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]]
+
[[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_June_2020|June]]
  
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
[[WormBase-Caltech_Weekly_Calls_September_2019|September]]
+
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
  
  
== October 3, 2019 ==
+
== September 3, 2020 ==
  
=== SObA comparison graphs ===
+
=== WS279 Citace upload ===
* Raymond and Juancarlos have worked on a SObA-graph based comparison tool to compare two genes for ontology-based annotations
+
* September 25
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 1]
+
* Local CIT upload (to Wen) Tuesday September 22 by 10am Pacific
** [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 ===
+
=== New AFP datatype for curation status form (CSF)? ===
* 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"
+
* afp_othergenefunc (to capture gene function other than enzymatic activity)
* 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"
+
* Can wait a bit before adding to CSF; if there will be dedicated curation for that data type we may add later
** [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 ===
+
=== GO annotation for description ===
* 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
+
* Kimberly will look into 'male tail tip developement' terms for description
* 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
 
  
 +
=== Migrate wobr1 server to AWS ===
 +
* SOLR, WOBr, SObA, Enrichment analysis
 +
* Working with Sibyl on the process
 +
* Will try migrating wobr1 first, as a test case
 +
* May eventually move, for example, Tazendra
 +
** Will there be drawbacks to doing this?
 +
** Can we regularly ssh into Tazendra on AWS without issue? Costs for transferring large files
 +
* Don't yet know the details of the costs, but we can try and keep track
 +
* We should move into WB or Alliance AWS instances (or Stanford)
  
== October 10, 2019 ==
+
=== WormBase talk at Boston Area Worm Meeting ===
 +
* https://www.umassmed.edu/ambroslab/meetings/bawm/
 +
* Meeting will be virtual on Zoom
 +
* Chris will give a talk September 23rd, 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
 +
* Send topic requests to Chris for the talk
 +
* Current topics:
 +
** Micropublications
 +
** Author First Pass
 +
** Automated Gene Descriptions
 +
** Community Curation
 +
** WB Query Tools
 +
* Chris will ask organizers if others can join: post on WormBase blog? May draw too large an audience for the zoom channel;
 +
* If the organizers record the talk, we can post it on the blog and WB YouTube channel
  
=== Biocuration 2020 ===
 
* Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
 
* Dates: Sunday May 17th to Wednesday May 20th, 2020
 
* Will have 3rd POTATO workshop
 
* [https://www.jax.org/education-and-learning/education-calendar/2020/05-may/biocuration-2020-conference Meeting website]
 
* Key Dates
 
** 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 ===
+
== September 10, 2020 ==
* International Conference on Biomedical Ontologies
 
* [https://icbo2020.inf.unibz.it/ Meeting website]
 
* Held in Bozen-Bolzano, Italy
 
* 16 - 19 September 2020
 
  
=== SObA comparison tool ===
+
=== GO GAF Files ===
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
+
* WS278 GO GAF is using the new 2.2 file format
 +
* [https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md Specifications]
 +
* GO will not be emitting GAF 2.2 until the end of the year (will try to get a fixed date)
 +
* Implications for gene descriptions, but what about other tools, applications at WB?
 +
* Some errors in the current WS278 GAF, but will get fixed soon
 +
** Impacts gene descriptions for WS278, so using WS277 for now; will be OK once source GAF is fixed
  
=== Textpresso derived paper connections ===
+
===Disease files on FTP===
* For example for strains and constructs, maybe anatomy terms?
+
*No changes for WS278 FTP files, except an extra custom file that Hinxton is producing mostly for gene descriptions so that we don't get the wrong human diseases via poor orthology calls (see GitHub issue https://github.com/WormBase/website/issues/7839)
* May want to flag Textpresso predictions (as opposed to manually connected)
+
*Will be some consolidation of disease data possibly for WS279 FTP files, implications for downstream tools--gene descriptions, WOBR, ??
* 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
 
  
 +
=== WormBase talk at Worcester Area Worm Meeting ===
 +
* Chris set to give talk on December 1st, 2020, via Zoom, 4pm (or 4:30pm) EST / 1pm Pacific
 +
* 30 minute slot; complementary to BAWM talk?
 +
* WormBase members can attend
  
