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]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
−
= 2018 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
== February 1, 2018 ==
+
==April 18th, 2024==
 +
*NNC pipeline being switched off locally and moving into the Alliance ABC.
  
−
=== Automated gene descriptions - orthology ===
+
==April 11th, 2024==
−
* Some genes have human orthology mentioned in automated descriptions, even though the orthology call has not been called in DIOPT
+
*Caltech WS293 ace files ready for the upload
−
* WormBase uses EnsemblCompara and other methods (not aggregate method like DIOPT)
 
−
* Orthology synchrony is a challenge; WormBase and FlyBase may need to pay special attention to orthology calls and discrepancies
 
−
* DIOPT is purely automated, does not consider other information about orthology evidence
 
−
* We should be clear about how the orthology calls are made
 
  
−
=== Next upload ===
+
==April 4th, 2024==
−
* Unclear of exact date
+
* Continued discussion on sustainability
−
* Probably end of March
+
* CZI, single cell RNAseq for Alliance -> anything happening will be few months down the road
 +
** Data is still going to SPELL and enrichment analysis
 +
** Peter Roy asking about expression profile of a condition and find similar expression profiles (SPELL like analysis) but SPELL cannot currently deal with scRNAseq data. Wen says it is possible (regarding each cell group as an experiment). Can try loading the into SPELL. Doe it improve the function of SPELL? Only 5-10 datasets. These data are a bit different from bulk RNAseq.
 +
* Textpresso: good to have a presentation for other MODs to show Textpresso capabilities? Yes. Maybe during sprint review
 +
* Michael's presentation on LLMs - Named Entity Recognition (NER)
  
−
=== SimpleMine issue ===
+
==March 14, 2024==
−
* Redundant genes in input list are merged
 
−
* Should SimpleMine provide an option to keep redundancies?
 
−
** Give option up front? Provide submission step to point out redundancies? Ask for choice?
 
−
* We can default to show row-by-row correspondence, and display the number of redundant entries
 
−
* Conclusion: Make an option for users to indicate if they want row-by-row correspondence or a merged list
 
  
−
=== Cell type expression ===
+
=== TAGC debrief ===
−
* Waterston paper
 
−
* 40,000 random cells, clusters sequenced individually to a depth of 20,000 reads; ~1000 genes per cell; cluster data; make judgement call as to what cell types they likely are
 
−
* For now, we can do a simple annotation: significantly expressed genes for each cell type
 
−
* Supplemental table S5 for neurons
 
−
* Maybe just ignore the hybrid calls like AQM/PVM, etc.
 
−
* It may be good to isolate the single cell data from other expression data
 
−
* We should annotate/capture the expression clusters
 
−
* Would be good to be able to do enrichment analysis on the clusters; compare data sets
 
−
* Data has not been placed in SPELL yet, Gary considered the data a work in progress
 
−
* We can communicate with Waterston group; are they collecting more data?
 
−
* Wen will take another look at the data
 
−
* Gary W. concerned about the reported/assumed/inferred identity of the cells in the paper
 
−
* Probably cannot curate to individual cells, but we can annotate to a higher level term
 
−
* We want to annotate and display expression enrichment as well as presence/absence calls
 
  
 +
==February 22, 2024==
  
−
== February 8, 2018 ==
+
===NER with LLMs===
  
−
=== Release schedule ===
+
* Wrote scripts and configured an LLM for Named Entity Recognition. Trained an LLM on gene names and diseases. Works well so far (F1 ~ 98%, Accuracy ~ 99.9%)
−
* Wen will ask Hinxton to update the published release schedule (for next data upload)
 
  
−
=== New York Worm Meeting ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
* Wen and Kimberly will present a WormBase tutorial on March 24
 
−
* Wen communicated to Oliver Hobert; suggested topics:
 
−
** Multi-gene (batch) search tools
 
−
** How literature info gets into WormBase? Curation process?
 
−
** Should we discuss completeness?
 
