Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
= 2022 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_January_2022|January]]
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_February_2022|February]]
 
  
−
[[WormBase-Caltech_Weekly_Calls_March_2022|March]]
+
==March 14, 2024==
  
−
[[WormBase-Caltech_Weekly_Calls_April_2022|April]]
+
=== TAGC debrief ===
  
−
[[WormBase-Caltech_Weekly_Calls_May_2022|May]]
+
==February 22, 2024==
  
 +
===NER with LLMs===
  
−
== August 31st, 2023 ==
+
* 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%)
−
=== Alliance Migration: Review flagged data types ===
 
−
* Discuss future of the different data types and flagging methods in context of transferring data to the Alliance infrastructure
 
−
* Initially thought we were planning to transfer everything we have currently at Caltech
 
−
* But are there data types that we don't need to transfer, and if so, what are the implications for:
 
−
** Alliance data storage - any limitations?
 
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** Storing and accessing existing Caltech legacy data
 
−
** If we don't transfer legacy data, but a flagging pipeline still runs, do we stop the flagging pipeline? Keep the flagging pipeline but don't transfer any data?
 
  
−
{| class="wikitable"
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
!Data Type in Curation Status Form
 
−
!Data Type Definition
 
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!Flagging method(s)
 
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!Usage - which flagging methods are used for curation
 
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!Curators
 
−
|-
 
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|rowspan="1"|Antibody
 
−
|
 
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|NNC, SVM, String Match, cfp, afp, oa, curation status
 
−
|
 
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|Daniela, Wen, Xiaodong
 
−
|-
 
−
|}
 
  
 +
* 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==
  
−
* Next citace upload using dockerized tazendra
+
=== Literature Migration to the Alliance ABC ===
−
** Documentation for SOP
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
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*** I started my own documentation but immediately ran into some questions (Kimberly)
+
===== 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
  
−
== August 24th, 2023 ==
+
===== Manually validate paper - topic flags without curating =====
−
*Using name server as a backdoor for curation
+
*Facet for topic
−
*Minting WBIDs for Tier3 and 4 species
+
*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?
  
−
== August 3rd, 2023 ==
+
==February 8, 2024==
−
=== Caltech ===
+
* TAGC
−
* Reminder to do research integrity training
+
** Prominent announcement on the Alliance home page?
−
* Not everyone at WormBase got the email - Paul S. can double-check if this was based on job titles or something else
 
  
−
=== Genetics Database Update Paper ===
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
* Is there enough material for a WB update?
 
−
** Explanation of transition to the Alliance
 
−
*** Start by creating a table of data types in WB vs Alliance
 
−
** New WB data, e.g. single cell data
 
−
* If so, who's turn is it to write it?
 
  
−
== July 20th, 2023 ==
+
==February 1, 2024==
−
=== Remaining debrief from IWM ===
+
* Paul will ask Natalia to take care of pending reimbursements
−
* PIs wanting to undergraduates to do more in terms of curation and training
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
−
** check into training support with NSF community outreach grants
 
−
=== Motivating the community ===
 
−
** Chris's trophys a huge hit - people wanted pictures and were motivated
 
−
** $250 uPub voucher useful
 
−
** Paul's sense of swag is off, staff have great ideas
 
−
** WB blog supports images - can post pictures of trophy winners
 
  
−
== Place for teaching material ==
+
==January 25, 2024==
−
want to have a public location to for people to access webinars and slides etc. ex. XenBase<br>
 
−
Paul suggests we use an Alliance Forum to post these, will also motivate alliance members to do the same><br>
 
−
Chris suggests the Alliance User Forum<br>
 
−
Todd suggests Google drive is good, but many problems with things getting muddled, e.g, by inconsistent naming = things get lost and hard to find<br>
 
−
If we use google drive, need to have some management<br>
 
−
Do we want a place for the community to share things with the community<br>
 
−
Alliance User Support Group should be tapped for help here, and we can reach out to GSA to see what they do to organize community teaching docs. <br>
 
−
Raymond - CMS system is designed for this, but we would need to set that up == Wen is interested<br>
 
−
Todd- need to identify what type of material would we be putting up. Slide shows? - maybe use a ready built CMS that is good with side-shows, will also need to have maintenance over time. <br>
 
−
Maybe the lowest hanging fruit is just Maintaining an Index page for these, then it doesn't matter where the material really exits<br>
 
−
Start with generic index page at Alliance, with brief metadata - can we store it in CaltechData = Karen and Wen will talk to the library
 
  
−
== Making Web pages for uPub papers ==
+
=== Curator Info on Curation Forms ===
−
Immediate problem - make a splash page for paper not found at WB.  
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
−
something more general - ask Alliance for splash page <br>
 
−
gene paper links is going to be more complicated
 
  
−
== WormBook and GSA ==
+
=== ACKnowledge Author Request - WBPaper00066091 ===
−
Genetics thinking that WormBook is not that active, but possibly they are missing out on activity since community uses WormBook.org as index to find articles. <br>
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
−
Dainel has been adding Genetics WormBook chapters to WormBook.org, so they should be available there and findable.  
 