== October 17, 2019 ==
+
=== WormBase talk at Boston Area Worm Meeting ===
 +
* https://www.umassmed.edu/ambroslab/meetings/bawm/
 +
* Chris will give a talk September 23rd (< 2 weeks), 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
 +
* WormBase members can attend; Zoom link will be sent next Monday
  
=== Alliance All Hands Face-to-Face ===
+
=== Worm Anatomy Ontology Fixes ===
* Flights: has everyone already booked? No, not yet
+
* Raymond working on addressing warnings and errors (missing definitions, duplicate labels, duplicate definitions)
* Any coordination of flights from Pasadena/LA?  
+
* Assessing the best way to address them
** Ranjana and Valerio got a direct flight from Burbank to Boston on Sunday for premeetings
+
* Would be good to be able to automate some edits; options:
 +
** Use OWL API (need someone proficient in coding with OWL API)
 +
** Convert to OBO, programmatically edit, convert back to OWL?
 +
** Use Cellfie plugin for Protege?
 +
** Should discuss with Nico once we have a sense as to what changes need to be made
  
=== SObA Comparison Tool ===
+
=== Dead Variations in Postgres ===
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
+
* Currently pulling in variations/alleles from Postgres to populate "allele" and "genetic perturbation" categories in Textpresso
* Prototype discussed last week, updated with feedback from prior discussions
+
* Noticed that many transgene names were being included, which can result in false positives for the categories
* Would this be a stand-alone tool discoverable under the Tools menu?
+
* Looking at Postgres table "obo_data_variation", there are ~100,000 entries, ~40,000 with status "Dead" and ~60,000 with status "Live"
** Possibly; could be a gene page widget, but may be out of place
+
* Trying to determine the history of the "Dead" variations, where most of the transgene names are coming from
** Stand-alone tool probably makes more sense
+
* May still want to include "Dead" variations/alleles in Textpresso category for historical reasons
* Life stage graph doesn't specify expression pattern vs. expression cluster; pretty much only expression patterns (no clusters)
+
* We could use pattern matching to filter out transgene names
 +
* Possible to search C. elegans corpus for all "real" allele public names in the "Dead" set to see if they should still be included in categories
  
=== SObA ===
+
=== WS279 Citace Upload ===
* Raymond intending to share progress on SObA at December Alliance All-Hands Face-to-Face
+
* Local Caltech upload to Spica, Tuesday September 22, 10am Pacific
* 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 ===
 
* Kimberly can give update on recent updates to GO from the recent GO meeting
 
* Slides are shared online
 
  
=== "all stages Ce" life stage ===
+
== September 17, 2020 ==
* Currently used to annotate that RNA was collected from, or a gene was observed to be expressed during, all C. elegans life stages
 
* "all stages Ce" is currently the root node of the C. elegans branch, but needs to change to generic "C. elegans life stage"
 
* Should we:
 
** 1) Create a "C. elegans life span" or "C. elegans life cycle" term to represent the entire life span and annotate to that?
 
*** Does this mean that, for example, a gene is expressed at some point during the life cycle or consistently throughout the entire life span?
 
** 2) Annotate instead to, for example, "embryo Ce", "larva Ce", and "adult Ce" individually
 
* Note: authors are often vague in their descriptions simply saying "during all stages" possibly stating a beginning and end of the range
 
* 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
 
* 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
 
  
=== Gene class missing description ===
+
=== Species errors in CITace ===
* 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)
+
* Wen is reviewing species coming from CIT and will send individual curators lists of species that need correction
* Jae or Ranjana will create a ticket and assign it to someone at Hinxton
 
  
 +
=== Webinars ===
 +
* We could perform a general WormBase webinar to cover all of WormBase, maybe one hour long
 +
* Allow 20-30 minutes for discussion? Can allow interruptions but plan for one hour
 +
* Follow up with more specific webinars in following months: JBrowse, WormMine, Micropublication, AFP, Textpresso Central, Ontology browser & Enrichment tools, SPELL, ParaSite BioMart
 +
* Chris and Wen can discuss how to setup
 +
* Should we have people register? Maybe
 +
* AFP probably doesn't need an hour; maybe split an hour across micropublications and AFP?
  