  
−
=== GO curation ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
* New simple input form for Noctua, being developed at USC
 
−
* Not very much GO curation happening at WB right now
 
−
* Protein-2-GO pipeline
 
−
* Do we have a good Phenotype-2-GO(Process) mapping pipeline? We have our old mappings; not very reliable; would need to spend more time expanding the worm phenotype ontology and GO to improve
 
−
* Cellular component curation will come in from WB expression curation
 
−
* Don't have pipeline for Interactions-2-GO
 
−
* Textpresso Molecular Functions pipeline?
 
−
* geneprod and catalyticact data types for molecular function pipeline
 
−
* Textpresso can send molecular function annotations to Noctua
 
−
* For high-level pathway curation; we should probably read WormBook chapters (or other reviews) and develop pathways (using non-experimental evidence codes)
 
−
* We could potentially seed Noctua models from Reactome
 
−
* We would like to have complete curation for major pathways for gene enrichment analysis
 
−
* Roles of small molecules in Noctua models still being worked out
 
  
−
=== Phenotype curation ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
* Chris has had community curation pipeline on back burner while updating Wiki and dealing with AGR, WormMine, etc.
 
−
* Will get back to soon; will resend email requests for newer papers sent over a year ago
 
  
−
=== Expression curation ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
* Daniela getting back to expression curation after Micropublication stuff has quieted down
 
  
−
=== Gene regulation curation ===
 
−
* April came across dataset involving regulation of siRNAs that don't seem to have gene objects in WB
 
−
* May need to instantiate genes for these?
 
  
−
=== Physical interaction curation ===
 
−
* SVM classification; do we flag a paper as negative that has protein interactions but no interactions for C. elegans
 
−
* Can we generate a good SVM that only identifies WB-curatable papers?
 
  
−
=== Disease curation ===
+
==February 15, 2024==
−
* Now curating the specific genetic entities involved in a disease model
 
−
* Will also capture environmental conditions, treatments (e.g. ameliorates, exacerbates)
 
−
* Curation in-line with AGR standards
 
−
* Evidence code needed for assertions that an animal is a model of disease in which the assertion is based on background knowledge and experimental evidence, together
 
−
* Evidence Code Ontology (ECO) is developing a new term to accommodate
 
−
* Disease curators can use new evidence code as well as any existing codes
 
−
* Is there a definition of a "disease model"?
 
−
* What are the minimal criteria for considering something a disease model?
 
−
* WB and FB curators focus on cellular phenotype and relation to the disease
 
  
−
=== Expression cluster curation ===
+
=== Literature Migration to the Alliance ABC ===
−
* 27 papers in pipeline
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
−
* Will then work on "single-cell" RNAseq
+
===== Find papers with a high confidence NN classification for a given topic that have also been flagged positive by an author in a community curation pipeline and that haven’t been curated yet for that topic =====
−
** Wen, Raymond, and David should discuss
+
*Facet for topic
 +
*Facet for automatic assertion
 +
**neural network method
 +
*Facet for confidence level
 +
**High
 +
*Facet for manual assertion
 +
**author assertion
 +
***ACKnowledge method
 +
**professional biocurator assertion
 +
***curation tools method - NULL
  
−
=== April and May Worm Meetings ===
+
===== Manually validate paper - topic flags without curating =====
−
* Midwest and Colorado meetings
+
*Facet for topic
−
* Wen submitting abstracts
+
*Facet for manual assertion
−
* Wen and Kimberly can write up abstract template for New York meeting and send around to be modified for future meetings
+
**professional biocurator assertion
 +
***ABC - no data
  
−
=== WormBook ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
* Published last version for legacy site
+
* Search ABC with paper identifier
 +
* Migrate to Topic and Entity Editor
 +
* View all associated data
 +
* Manually validate flags, if needed
  
−
=== Papers ===
+
=== PDF Storage ===
−
* Daniel requested 13 (older) papers from Caltech library through inter-library process
+
* At the Alliance PDFs will be stored in Amazon s3
−
* Received more than half as images; would need optical character recognition (OCR) for Textpresso purposes
+
* We are not planning to formally store back-up copies elsewhere
−
* What is the state of the art of OCR now? How good is it? Can we ask Caltech library for the service?
+
* Is this okay with everyone?
−
* Are these high priority papers? Need to check to see if worth processing
 
