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
 
  
  
= 2019 Meetings =
 
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
+
= 2020 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
 
  
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
+
== June 4, 2020 ==
  
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
+
=== 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
  
== October 3, 2019 ==
+
=== 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
  
=== SObA comparison graphs ===
+
=== Alliance SimpleMine ===
* Raymond and Juancarlos have worked on a SObA-graph based comparison tool to compare two genes for ontology-based annotations
+
* Any updates? 3.1 feature freeze is tomorrow
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 1]
+
* Pending on PI decision; Paul S. will bring it up tomorrow on the Alliance PI call
** [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=annotSummaryCytoscape&filterForLcaFlag=1&filterLongestFlag=1&showControlsFlag=0&datatype=phenotype&geneOneValue=lin-3%20(Caenorhabditis%20elegans,%20WB:WBGene00002992,%20-,%20F36H1.4)&autocompleteValue=let-23%20(Caenorhabditis%20elegans,%20WB:WBGene00002299,%20-,%20ZK1067.1 Example comparison between lin-3 and let-23]
 
* [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 2]
 
** [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=annotSummaryCytoscape&filterForLcaFlag=1&filterLongestFlag=1&showControlsFlag=0&datatype=phenotype&geneOneValue=lin-3%20(Caenorhabditis%20elegans,%20WB:WBGene00002992,%20-,%20F36H1.4)&autocompleteValue=let-23%20(Caenorhabditis%20elegans,%20WB:WBGene00002299,%20-,%20ZK1067.1) Example comparison between lin-3 and let-23]
 
* What information does a user most care about?
 
# What terms (nodes) are annotated to gene 1 and what terms to gene 2
 
# For a given term, what is the relative number of annotations between gene 1 and gene 2.
 
# For a given node, what is the relative number of annotations each gene has to the total annotations of that gene.
 
* # 3 is actually what we applied to size the nodes in the single-gene version of SObA. Thus, not surprisingly, I think it is important.
 
* Generally people like Prototype 2 as a default view; we could possibly have a toggle to see the other view
 
* In either case users need a good legend and/or documentation
 
* Jae, it would be good if a user could specifically highlight nodes specific to each gene and gray-out or de-emphasize the common nodes
 
  
=== Germ line discussion ===
 
* Currently, the anatomy ontology has "germ line" as a type of "Cell" and a type of "Tissue", and "germ cell" as a type of "germ line"
 
* Chris would like to (1) remove "germ line" from under "Cell" and leave it under "Tissue" and (2) move "germ cell" out from under "germ line" and place directly under "Cell"
 
** [https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/pull/23 Made pull request]
 
* Chris will update pull request to include a change to move "germline precursor cell" out from under "germ line" and place it under "Cell" (done)
 
  
=== Script to remove blank entries from Postgres ===
+
== June 11, 2020 ==
* Chris stumbled across several entries in the OA that were blank (empty strings) or consisted of only whitespace, some of which were causing errors upon upload to ACEDB
 
* Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
 
* Does anyone object to removing these entries throughout Postgres?
 
* Juancarlos will remove all the empty fields identified by his script
 
  
 +
=== 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::' " ` / < > [ ] { } ? , . ( ) * ^ & % $ # @ ! \ | &alpha; &beta; Ω ≈ µ ≤ ≥ ÷ æ … ˚ ∆ ∂ ß œ ∑ † ¥ ¨ ü i î ø π “  ‘ « • – ≠ Å ´ ∏ » ± — ‚ °
 +
* Juancarlos will look into and try to fix
  
== October 10, 2019 ==
+
=== 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?
  
=== Biocuration 2020 ===
+
=== Alliance priorities? ===
* Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
+
* Transcription regulatory networks
* Dates: Sunday May 17th to Wednesday May 20th, 2020
+
* Interactions can focus on network viewer eventually
* Will have 3rd POTATO workshop
+
** May want different versions/flavors of interaction viewers
* [https://www.jax.org/education-and-learning/education-calendar/2020/05-may/biocuration-2020-conference Meeting website]
+
** May also want to work closely with GO and GO-CAMs
* Key Dates
+
* Gene descriptions can focus on information poor genes, protein domains, etc.
** October 31, 2019 - Paper Submission Deadline
 
** January 24, 2020 - Abstract  and Workshop Submission Deadline
 
** March 6, 2020 - Notification of Acceptance
 
** April 6, 2020 - Early Bird Registration Ends
 
** May 8, 2020 - Registration Deadline
 
* Academic ISB Member, early bird registration fee is $250
 
* Author First Pass form paper, submitting to Database, biocuration issue (managed by biocuration group); authors have an opportunity to present at Biocuration conference
 