== October 24, 2019 ==
+
=== Transcription factors and regulatory networks ===
 +
* Had another question about TFs, asking for common TFs for a list of genes
 +
* An issue is that the TF binding data we have is in disparate forms, trying to reconcile
 +
* We have a ?Transcription_factor class; it would be good to update and integrate with other related data types
  
=== Textpresso links from WB page References widgets ===
+
=== Alzheimer's disease portal ===
* Discussed with Sibyl and Adam on last week's Textpresso call
+
* Funding has been awarded for Alzheimer's research
* Sibyl working on mockups for including Textpresso derived paper associations in the References widget
+
* Ranjana: should the disease working group consider more about an Alliance Alzheimer's disease portal?
* Had originally considered for the following classes
+
* Paul S: Alliance SAB tomorrow; we'll see what the SAB says
** Strain
+
* Can look at other resources like RGD disease portals and Reactome disease-related pathway models
** Gene
+
* Ruth Lovering is doing some work in this regard
** Variation
 
** Transgene
 
** 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
 
  
 +
=== GO meeting ===
 +
* All are welcome to attend
 +
* Will discuss GAF format changes, etc.
 +
* Ranjana: should she and Valerio attend to learn about GO changes that affect the gene descriptions pipeline?
 +
** Kimberly: there could be a particular breakout group that Ranjana and Valerio could attend to discuss
  
=== Updates from GOC Meeting, Berkeley ===
+
=== New GAF 2.2 file ===
* Status of MOD Imports into Noctua
+
* Kimberly has reviewed and sent feedback to Michael P
** Starting with WormBase and MGI GO annotations into GO-CAM
+
* Valerio would like to stay in the loop to test the new files
** 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 ===
 
* Gene comparison tool
 
* Enriched term list tool
 
  
=== ?Genotype class ===
+
=== Data mining tool comparison sheet ===
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing Working data model document]
+
* https://docs.google.com/spreadsheets/d/1vBTDBOKfXn9GcdpF1bXI62VEJ7hwyz2hOyAZcoV1_ng/edit?usp=sharing
* Several classes have a "Genotype" tag with text entry
+
* Needs an update
** Strain
+
* Could we make this available to users? A link in the Tools menu?
** 2_point_data
+
* Is this useful to users? Would they understand it? Maybe be better as a curator resource
** Pos_neg_data
+
* Could this be micropublished?
** Multi_pt_data
+
** Possible; may want to consider a series of publications with videos of webinars, etc.
** 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)"
 

Revision as of 16:39, 17 September 2020

Previous Years

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2014 Meetings

2015 Meetings

2016 Meetings

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2020 Meetings

January

February

March

April

May

June

July

August


September 3, 2020

WS279 Citace upload

  • September 25
  • Local CIT upload (to Wen) Tuesday September 22 by 10am Pacific

New AFP datatype for curation status form (CSF)?

  • afp_othergenefunc (to capture gene function other than enzymatic activity)
  • Can wait a bit before adding to CSF; if there will be dedicated curation for that data type we may add later

GO annotation for description

  • Kimberly will look into 'male tail tip developement' terms for description

Migrate wobr1 server to AWS

  • SOLR, WOBr, SObA, Enrichment analysis
  • Working with Sibyl on the process
  • Will try migrating wobr1 first, as a test case
  • May eventually move, for example, Tazendra
    • Will there be drawbacks to doing this?
    • Can we regularly ssh into Tazendra on AWS without issue? Costs for transferring large files
  • Don't yet know the details of the costs, but we can try and keep track
  • We should move into WB or Alliance AWS instances (or Stanford)

WormBase talk at Boston Area Worm Meeting

  • https://www.umassmed.edu/ambroslab/meetings/bawm/
  • Meeting will be virtual on Zoom
  • Chris will give a talk September 23rd, 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
  • Send topic requests to Chris for the talk
  • Current topics:
    • Micropublications
    • Author First Pass
    • Automated Gene Descriptions
    • Community Curation
    • WB Query Tools
  • Chris will ask organizers if others can join: post on WormBase blog? May draw too large an audience for the zoom channel;
  • If the organizers record the talk, we can post it on the blog and WB YouTube channel