  
−
=== AGR ===
+
==February 8, 2024==
−
* Disease working group setting up a face-to-face meeting
+
* TAGC
−
* Variant working group may need a face-to-face meeting as well
+
** Prominent announcement on the Alliance home page?
−
* Expression working group working out initial AGR site data display mockups
 
−
* Interaction working group; we will want to incorporate miRNA/target interactions (RNA-RNA interactions); will look at miRBase
 
  
 +
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
−
== February 15, 2018 ==
+
==February 1, 2024==
 +
* Paul will ask Natalia to take care of pending reimbursements
 +
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
  
−
=== Model changes ===
+
==January 25, 2024==
−
* Models freeze March 2nd
 
−
* Will need to get model changes proposed and tested by then
 
  
−
=== Sys admin of Tazendra/Mangolassi ===
+
=== Curator Info on Curation Forms ===
−
* Raymond will discuss with Juancarlos to centralize
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
* Need good documentation for forms, tools, etc.
 
−
* Will be a push to put all code for tools and forms on GitHub
 
  
−
=== Tazendra forms, tools bug this week ===
+
=== ACKnowledge Author Request - WBPaper00066091 ===
−
* There is a dependency on Mangolassi for some tools
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
−
* Mangolassi went down and caused problems
 
−
* Would be good to decouple the two machines
 
  
−
=== AGR ===
+
* The paper conducts an analysis of natural variations within 48 wild isolates. To enhance the reliability of the variant set, I utilized the latest variant calling methods along with a custom filtering approach. The resulting dataset comprises 1,957,683 unique variants identified using Clair3. Additionally, Sniffles2 was used to identify indels of >30 bp, which numbered in the thousands to tens of thousands for most wild isolates. It is worth noting that variants identified with Sniffles2 have less reliable nucleotide positions in the genome.
−
* May not get an AGR all-hands face-to-face meeting before the summer
 
−
* Working groups can decide to have face-to-face meeting
 
−
* People should speak up if they have interest in visiting other MODs/sites; can be arranged
 
−
* Consider what grant proposals could come out of such meetings/visits
 
−
* Currently no ontology working group, no anatomy working group
 
−
* Could establish a preliminary working group; reach out to relevant people
 
−
* Anatomy working group issues may come up in expression working group
 
−
** Daniela will keep Raymond updated on relevant issues that come up with the expression group
 
  
−
=== Ontology Browser gene lists ===
+
* I am reaching out to inquire whether WormBase would be interested in incorporating this dataset. An argument in favor is the higher quality of my data. However, I am mindful of the potential substantial effort involved for WormBase, and it is unclear whether this aligns with your priorities.
−
* Chris requesting change to gene list display from WOBr
 
−
* https://github.com/WormBase/website/issues/6190
 
−
* Should provide WBGene IDs, not just gene public names
 
−
** That was the original intent, but using WBGene IDs was, for some reason, causing issues when developing the tool; will need to revisit that issue to get WBGene IDs displayed
 
  
 +
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
  
−
== February 22, 2018 ==
+
=== Update on NN Classification via the Alliance ===
 +
* Use of primary/not primary/not designated flag to filter papers
 +
* Secondary filter on papers with at least C. elegans as species
 +
* Finalize sources (i.e. evidence) for entity and topic tags on papers
 +
* Next NN clasification scheduled for ~March
  
−
=== Making MOD data publicly available in a central location===
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
−
* Meets the NIH mandate for WB as a publicly-funded project and helps researchers get their data highlighted faster than waiting for the db build
+
* NNC html pages will show NNC values together with species.
−
**would put in filters to avoid releasing sensitive data  or incomplete curation annotations
+
* Show all C. elegans papers first and other species in a separate bin.
−
**would be good for journal hyperlinking project since it needs access to up to date data--see more below about project
 
−
** Central data repository for all data (MOD) files would be helpful to developers (and users)
 
−
** Does Caltech have an FTP site that could be used?
 
  
−
===Journal Hyperlinking project goals===
+
=== Travel Reimbursements ===
−
Hyperlinking project, has been in production since 2009, links bioentities in worm, yeast, and fly research articles to relevant databases, requires the latest data from WormBase, SGD, and FlyBase - could use a central repository to pull entities (name, ids, synonyms) from
+
* Still waiting on October travel reimbursement (Kimberly)
−
**MOD Curators check link accuracy and check for missed links (needs ongoing fte support)
+
* Still waiting on September and October travel reimbursements (Wen)
−
**supporting this project is not in the remit of any of the MODs, project is not sustainable without outside funding, hence finding funding outside of WB.
 