  
=== ICBO 2020 ===
+
=== Sandbox visual cues ===
* International Conference on Biomedical Ontologies
+
* 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)
* [https://icbo2020.inf.unibz.it/ Meeting website]
+
* AFP and Micropub dev sites have indicators
* Held in Bozen-Bolzano, Italy
+
* Could play with changing the background color? Maybe too hard to look at?
* 16 - 19 September 2020
+
* 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
  
=== SObA comparison tool ===
+
=== Evidence Code Ontology ===
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
+
* Kimberly and Juancarlos have worked on a parser
 +
* Will load into ACEDB soon
  
=== Textpresso derived paper connections ===
 
* For example for strains and constructs, maybe anatomy terms?
 
* May want to flag Textpresso predictions (as opposed to manually connected)
 
* Couple of options:
 
** 1) At time of build, populate the papers (in ACEDB/Datomic) into a 'Putative_reference' tag and display in a distinct 'Putative references' widget
 
** 2) Not part of database build, but make associations live (using RESTful API to link out to Textpresso and submit search with URL) using Textpresso with links to Textpresso and Textpresso results, giving users chance to see context of matches in sentences at the Textpresso site
 
*** A link to Textpresso could be done regardless of other approaches; low-hanging fruit?
 
*** Do a diff so that Textpresso pulls up only additional papers (not already associated)?
 
** 3) Could populate WB page with connections made through a Textpresso API call (could cache results? maybe, but might as well choose 1st option?)
 
* Transgene pipeline:
 
** Arun wrote script, matching transgene names (using regex; Is and Si transgenes) to papers, automatically populate OA
 
** Another script, captures Ex transgenes as well, automatically connects to construct objects
 
** WB only displays verified papers; unverified (predicted) associations are not dumped
 
* Could integrate author verification as part of AFP pipeline, even for older papers? Would we want to re-request AFP results for authors that have already replied in the past? Probably not
 
* Could embed AFP predictions in WB display with link to AFP form for authors (and others?) to verify, via logged-in users? Or via a validation token sent via email?
 
* Chris will make GitHub ticket to ask WB web team to add a link to Textpresso search from References widget on respective page; will require a Textpresso URL constructor
 
* Can apply to: genes, transgenes, constructs, strains, alleles, AFP-vetted entities
 
  
 +
== June 18, 2020 ==
  
== October 17, 2019 ==
+
=== 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)
  
=== Alliance All Hands Face-to-Face ===
+
=== Special characters in OA/Postgres ===
* Flights: has everyone already booked? No, not yet
+
* There are many special characters in free text entries in the OA; probably all from copy-pasting directly from PDF
* Any coordination of flights from Pasadena/LA?
+
* In some cases it seems the special characters cause problems for downstream scripts (e.g. FTP interactions file generator)
** Ranjana and Valerio got a direct flight from Burbank to Boston on Sunday for premeetings
+
* 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
  
=== SObA Comparison Tool ===
+
=== Citace upload ===
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
+
* July 10th citace-to-Hinxton upload
* Prototype discussed last week, updated with feedback from prior discussions
+
* July 7th citace upload, but Wen will be on vacation so will upload to Wen on Tuesday, June 30th
* Would this be a stand-alone tool discoverable under the Tools menu?
 
** Possibly; could be a gene page widget, but may be out of place
 
** Stand-alone tool probably makes more sense
 
* Life stage graph doesn't specify expression pattern vs. expression cluster; pretty much only expression patterns (no clusters)
 
  
=== SObA ===
 
* Raymond intending to share progress on SObA at December Alliance All-Hands Face-to-Face
 
* For example, share GO SObA graph for other species
 
* Will need to be dependent on a SOLR server with all species data
 
** Raymond has run into problems trying to setup his own SOLR server
 
** Raymond asked Seth Carbon if we could us GO server, but he prefers not
 
** Appear to be software versioning issues, possible memory issues
 
  
=== GO meeting ===
+
== June 25, 2020 ==
* Kimberly can give update on recent updates to GO from the recent GO meeting
 
