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November 14, 2024

• TIFF PDF in ABC

WormBase has a complete collection of worm literature, including over 2000 papers that have no full text online, most of them were from the 90's. When we started WormBase in 2000, we collected reprints of all worm-related papers, scanned them, and converted them into text PDFs. --Wen

- We have PDFs at ABC, and that's the Source of Truth, because manual curator modification of files happens there.
- Daniel downloads PDFs to a computer, and uses Valerio's script / my CGI to upload them to ABC
- It's hard to see where the files ended up, so we'd like to have a way to see that things are actually properly stored and available somewhere.
- We have a bunch of old PDFs on tazendra, that would be very hard to get back, if we lost the copies at ABC (which are in s3).  So we'd like to back these up for sure (?)
- We might also want to back up the new ones, as they get uploaded, so we can be sure that we can see them on the server through the file system.
- - Valerio thinks it'd be easy to expand the disk on the dockerized prod server, and it would only cost $100 or so a year, and we can modify the CGI to put them there, where anyone can ssh into the directory and see them.  Do we want to do this ?  (Discuss in this email / at the next WB call)
- - Raymond would like them to be accessible through the old CGI that listed all the PDFs by WBPaper ID.  If we want that at ABC, it would go through Ceri / Blue team prioritization, if we want that at Caltech, I can do that.  The Caltech version won't be the SoT, it would be just of what Daniel uploaded (so any edits by curators won't be there)
- - Curators don't want to bring back access to the PDFs through the paper editor directly, like they used to before, because ABC is the SoT (discuss, if that's not the case).

We didn't realize that Daniel wasn't keeping local copies of what he was uploading, so storing them somewhere sounds good.

-- Juancarlos + Valerio

November 7, 2024

Wen has been in discussion with Eduardo and his student regarding an AI/Textmining project for finding publications of allele sequence changes. They will make use of Textpresso, by way of Wen's private token for access. Daniela mentioned that she's interested in incoporating this into author flagging pipeline, when that becomes practical.

October 31, 2024

(Zoom AI summary, edited by Raymond)

Quick recap

The team discussed the progress of mapping Allele variations to gene names, the development of a training set for a project, and the process of generating and validating data sets for training.

Next steps

• Chris to compile training sets for gene interactions, gene regulation, new mutant, overexpression, and RNAi data types.
• Karen to create training sets for overexpression data type using the curation status form.
• Wen to explore ways to identify papers publishing sequence details for alleles.

Summary

Allele Variations Mapping and Challenges

Wen reported on the progress of mapping Allele variations to gene names, identifying about 3,000 alleles without gene names. She successfully mapped 2,549 alleles through their strain phenotype and another 453 through textpresso screens. These were sent to Stavros for loading into the database. Wen also mentioned her intention to start curating sequence changes, but faced challenges in identifying papers that mention sequence details. Kimberly suggested searching through positive lists of papers with Allele designation or string, while Hans-Michael questioned the accuracy of old models for sequence changes. Chris and Juancarlos discussed the need for models for new data types like mutant, gene regulation, and overexpression phenotypes, with the understanding that some data may need to be manually generated.

Training Set Development and Validation

The team discussed the development of a training set for a project. Juancarlos mentioned that they were considering using the duration status form for this purpose, but needed feedback on what information to include. Chris suggested a target number of 100 papers for both positive and negative sets. Ranjana proposed an Excel spreadsheet as a starting point, which Valerio could help develop into a programmatic way of validating the data. Daniela suggested bringing back the data into the curation status form to avoid double work. The team agreed to work on this, with the aim of having a programmatic way to validate the data. Data Set Generation and Validation The team discussed the process of generating and validating data sets for training. They considered using the curation status form and spreadsheets for this task. The team also discussed the need for more training data, particularly for overexpression and new mutant data types. It was suggested that the Blue Team could generate a random set of papers for validation. The team also discussed the need for more negatives in the genetic interaction data type. Chris offered to compile the overexpression data set. The team agreed to use the curation status form to extract existing sets of validated positives and negatives. They also discussed the process of creating tickets for generating data sets.

October 24, 2024

• NNC classification is going away (maybe ? I don't actually know)
• Blue Team is taking over automated dataset generation
• We need positive/negative sets to retrain the data
• Some datatypes have already generated dataset
• Chris G + Jae + Kimberly + Valerio discussed how to generate Physical Interaction data.
  • There will be two sets of data using geneprod
  • physical_interaction_c_elegans
    • Papers validated positive 2563
    • Papers validated negative 8068
  • physical_interaction_general
    • Same positive set
    • Negative set exclude those that have a manual text comment. SELECT COUNT(*) FROM cur_curdata WHERE cur_datatype = 'geneprod' AND cur_curdata = 'negative' AND cur_txtcomment = ;
• Curators need to figure out what datasets they want to generate training data for, or it won't be at ABC.
• Kimberly suggests doing a controlled vocabulary at ABC instead of manual comments.
• Wen talked about gene name entity extraction.