−
**Since inception, project links bioentities in GSA papers (Genetics and G3)
 
−
**C. elegans genes, alleles, rearrangements, strains, clones, short phenotype names, and transgenes are linked in these papers
 
−
**Karen's (InSilico) grant goals are to
 
−
***expand the pipeline to  other journals, specifically eLife (then to PLoS)
 
−
***expand to all AGR member mods in addition to SGD and FlyBase. Also bring in PomBase
 
−
***not planning on expanding linking beyond simple text recognition of known lexica and entities that follow a regex
 
−
***SBIR commercialization plan is to extend entity identification to commercial reagents and collect data for subscription-based access from biotech suppliers.
 
−
***need data from postgres, which is not available in geneace dump.  Could possibly just dump all Postgres data into one place, Karen's developers could write scripts to process that data;
 
−
***** Juancarlos will setup a URL that can be used to access the data; will setup on cronjob every day at 8pm
 
−
***InSilico hyperlinks go through InSilico page to embedded i-frames of MOD entity page
 
−
****allows trackability of link access, stats that will be given to the MODS
 
−
****allows monitoring and resolution of links that go dead
 
−
****allows splash pages for silent links
 
  
−
=== Alliance SAB meeting ===
+
=== UniProt ===
−
* SAB critical of:
+
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
−
** not being unified
+
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
−
** not being organized
+
* Stavros escalates the issue on Hinxton Standup.
−
* Now everyone has committed
+
* Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.
−
* Concern still exists about autonomy of MODs
 
−
** Will each user community still be served effectively by the Alliance?
 
−
* Organization is easier when all are committed
 
−
* Maybe bring in a professional organizer/project manager (long term)
 
−
* New aggressive timeline for progress
 
−
** April 23rd meeting; need to give material a week earlier
 
−
** Need year and a half plan; each working group will provide details
 
−
* Only 2 full time Alliance staff; may need more on project; difficult for individuals to split time/effort
 
−
* SAB member: curation involves expert decision making/analysis on issues, not just straight-forward data acquisition
 
−
* Maybe we would have better curation consistency if individual curators focused on particular topics; became experts for certain subject matter
 
−
* Possibility to have Alliance all-hands call in Fall
 
−
* Working groups can have face-to-face meetings; have travel/meeting budget until July 31st then resets
 
  
−
=== Automated gene descriptions ===
+
==January 18, 2024==
−
* Difficult to handle genes with high information content; many ontology term annotations
+
* OA showing different names highlighted when logging in the OA, now fixed on staging
−
* How do we simplify descriptions? Using higher-level terms, slim terms? Gets tricky
 