September 10, 2020

GO GAF Files

  • WS278 GO GAF is using the new 2.2 file format
  • Specifications
  • GO will not be emitting GAF 2.2 until the end of the year (will try to get a fixed date)
  • Implications for gene descriptions, but what about other tools, applications at WB?
  • Some errors in the current WS278 GAF, but will get fixed soon
    • Impacts gene descriptions for WS278, so using WS277 for now; will be OK once source GAF is fixed

Disease files on FTP

  • No changes for WS278 FTP files, except an extra custom file that Hinxton is producing mostly for gene descriptions so that we don't get the wrong human diseases via poor orthology calls (see GitHub issue https://github.com/WormBase/website/issues/7839)
  • Will be some consolidation of disease data possibly for WS279 FTP files, implications for downstream tools--gene descriptions, WOBR, ??

WormBase talk at Worcester Area Worm Meeting

  • Chris set to give talk on December 1st, 2020, via Zoom, 4pm (or 4:30pm) EST / 1pm Pacific
  • 30 minute slot; complementary to BAWM talk?
  • WormBase members can attend

WormBase talk at Boston Area Worm Meeting

Worm Anatomy Ontology Fixes

  • Raymond working on addressing warnings and errors (missing definitions, duplicate labels, duplicate definitions)
  • Assessing the best way to address them
  • Would be good to be able to automate some edits; options:
    • Use OWL API (need someone proficient in coding with OWL API)
    • Convert to OBO, programmatically edit, convert back to OWL?
    • Use Cellfie plugin for Protege?
    • Should discuss with Nico once we have a sense as to what changes need to be made

Dead Variations in Postgres

  • Currently pulling in variations/alleles from Postgres to populate "allele" and "genetic perturbation" categories in Textpresso
  • Noticed that many transgene names were being included, which can result in false positives for the categories
  • Looking at Postgres table "obo_data_variation", there are ~100,000 entries, ~40,000 with status "Dead" and ~60,000 with status "Live"
  • Trying to determine the history of the "Dead" variations, where most of the transgene names are coming from
  • May still want to include "Dead" variations/alleles in Textpresso category for historical reasons
  • We could use pattern matching to filter out transgene names
  • Possible to search C. elegans corpus for all "real" allele public names in the "Dead" set to see if they should still be included in categories

WS279 Citace Upload

  • Local Caltech upload to Spica, Tuesday September 22, 10am Pacific


September 17, 2020

Species errors in CITace

  • Wen is reviewing species coming from CIT and will send individual curators lists of species that need correction

Webinars

  • We could perform a general WormBase webinar to cover all of WormBase, maybe one hour long
  • Allow 20-30 minutes for discussion? Can allow interruptions but plan for one hour
  • Follow up with more specific webinars in following months: JBrowse, WormMine, Micropublication, AFP, Textpresso Central, Ontology browser & Enrichment tools, SPELL, ParaSite BioMart
  • Chris and Wen can discuss how to setup
  • Should we have people register? Maybe
  • AFP probably doesn't need an hour; maybe split an hour across micropublications and AFP?

Transcription factors and regulatory networks

  • Had another question about TFs, asking for common TFs for a list of genes
  • An issue is that the TF binding data we have is in disparate forms, trying to reconcile
  • We have a ?Transcription_factor class; it would be good to update and integrate with other related data types

Alzheimer's disease portal

  • Funding has been awarded for Alzheimer's research
  • Ranjana: should the disease working group consider more about an Alliance Alzheimer's disease portal?
  • Paul S: Alliance SAB tomorrow; we'll see what the SAB says
  • Can look at other resources like RGD disease portals and Reactome disease-related pathway models
  • Ruth Lovering is doing some work in this regard

GO meeting

  • All are welcome to attend
  • Will discuss GAF format changes, etc.
  • Ranjana: should she and Valerio attend to learn about GO changes that affect the gene descriptions pipeline?
    • Kimberly: there could be a particular breakout group that Ranjana and Valerio could attend to discuss

New GAF 2.2 file

  • Kimberly has reviewed and sent feedback to Michael P
  • Valerio would like to stay in the loop to test the new files

Data mining tool comparison sheet