October 10, 2024

• Laboratory history will need schema changes
  • Change of PIs/Lab representative.
  • Lab was dismissed (PI retired or deceased)
  • We would document these at the Alliance level. Juancarlos will involve Wen when it is time to work on the schema.

• Area meeting information
  • We documented some area meetings for the outreach purpose but these are outdated: https://wiki.wormbase.org/index.php/Meetings
  • Shall we update and publish them? Yes, Raymond will create a public page so that everyone in the Worm community can update the page.

• Privacy issue
  • Will the above information be abused by companies or individuals to sell their products?
  • SimpleFind allows users to download all Lab information. Bhagwati Gupta downloaded the table to promote online seminars. https://caltech-curation.textpressolab.com/pub/cgi-bin/forms/simplefind.cgi
  • We should remove the emails from SimpleFind Lab results.

Minutes

• Lab info, area meetings, and privacy

When Labs change PIs, we can change the PI name but we are not keeping track of old PIs (in acedb). We should add a field for "previous PIs and CGC representatives" to the schema, and keep track of all data in the lab object for old PIs. We have the data about old PIs in postgres in the old_pis table. The timestamp we have in the table is when Cecilia recorded the change, but there's no indication on the date when the PI became an "old PI". Wen: we could set old labs to "not active" in case their PIs passed away or we could check if they are actively publishing. Keeping track of labs is really important for uPublication to check if submissions are legit. We could do these changes in the Alliance (blue team). Paul suggests that we should do this directly at the Alliance. Wen: we need curation to make sure that history of lab info is accurate. Wen also keeps a wiki page of area meetings and can provide these data to the Alliance. We decided to remove lab info from simple find to avoid giving contact information to spammers. The lab info can stay but not contact information. This is a general privacy concern but we agree that it's fine to keep the info.

• Discussion with Erik Andersen (CeNDR, the Caenorhabditis elegans natural diversity resource)

Paul invited him to a WB meeting to discuss what they need when Stavros is also present. If they have additional gene info they should provide linkouts that can be connected to Alliance and WB gene pages. There was also a discussion about Textpresso. Another thing they are interested in is that they would like to curate traits instead of phenotype. This could be a huge task (creating a traits ontology). We should lear from people who already worked on traits ontologies. We also mentioned worm anatomy ontology. The main purpose of the ontology discussion is to plant seeds for future collaboration and to reduce overlap of efforts.

September 12, 2024

Help Desk

• Email from Anayah Chowdhury about Alzheimer strains. Can someone respond?

WS295 Citace Upload Deadline

• According to WB Release Schedule, data freeze/upload is 07-Oct-2024
• Local citace upload deadline of prior Tuesday, October 1st?

September 5, 2024

Acknowledge pipeline

• Acknowledge (program officer) excited; interested in implications for medical records
• Renewal possible in November (or March)

Call for scientific software engineers

• Possible funding source for more software?

August 29th, 2024

• Helpdesk question on Hi-C and Chip-seq data sets
• Included in SPELL datasets directory? Or other sources like GEO?

August 22nd, 2024

• Loading transgenic allels associated with references into the ABC
  • Species questions - thank you to Chris and Karen for the info
    • Multi-species transgenes
      • Species is captured in the construct object
    • Species value in the OA and WB
      • Represents the species into which the construct was introduced and thus where the transgene exists
      • Any additional value to back-populating the species field in the OA to match what is happening at the level of dumping the .ace file? What is the implication wrt understanding how that information got added, i.e. manually by a curator or automatically by a script?
    • For the ABC topic/entity editor, we'll need to agree on, and document, what species for a transgene flag really means.
• GFT/GFF files for CB4856 - helpdesk question
  • What files are useful for people and does WB have the bandwidth to produce them?
  • If we don't actually have content for files, should there be a link on the https/ftp site?

August 8th, 2024

• Some curators rely on knowing when a new WB release is out on the website for their work, eg., for updating SOBA, WOBR, SimpleMine, etc. WS293 has been released now
• Raymond will try to write a script/chron job to alert curators to a new release
• Blogpost done to alert users to WS293 and availability of balancers in SimpleMine
• Some workshop proposals already submitted for 2025 Biocuration workshops--AI, Acknowledge, microPub to be submiited

July 18, 2024

• Shall we keep caltech-curation-dev up year-round with less RAM and CPU?
  • We need this dev site to test new features for the current tools and pipelines like SimpleMine, the one-button feature for curators to test ace files for upload. A quarter of the current RAM and CPU may work if it can reduce 75% of the cost.
  • Yes keep both instances up and reduce RAM and CPU.
• We added Balancers (with their rearrangement type and reference strains) to SimpleMine.
  • It will go live with WS293 on July 26. Here is the dev site with the new feature: https://caltech-curation-dev.textpressolab.com/pub/cgi-bin/forms/simplemine.cgi
  • Received feedback for Reagent Help. Need more work on the Gene search. Also need a new name for the tool.