  
−
=== Micropublications ===
 
−
* Michael Elowitz tweeted out micropublication stuff
 
−
* Received feedback on Twitter; worth looking at threads, comments
 
  
−
=== Community curation plan ===
+
==January 11, 2024==
−
* Alliance need for community curation
+
* Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
−
* Micropublications are a bit of a pilot for community curation
+
** Curators should make sure that, when pasting special characters, the duplicate function works
−
* Need shared curation/submission forms; fit shared data models?
+
* OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
 +
** If you want to bookmark an OA url for your datatype and user, log on once, and bookmark that page (separately for prod and dev)
 +
* Chris tested on staging and production the phenotype form and the data are still going to tazendra
 +
** Chris will check with Paulo. Once it is resolved we need to take everything that is on tazendra and put it on the cloud with different PGIDs
 +
** Raymond: simply set up forwarding at our end?
 +
* AI working group: Valerio is setting up a new account for open AI -paid membership for ChatGPT4. We can also use Microsoft Edge copilot (temporary?)
 +
* Chris getting ready to deploy a 7.0.0. public release - February 7th. Carol wanted to push out monthly releases. This will include WS291. For subsequent releases the next several releases will be WS 291 until WS292 is available.
 +
* Valerio would like to use an alliancegenome.org email address for the openAI account
 +
* New alliance drive: https://drive.google.com/drive/folders/0AFkMHZOEQxolUk9PVA
 +
** note: please move shared files that you own to new Alliance Google Drive.  Here is the link to the information that Chris Mungall sent:  For more instructions see the video and SOP here:https://agr-jira.atlassian.net/browse/SCRUM-925?focusedCommentId=40674
 +
* Alliance logo and 50 word description for TAGC> Wen will talk to the outreach WG
 +
* Name server. Manuel working on this, Daniela and Karen will reach out to him and let him know that down the road micropublication would like to use the name server API to generate IDs in bulk
 +
* Karen asking about some erroneous IDs used in the name server. Stavros says that this is not a big deal because the "reason" is not populating the name server
 +
* It would be good to be able to have a form to capture additional fields for strains and alleles (see meeting minutes August 31st 2023. https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls_2023#August_31st.2C_2023). This may happen after Manuel is done with the authentication.
 +
* Michael: primary flag with Alliance. Kimberly talked about this with the blue team. They will start bringing that over all papers and fix the remaining 271 items later.
  
−
=== RNAi secondary targets ===
+
==January 4, 2024==
−
* WormMine and WormBase gene/RNAi pages include secondary RNAi targets but WOBr and SObA do not
+
* ACKnowlegde pipeline help desk question:
−
* Should we include or exclude secondary targets? We want consistency across data sets
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
* No gold standard RNAi target prediction algorithm
+
* Citace upload, current deadline: Tuesday January 9th
−
* We should be transparent about primary/secondary status wherever we include secondary targets in display
+
** All processes (dumps, etc.) will happen on the cloud machine
−
* Could be addressed with phenotype display proposal
+
** Curators need to deposit their files in the appropriate locations for Wen
−
* Should probably remove secondary targets from bulk data sets
+
* Micropublication pipeline
 +
** Ticketing system confusion
 +
** Karen and Kimberly paper ID pipeline; may need sorting out of logistics

Latest revision as of 16:04, 18 April 2024

Previous Years

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2012 Meetings

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2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

2022 Meetings

2023 Meetings

April 18th, 2024

  • NNC pipeline being switched off locally and moving into the Alliance ABC.

April 11th, 2024

  • Caltech WS293 ace files ready for the upload

April 4th, 2024

  • Continued discussion on sustainability
  • CZI, single cell RNAseq for Alliance -> anything happening will be few months down the road
    • Data is still going to SPELL and enrichment analysis
    • Peter Roy asking about expression profile of a condition and find similar expression profiles (SPELL like analysis) but SPELL cannot currently deal with scRNAseq data. Wen says it is possible (regarding each cell group as an experiment). Can try loading the into SPELL. Doe it improve the function of SPELL? Only 5-10 datasets. These data are a bit different from bulk RNAseq.
  • Textpresso: good to have a presentation for other MODs to show Textpresso capabilities? Yes. Maybe during sprint review
  • Michael's presentation on LLMs - Named Entity Recognition (NER)

March 14, 2024

TAGC debrief

February 22, 2024

NER with LLMs

  • Wrote scripts and configured an LLM for Named Entity Recognition. Trained an LLM on gene names and diseases. Works well so far (F1 ~ 98%, Accuracy ~ 99.9%)
  • Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  • There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.


February 15, 2024

Literature Migration to the Alliance ABC

Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)?

Find papers with a high confidence NN classification for a given topic that have also been flagged positive by an author in a community curation pipeline and that haven’t been curated yet for that topic
  • Facet for topic
  • Facet for automatic assertion
    • neural network method
  • Facet for confidence level
    • High
  • Facet for manual assertion
    • author assertion
      • ACKnowledge method
    • professional biocurator assertion
      • curation tools method - NULL
Manually validate paper - topic flags without curating
  • Facet for topic
  • Facet for manual assertion
    • professional biocurator assertion
      • ABC - no data
View all topic and entity flags for a given paper and validate, if needed
  • Search ABC with paper identifier
  • Migrate to Topic and Entity Editor
  • View all associated data
  • Manually validate flags, if needed

PDF Storage

  • At the Alliance PDFs will be stored in Amazon s3
  • We are not planning to formally store back-up copies elsewhere
  • Is this okay with everyone?