  
−
== Connectome ==
+
* 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.
−
Raymond fixed the link-outs to these sites, not updated on the site yet<br>
 
−
Todd- hotfix will be run that should fix all of that
 
  
−
== Release announcements ==
+
* 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.
−
Not automated, Caltech needs to synchronize things, Raymond and Wen will be added to Slack release channel.  
 
  
 +
* 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.
  
−
== July 13th, 2023 ==
+
==January 18, 2024==
−
=== Update/Discussion on WormBase -> Alliance paper pipeline migration ===
+
* OA showing different names highlighted when logging in the OA, now fixed on staging
−
* [https://docs.google.com/drawings/d/1dUt5PwBMBYf-x0ugzbJgMcsFWF-SvPU0bcYTo9YKI4s Alliance data model] for entity/topic tagging
 
−
* [https://alpha-curation.alliancegenome.org/#/ontology/atp Alliance Tags for Papers Ontology]
 
−
* [https://github.com/evidenceontology/evidenceontology/issues ECO requests]
 
−
* Bibliographic data - Alliance will be the source of truth for all references in PubMed (except legacy author data); WB will be the source of truth for all other paper, e.g. meeting abstracts
 
−
* Entity tags
 
−
** Species
 
−
*** Modeling evidence
 
−
**** 'Manually_connected' plus 'Curator_confirmed' - Alliance doesn't yet have people, so we will store 'WBPerson' in a created_by field
 
−
**** 'Inferred_automatically' text string (from ACKnowledge pipeline)
 
−
**** No explicit evidence in postgres, but notes on what we did, e.g. scripts and string matching
 
−
** Genes
 
−
*** Modeling evidence
 
−
* Topic tags
 
−
** Will port over the WB topic and map to an ATP ontology term
 
−
** Will not populate species (we don't know this definitively at WB)
 
−
** Each flagging 'method' will be a unique combination of: source, source details, MOD, and creator
 
−
*** For example, author, ACKnowledge, WB, WBPerson625
 
−
*** For example, author, Fast Track Your Paper, FB, Norbert Perrimon
 
−
** Some data types, e.g. antibody, are modeled as topics and entities; we will only populate topic unless we also have a specific curie to populate an entity value
 
−
*** New topic tags: antibody data
 
−
** Existing validation will come from manual curator entries in curation status form and from OA values and from author ACKnowledge submissions
 
−
*** Each validation is tracked separately; no manual validation will overwrite any other manual validation
 
−
*** Manual entries will validate AI entries (more specific entries can validate less specific entries)
 
−
** Modeling and porting over curation status pre-canned comments
 
−
*** SVM positive, curation negative
 
−
**** Validated right by curator, but not curatable for WB (will be a new workflow ATP tag)
 
−
**** WB may not have always been consistent here, so we may want to think about clean up after migration
 
−
*** C. elegans as heterologous expression system
 
−
*** GO curation (will not port over; we can get this information from a GAF, if need be)
 
−
*** BioGrid and BioGrid/GO - keep?
 
−
*** Curation negative, no strain name given in paper
 
−
*** Toxicology - create an ATP value?
 
−
*** Host-pathogen virulence - create an ATP value?
 
  
−
== July 6th, 2023 ==
 
  
−
== June 8th, 2023 ==
+
==January 11, 2024==
−
*Update on WormBase -> Alliance paper pipeline migration
+
* Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
−
** Newly added WB papers for retraction notices and corrections
+
** 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.
  
−
== June 1st, 2023 ==
+
==January 4, 2024==
−
*Raymond: We need to prepare some slides to introduce our tools at IWM. It would be better to drop them to the google doc folder for IWM.
+
* ACKnowlegde pipeline help desk question:
−
*From Tazendra to Amazon Cloud server: Valerio finished the backup setting and now restoring data on the cloud server. Now testing Wen's script and the full build will be tested after IWM
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
*Textpresso will be modified and prepared for ABC in Alliance. This will be discussed again after IWM.
+
* Citace upload, current deadline: Tuesday January 9th
−
 
+
** All processes (dumps, etc.) will happen on the cloud machine
−
== May 25th, 2023 ==
+
** Curators need to deposit their files in the appropriate locations for Wen
−
* Waterston data
+
* Micropublication pipeline
−
**Noticed that Bob's list had 69 dead genes and that the graphs were displayed on the dead gene page
+
** Ticketing system confusion
−
 
+
** Karen and Kimberly paper ID pipeline; may need sorting out of logistics
−
<pre>e.g. WBGene00009022
 
−
https://wormbase.org/species/c_elegans/gene/WBGene00009022#0g1--10 </pre>
 
−
 
 
−
**Asked Paulo to map the dead genes to the live ones and display on the live gene page.
 
