • Since April 24, the class has submitted 171 annotations from 23 papers (some redundant and some still under review)

Special characters in OA/Postgres

  • There are many special characters in free text entries in the OA; probably all from copy-pasting directly from PDF
  • In some cases it seems the special characters cause problems for downstream scripts (e.g. FTP interactions file generator)
  • It would probably be good to script the replacement of special characters with their appropriate simple characters or encoded characters
  • Juancarlos wrote Perl script on Mangolassi at:
    • /home/postgres/work/pgpopulation/grg_generegulation/20200618_summary_characters/get_summary_characters.pl
    • Will find bad characters and their pgids for a given Postgres table
    • Will find bad data and their pgids for the same table
    • People can query their data tables for these characters
  • Chris & Wen will work on compiling a list of bad characters that tend to come up

Citace upload

  • July 10th citace-to-Hinxton upload
  • July 7th citace upload, but Wen will be on vacation so will upload to Wen on Tuesday, June 30th


June 25, 2020

Caltech Summer Student

  • Paul has new summer student
    • Molecular lesion curation, maybe
    • Are early stops more or less likely to be null mutations?
    • Alleles are flagged as null in WB in the context of phenotypes
    • Would be good to query Postgres for null alleles and work from there
  • Fernando
    • Anatomy function
    • GO curation? Curating transcription factors?
      • Checking for consistent curation

Worm Community Diversity Meeting

  • Organized by Ahna Skop and Dana Miller
  • Invite posted on Facebook "C. elegans Researchers" group
  • Two meetings held: one Thursday (June 18th), one Friday (June 19th)
  • Chris attended last Friday (June 19th)
  • Worm Board looking to take input and ideas from this meeting and incorporate into meetings and events
  • One idea was to document and track outreach efforts and what people have learned from them and organize them in a central location, maybe WormBase or Worm Community Forum
  • Also, there was a suggestion to have a tool that could inform potential students of worm labs in their respective local area
    • Ask Todd; he used to have a map of researchers; Todd had asked Cecilia to curate lab location and institution
  • Person and Laboratory addresses in ACEDB have a different format, so looking to reconcile
  • Do we know how many labs are still viable? Check for a paper verified in the last 5 years, or requested strains from the CGC recently
    • Most labs were real

C_elegans Slack group

  • Called "C_elegans"
  • Chris made a "WormBase" channel for people to post questions, comments
  • Chris will look into inviting everyone and possibly integrating with help@wormbase.org email list

WormBase Outreach Webinars

  • While travel is still restricted, we should consider WormBase webinars
  • Scott working on a JBrowse webinar
  • Could have a different topic each month
  • Should collect topics to cover and assign speakers (maybe multiple speakers per topic; keep it lively)
  • Should set up a schedule
  • How should we advertise? Can post on blog, twitter, etc.

New transcripts expanding gene range

  • Will bring up at next week's site-wide call
  • Possibly due to incorporation of newer nanopore reads
  • Many genes coming in WS277 have expanded well beyond the gene limits as seen in WS276
    • Example genes: pes-2.2, pck-2, herc-1, atic-1
  • Has several repercussions:
    • WormBase does not submit alleles affecting more than one gene; with these gene expansions suddenly alleles once only affecting a single gene are now affecting two genes, and so are now omitted from loading into the Alliance (including any phenotype and/or disease annotations)
    • Some expanded genes are now being attributed with thousands of alleles/variants

Citace upload

  • Upload files to Spica/Wen by Tuesday (June 30th) 10am
  • Wen will clean up folders in Spica (older files from WS277 not cleared out for some reason)

July 9th, 2020

Gene names issue in SimpleMine and other mining tools

  • Wen: Last week, Jonathan Ewbank raised the issue of gene names that may refer to multiple objects.
  • this can be an issue for multiple data mining tools including WormMine, BioMart, and Gene Set Enrichment.
  • Perhaps have a standalone approach to check if any gene name among a list may refer to multiple objects (users check their name lists before submitting them to any data mining tool).
  • Jae: The public name issue has heterogeneous natures. That means there may be no single solution to solve all those problems.
  • Gene list curation from high-throughput studies, confusing usage of public names probably less than 2% (still cannot be ignored). See examples below--
    • single public name is assigned to multiple WBgene ID, Wen has a list of these genes
    • overlapped or dicistronic genes, ex. mrpl-44 and F02A9.10
    • overlapped or dicistronic, but has a single sequence name, examples:
   exos-4.1 and tin-9.2 (B0564.1)
   eat-18 and lev-10 (Y105E8A.7)
   cha-1 and unc-17 (ZC416.8)
    • simple confusion from authors, ex. mdh-1 and mdh-2
  • One of the most significant problems is a propagation to other DB and papers of these gene name issues.
  • We can make a special note for each gene page, but the people using batch analysis could not catch that easily.
  • Conclusion: Jae and Wen will work on a tool that lets Users "sanitize" their gene lists before submission to data mining tools. They will also write a microPub explaining this issue to the community.

Wormicloud

  • Please test and leave any feedback on the word cloud tool (Wormicloud), https://wormicloud.textpressolab.com/
  • Valerio and Jae have worked on a tool that uses data in Textpresso; given a keyword, eg. "transposon", the tool generates a word cloud and word trend.
  • Any keyword can generate a graph that plots trends of occurence across the years in publication abstracts.

Noctua 2.0 form ready to use

  • Caltech summer student will try using Noctua initially for dauer (neuronal signaling) pathways

Nightly names service updates to postgres

  • Nightly using Matt's wb-names-export.jar to get full output of genes from datomic/names service, and updating postgres based on that.