* Slides are shared online
 
  
=== "all stages Ce" life stage ===
+
=== Caltech Summer Student ===
* Currently used to annotate that RNA was collected from, or a gene was observed to be expressed during, all C. elegans life stages
+
* Paul has new summer student
* "all stages Ce" is currently the root node of the C. elegans branch, but needs to change to generic "C. elegans life stage"
+
** Molecular lesion curation, maybe
* Should we:
+
** Are early stops more or less likely to be null mutations?
** 1) Create a "C. elegans life span" or "C. elegans life cycle" term to represent the entire life span and annotate to that?
+
** Alleles are flagged as null in WB in the context of phenotypes
*** Does this mean that, for example, a gene is expressed at some point during the life cycle or consistently throughout the entire life span?
+
** Would be good to query Postgres for null alleles and work from there
** 2) Annotate instead to, for example, "embryo Ce", "larva Ce", and "adult Ce" individually
+
* Fernando
* Note: authors are often vague in their descriptions simply saying "during all stages" possibly stating a beginning and end of the range
+
** Anatomy function
* Wen: not comfortable making a decision right now; want to discuss with Gary Williams and with other MOD members about how to handle large scale expression data
+
** GO curation? Curating transcription factors?
* Daniela: will look through existing (old and new) expression pattern annotations made to "all stages Ce" to see if it would be reasonable to annotate each case individually to "embryo Ce", "larva Ce", and "adult Ce" individually
+
*** Checking for consistent curation
  
=== Gene class missing description ===
+
=== Worm Community Diversity Meeting ===
* The gene class "aatf" has no description, so in the aatf-1 gene page Overview widget, the gene has empty parentheses next to the gene name where there should be a description of what "aatf" stands for (coming from the ?Gene_class description)
+
* Organized by Ahna Skop and Dana Miller
* Jae or Ranjana will create a ticket and assign it to someone at Hinxton
+
* 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
  
== October 24, 2019 ==
+
=== 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.
  
=== Textpresso links from WB page References widgets ===
+
=== New transcripts expanding gene range ===
* Discussed with Sibyl and Adam on last week's Textpresso call
+
* Will bring up at next week's site-wide call
* Sibyl working on mockups for including Textpresso derived paper associations in the References widget
+
* Possibly due to incorporation of newer nanopore reads
* Had originally considered for the following classes
+
* Many genes coming in WS277 have expanded well beyond the gene limits as seen in WS276
** Strain
+
** Example genes: pes-2.2, pck-2, herc-1, atic-1
** Gene
+
* Has several repercussions:
** Variation
+
** 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)
** Transgene
+
** Some expanded genes are now being attributed with thousands of alleles/variants
** Construct
 
** Anatomy_term
 
* Sibyl asks: could we put this link in all References widgets in WB?
 
** Classes with References widgets include:
 
*** Antibody
 
*** Clone
 
*** Construct
 
*** Expression cluster
 
*** Expression pattern
 
*** Gene
 
*** Interaction
 
*** Life stage
 
*** Rearrangement
 
*** RNAi
 
*** Strain
 
*** Transgene
 
*** Variation
 
*** Analysis
 
*** Molecule
 
*** Process
 
** Any Textpresso search on internal WB identifiers, like WBInteraction000###### or WBRNAi00######, or on long complicated names is certainly meaningless, so the following classes are probably ruled out:
 
*** Antibody
 
*** Expression cluster
 
*** Expression pattern
 
*** Interaction
 
*** RNAi
 
*** Analysis
 
** Otherwise it could probably be beneficial to include the additional classes, searching on public name:
 
*** Clone
 
*** Life stage
 
*** Rearrangement
 
*** Molecule
 
*** Process
 
* Created Google Doc summary [https://docs.google.com/document/d/19y5wNIHLmBRm4z7Rz6NG-NQYlZbtobXuQcH6dz0s8Rg/edit?usp=sharing here]
 
* So the current list of candidate classes is:
 
** Strain
 
** Gene
 
** Variation
 
** Transgene
 
** Construct
 
** Anatomy_term (no References widget currently)
 
** Clone
 
** Life stage
 
** Rearrangement
 
** Molecule
 
** Process
 
* Eventually, we may want to incorporate papers found by Textpresso directly into the References widget
 
** We would want predicted associations to be made explicitly so
 
** We could populate the database, but there are reservations about doing this
 
  
 
+
=== Citace upload ===
=== Updates from GOC Meeting, Berkeley ===
+
* Upload files to Spica/Wen by Tuesday (June 30th) 10am
* Status of MOD Imports into Noctua
+
* Wen will clean up folders in Spica (older files from WS277 not cleared out for some reason)
** Starting with WormBase and MGI GO annotations into GO-CAM
 
** GPAD/GPI is standard import format
 
* GO-CAM Specifications and Validation
 
* Noctua Form
 
* Pathways2GO
 
* Priorities for next 6 months:
 
** Create gene-centric Noctua views
 
** Create pathway-centric Noctua views
 
 
 
 
 
== October 31, 2019 ==
 
 
 
=== Alliance 2.3 release ===
 
* Are variants listed on gene pages? Yes, in Alleles and Variants table
 
* Should we be listing strains as models if they don't have phenotype or disease data?
 