−
**While doing this Paulo noticed that 55 genes had values for both dead and live genes, and the values are quite different.
 
−
 
 
−
<pre>https://wormbase.org/species/c_elegans/gene/WBGene00007084#0g1--10</pre>
 
−
 
 
−
**Notify Bob, can ditch dead genes
 
−
 
 
−
==May 11th, 2023==
 
−
* Waterston data update
 
−
** Generated a file with the correct mappings
 
−
** Renamed Canopus the image files on Canopus
 
−
** Generated a -D file for Citace Minus
 
−
*** Send the .ace file to stavros
 
−
*** Contact Paulo and Todd
 
−
** Tested on spica, all good
 
−
** Patch the file for WS289. What needs to be done?
 
−
* Next upload
 
−
** Falls right after the IWM and around the 4th of July holiday
 
−
** Do we want to do a trial upload with our new system beforehand?
 
−
** We will upload the files on spica as we normally do but will also test the new system as much as we can
 
−
** Will do upload on July 11th
 
−
 
 
−
*IWM
 
−
** Finalize swag
 
−
*** Generic WB swag pens and frisbee (agreed blue with white logo): https://docs.google.com/document/d/1v8bCoL2Qy9hNQmJ57YOccg8HkmKXclulugfnYwGU7lM/edit
 
−
*** Community curation swag: https://www.crownawards.com/search?q=FIRDBW&lang=default
 
−
**** Trophies with custom logos: https://www.crownawards.com/Custom_Logo_Trophies?q=FIRDBW
 
−
** Booth
 
−
*** Ordered 2 chairs, a long desk, 1 electric outlet. Sarah D, Stavros will bring additional chairs
 
−
*** Carpeting. ok without
 
−
* Backup for new dockerized system
 
−
** Restic software -command line program that provides encrypted backup. Files compressed and store by md5sum
 
−
** want to avoid the encryption if we can
 
−
** Can include folders
 
−
** symlinks to the scripts -> will back up the links but not the files, which will be backed up with git
 
−
** Include/exclude list for files and folders
 
−
** Documentation will be provided in a readme file in github
 
−
** Backup files can be stored in aws S3
 
−
 
 
−
* Person wormbase_comments in acedb vs internal comments in postgres, but neither on WBPerson pages on website.
 
−
** No one recalls why they're in acedb, email sent to wormbase@caltech with questions for Cecilia.  There are ~14k wormbase_comments
 
−
 
 
−
==May 4th, 2023==
 
−
* Bug with molecule OA
 
−
** JSON parse failed error -> fixed
 
−
** Juancarlos will look into this
 
−
* Alliance postgres migration
 
−
** Chris started working on this
 
−
 
 
−
==April 27th, 2023==
 
−
* 445 image files provided by Bob Waterston contain the wrong WBGene name, e.g. egl-1_WBGene00001186_embryo_lineage.jpg (egl-1 is WBGene00001170)
 
−
* noticed while doing spot check in discussing Eyleen J. O'Rourke data
 
−
* Paulo programmatically went through the files, the graphs are unaffected, the images are.
 
−
* Option 1: ask Juancarlos to rename the wrong image files, based on gene public name. Prepare a -D file for CitaceMinus and re-upload a .ace file for the wrong objects.
 
−
* Option 2: ask Bob to send again the original files with the right name.
 
−
* Regardless, notify Bob
 
−
 
 
−
==March 23rd, 2023==
 
−
#Some updates on Neural Networks development (postponed)
 
−
 
 
−
==March 16th, 2023==
 
−
# Getting data from acedb to load postgres.  (e.g. Variation)  Do we still need this ?  Automated scripts seemed to break a lot, while running them manually always worked.
 
−
 
 
−
==March 9th, 2023==
 
−
#[[https://docs.google.com/document/d/1aJ-TOd2xIxNV2VZG5T57brz3T82MMcgbyXWohVH27NU/edit?usp=sharing|Postgres migration to the cloud]]
 
−
##The generic.cgi, we need to know who uses these:
 
−
###tempVariationObo: this brings in variations into the OA that are in WB but not in the OA. Note this is a different functionality compared to the Name server. We need this. Used by Ranjana, ??
 