February 8, 2024

  • TAGC
    • Prominent announcement on the Alliance home page?
  • Fixed login on dockerized system (dev). Can everybody test their forms?

February 1, 2024

  • Paul will ask Natalia to take care of pending reimbursements
  • Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.

January 25, 2024

Curator Info on Curation Forms

  • Saving curator info using cookies in dockerized forms. Can we deploy to prod?

ACKnowledge Author Request - WBPaper00066091

  • I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  • The paper conducts an analysis of natural variations within 48 wild isolates. To enhance the reliability of the variant set, I utilized the latest variant calling methods along with a custom filtering approach. The resulting dataset comprises 1,957,683 unique variants identified using Clair3. Additionally, Sniffles2 was used to identify indels of >30 bp, which numbered in the thousands to tens of thousands for most wild isolates. It is worth noting that variants identified with Sniffles2 have less reliable nucleotide positions in the genome.
  • I am reaching out to inquire whether WormBase would be interested in incorporating this dataset. An argument in favor is the higher quality of my data. However, I am mindful of the potential substantial effort involved for WormBase, and it is unclear whether this aligns with your priorities.
  • Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.

Update on NN Classification via the Alliance

  • Use of primary/not primary/not designated flag to filter papers
  • Secondary filter on papers with at least C. elegans as species
  • Finalize sources (i.e. evidence) for entity and topic tags on papers
  • Next NN clasification scheduled for ~March
  • We decided to process all papers (even non-elegans species) and have filters on species after processing.
  • NNC html pages will show NNC values together with species.
  • Show all C. elegans papers first and other species in a separate bin.

Travel Reimbursements

  • Still waiting on October travel reimbursement (Kimberly)
  • Still waiting on September and October travel reimbursements (Wen)

UniProt

  • Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
  • Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
  • Stavros escalates the issue on Hinxton Standup.
  • Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.

January 18, 2024

  • OA showing different names highlighted when logging in the OA, now fixed on staging


January 11, 2024

  • Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
    • Curators should make sure that, when pasting special characters, the duplicate function works
  • OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
    • If you want to bookmark an OA url for your datatype and user, log on once, and bookmark that page (separately for prod and dev)
  • Chris tested on staging and production the phenotype form and the data are still going to tazendra
    • Chris will check with Paulo. Once it is resolved we need to take everything that is on tazendra and put it on the cloud with different PGIDs
    • Raymond: simply set up forwarding at our end?
  • AI working group: Valerio is setting up a new account for open AI -paid membership for ChatGPT4. We can also use Microsoft Edge copilot (temporary?)
  • Chris getting ready to deploy a 7.0.0. public release - February 7th. Carol wanted to push out monthly releases. This will include WS291. For subsequent releases the next several releases will be WS 291 until WS292 is available.
  • Valerio would like to use an alliancegenome.org email address for the openAI account
  • New alliance drive: https://drive.google.com/drive/folders/0AFkMHZOEQxolUk9PVA
  • Alliance logo and 50 word description for TAGC> Wen will talk to the outreach WG
  • Name server. Manuel working on this, Daniela and Karen will reach out to him and let him know that down the road micropublication would like to use the name server API to generate IDs in bulk
  • Karen asking about some erroneous IDs used in the name server. Stavros says that this is not a big deal because the "reason" is not populating the name server
  • It would be good to be able to have a form to capture additional fields for strains and alleles (see meeting minutes August 31st 2023. https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls_2023#August_31st.2C_2023). This may happen after Manuel is done with the authentication.
  • Michael: primary flag with Alliance. Kimberly talked about this with the blue team. They will start bringing that over all papers and fix the remaining 271 items later.

January 4, 2024

  • ACKnowlegde pipeline help desk question:
    • Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
  • Citace upload, current deadline: Tuesday January 9th
    • All processes (dumps, etc.) will happen on the cloud machine
    • Curators need to deposit their files in the appropriate locations for Wen
  • Micropublication pipeline
    • Ticketing system confusion
    • Karen and Kimberly paper ID pipeline; may need sorting out of logistics
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