July 11, 2024

• Juancarlos and Wen are developing a new CGI to filter entities like Gene, Allele, Transgene, Rearrangement, Antibody etc.
  • https://caltech-curation.textpressolab.com/pub/cgi-bin/forms/reagent_help.cgi
• WS294 upload this week
  • Shall we start the automatic dump of ace files and ontology files into the upload directory?

June 27th, 2024

ISB

• From Mary Ann Tuli: "Elections for the ISB Executive Committee are coming up in a few months. Someone from WormBase on the committee would be a great asset. Have a think."
• Possibility of an AI committee sponsored by the ISB - thoughts?

2025 Meetings

• Discuss who would like to attend what meetings and travel funds
• ISB 2025 - early April, Stowers Institute, Kansas City, MO
  • Possible workshop proposals:
    • AI - Valerio, Alliance AI working group, Elixir?
    • Community curation - Daniela, Kimberly, invited community members
    • microPublication - Daniela, Karen

Person curation

• Unsubscribe from WormBase and ACKnowledge email lists
  • Recently, an author expressed their desire not to receive ACKnowledge notifications, and we would like to ensure their preferences are respected.
  • We have an ‘omit’ form where curators can enter a WBPerson ID to omit them from notifications: https://caltech-curation.textpressolab.com/priv/cgi-bin/omit_form.cgi
  • How does being on the omit list for ACKnowledge requests affect other types of communications from WormBase? Cecilia uses postgres to unsubscribe and via the command line she can chose different levels of non-notifications:
    • hide : suppress whole object from acedb/WormBase
    • privacy : we keep track of email, we don't mass email, we don't put it in acedb/WormBase, but we can still do person-paper verification, and know that we don't need to find their email.
    • unsubscribe : _does_ show up in acedb/Wormbase. no mass emails, do contact for person-paper verifications.
    • omit form -> if someone is on the omit list they will not receive the email from Chris' phenotype community curation pipeline.
  • Do we need to modify the omit form to allow curators to choose what type of non-notification to assign to an author?
• Person curation: how does the current WB workflow fit with ACKnowledge and the transition to the ABC
  • When a new paper is included in the WormBase corpus, there are scripts that extract author's names and email addresses and match those names with WBPersons.
  • If an email was extracted, Cecilia sees that in the author-person form: https://caltech-curation.textpressolab.com/priv/cgi-bin/cecilia/person_editor.cgi?curator_two=two1&paper_id=00066889&action=Search+Paper
  • If no email was extracted, Cecilia checks the PDF. Example: https://caltech-curation.textpressolab.com/priv/cgi-bin/cecilia/person_editor.cgi?curator_two=two1&paper_id=00066861&action=Search+Paper
  • If the Person exists in the Database, and if the paper has a new email address: Cecilia updates the email address and also add that paper to their bibliography.
  • If the Person does not exist in the Database: Cecilia creates a new Person object and adds that paper to their bibliography.
  • For old papers with email addresses
    • Cecilia first checks if the authors exist as WBPerson, if yes she adds that paper to their bibliography and if not she creates a New Person object.
  • For old papers without email addresses
    • Cecilia searches the internet for author information. If she finds new data, she updates the record.

June 13th, 2024

• Donations, Raymond looking into it
• Paul looking into subscriptions vs fees
• Paul talking to Global BioData Coalition
• SAB
  • PI succession plan
    • Long term - Someone at WB with a faculty status? A WB PI?

May 30th, 2024

Entity association with references - Alliance ABC (Kimberly)

• Need to make sure we have the right classes in the ATP ontology for what WB wants to associate wrt transgenes
  • Variation
  • Construct
  • Transgene
  • Rearrangement
• Suggestion: create a new child of allele: transgenic allele and use that for WB transgenes
• Question: should affected genomic model be a child of entity?

May 23rd, 2024

• Publication bias workshop NINDS
  • Registered report -> the protocol is sent before publication
  • How many negative curated data? Do we want to pull this out?
  • Two billion dollars worth of research not published each year
  • Octopus.ac publishing platform

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)

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%)

• Is this similar to the FlyBase system? Recording of presentation https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK

• 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.

• Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024

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
  • 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.

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