 
 
=== New SObA tools ===
 
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Gene comparison tool]
 
** Select a data/ontology type, type in two genes, and graph will be generated/displayed
 
** Nodes colored red and blue respective to annotations from each gene
 
*** Absolute count slices - shows percentage of annotations to that node coming from each gene
 
*** Relative count slices - shows percentage of annotations to that node compared to all annotations for that gene
 
*** Percentage slices rendered after binning/rounding; will update to not round (be more precise) so that 80% doesn't fill the node portion
 
** Amigo/Solr now using MD5 Checksums instead of text strings; loss of data, may request rollback or some feature that can restore data; SObA now "frozen" at an older release of Amigo because of this
 
** Clicking on a node gives a total count of annotations to that node (direct and inferred); can we make an easy way for users to see all those annotations? Maybe provide a pop-up table that can be viewed and downloaded/exported?
 
** Node pop-ups for "Relative count slices" view says, for example, "75% of gene total". This is confusing; might be better to say "75% of total annotations to gene" or something.
 
** User interface updates
 
*** Right now, graph is automatically rendered after entering second gene; genes with no data do not show up in autocomplete
 
*** Will implement a "Submit" button so that user can make selections in various orders and then confirm
 
*** Problematic to allow a lookup on all possible genes because the tool is indexing the Solr database; if no data for a gene (for a data type) the gene does not appear to exist; Will change lookup to look at Postgres on Tazendra (or some other complete source)
 
*** We eventually want a gene name lookup service/API for the Alliance to provide all gene names for all species
 
*** It would be better to either:
 
**** (A) provide clear text that explains that a gene will not appear in the autocomplete if it has no data for the selected data type
 
**** OR (B) allow a user to type in their gene, but if it doesn't have data indicate so in the autocomplete (will need to consider when genes are entered but then user switches data type; will it then perform another lookup and indicate presence of data or not?)
 
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Terms+to+SObA+Graph Enriched term list tool]
 
 
 
== November 7, 2019 ==
 
 
 
=== ?Genotype class ===
 
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing Working data model document]
 
* Several classes have a "Genotype" tag with text entry
 
** Strain
 
** 2_point_data
 
** Pos_neg_data
 
** Multi_pt_data
 
** RNAi
 
** Phenotype_info
 
** Mass_spec_experiment (no data as of WS273)
 
** Condition
 
* Collecting all genotype text entries yields ~33,000 unique entries, with many different forms:
 
** Species entries, like "Acrobeloides butschlii wild isolate" or "C. briggsae"
 
** Strain entries, like "BA17[fem-1(hc-17)]" or "BB21" or "BL1[pK08F4.7::K08F4.7::GFP; rol-6(+)]"
 
** Anonymous transgenes, like "BEC-1::GFP" or "CAM-1-GFP" or "Ex[Pnpr-9::unc-103(gf)]"
 
** Complex constructs, like "C56C10.9(gk5253[loxP + Pmyo-2::GFP::unc-54 3' UTR + Prps-27::neoR::unc-54 3' UTR + loxP]) II"
 
** Text descriptions, like "Control" or "WT" or "Control worms fed on HT115 containing the L4440 vector without insert" or "N.A."
 
** Bacterial genotypes, like "E. coli [argA, lysA, mcrA, mcrB, IN(rrnD-rrnE)1, lambda-, rcn14::Tn10(DE3 lysogen::lavUV5 promoter -T7 polymerase]"
 
** Including balancers, like "F26H9.8(ok2510) I/hT2 [bli-4(e937) let-?(q782) qIs48] (I;III)"
 
** Reference to parent strain, like "Parent strain is AG359"
 
** Referring to RNAi, like "Pglr-1::wrm-1(RNAi)" or "Phsp-6::gfp; phb-1(RNAi)"
 
** Referring to apparent null or loss of function alleles, like "Phsp-4::GFP(zcIs4); daf-2(-)" or "ced-10(lf)"
 

Latest revision as of 19:13, 25 June 2020

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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)