−
#### CG: Yes, I need this
 
−
###UpdateVariationObo--can't get to this now on Tazendra
 
−
###AddToVariationObo--can't get to this now on Tazendra
 
−
###TempStrainObo --brings in strains into the OA that are in WB, seems to be the counterpart of the tempVariationObo for strains
 
−
####  CG: I need this
 
−
###AddTempObjectObo--used to add data to the database, used by AddToVariationObo and AddToStrainObo
 
−
###PapIdToWBPaper
 
−
#### CG: I need this
 
−
###  When people added things by mistake they would sometimes remove them from the flatfile, does anyone still do that ? -- Chris and Ranjana don't, Karen or Daniela might
 
−
###  Does the public need access to this, or should we move this to a private / protected URL ? -- Nick/micropub probably needs this
 
−
##WSVariation and nightly geneace variation file
 
−
###Overlapping but WSVariation has a lot more variation-related info, e.g. phenotype and phenotype_not_observed
 
−
###Confirming that we still need both
 
−
##There's also WpaXref and WpaXrefBackwards and ListPmids and ConvertPaperIdentifiers
 
−
##The only thing is that it writes to flatfiles so when cronjobs update variation/strains from nameserver or WS, it also loads from the flat files.  The location of the flatfiles isn't final yet, but it's dockerized.  People used to manually edit that when they wanted to remove them from the list, do people still want to manually edit those flatfiles ?
 
−
##ContinentPIs
 
−
##Valerio has set up ssh access into textpressolab.com
 
−
##There's 3 cases for using acedb: 
 
−
###your local use for testing stuff
 
−
###spica replacement for Wen
 
−
###extract things automatically for tazendra/postgres.  Do we need this ?
 
−
#Some updates on Neural Networks development
 
−
 
 
−
= Feb 23rd, 2023 =
 
−
== New paper folder organization may affect downstream pipelines ==
 
−
* Antibody string-matching pipeline was affected by recent changes in paper folder structure
 
−
** The pipeline started processing old papers, does this affect also papers processed for NN?
 
−
** http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=listCurationStatisticsPapersPage&select_datatypesource=caltech&select_curator=two12028&listDatatype=antibody&method=str%20pos%20nval&checkbox_cfp=on&checkbox_afp=on&checkbox_str=on&checkbox_nnc=on&checkbox_svm=on
 
−
 
 
−
= Feb 9th, 2023 =
 
−
== IWM 2023 booth cost ==
 
−
* From Mary Anne this morning: "I had the cost wrong, it would be $750 for you at cost. Sorry, I had been looking at the wrong line item."
 
−
 
 
−
= January 26th, 2023 =
 
−
 
 
−
== Alliance issues ==
 
−
* monitoring API usage?
 
−
** We have Google Analytics but since Patrick Kalita left, no one has been monitoring it
 
−
** Paul: we need for now a simple way of tracking number of users. Chris: seems reinventing the wheel to write something from scratch. tracking API calls would be useful for our funders.
 
−
** Olin said you can track UI events (e.g. page clicks) and API access (including programmatic access) but we are not currently. Chris will see how much work is involved in this. We need someone with Google Analytics experience.
 
−
** Would be good to put a call out to all people at Alliance asking who has experience with Google Analytics.
 
−
* Simplemine: reverse proxy hosted at alliancegenome.org. If it is dockerized we can do it, otherwise not. Eventually dockerize Simplemine and move it to Alliance servers.
 
−
** Olin concerned about security over CGI technology.
 
−
** We will talk about this (implementation and security concerns) at the developer call
 
−
* Embedding alliance tools or processes into MODs.
 
−
** The API is there but is not in all MOD interest to write code to pull the data out.
 
−
** iFrame is not very flexible on how you display data (e.g. narrow, little flexibility in configuration).
 
−
** Could set up widgets as we did for the GO ribbon. Still requires MOD implementation of code base.
 
−
** Paul: eventually MOD sites will be retired. Chris: One concern from Christian (ZFIN): clicking on a zebrafish gene name will open up an alliance page, could it link to ZFIN gene page or provide users with an option?
 
−
** Maybe opening up an Alliance widget at the MOD preferably happens in a separate window (e.g. pop-up window, new browser window/tab; as opposed to in the same page/tab).
 
−
 
 
−
== Alliance All Hands ==
 
−
* Not all the curators are going to be there. Focus on PI discussion and development teams?
 
−
 
 
−
= January 5th, 2023 =
 
−
 
 
−
*Chris will help to create a reverse proxy for the Alliance SimpleMine. It will function like WormBase SimpleMine. People will need to visit the Alliance before going to tazendra. It will prevent users from seeing the tazendra URL and create more traffic for the Alliance
 
−
*Alliance SimpleMine with XenBase data is ready but needs XenBase feedback before it goes public. It is based on Alliance 5.4.0 release, so it can be released when Alliance 5.4.0 goes public in late Jan or mid-Feb. 
 
−
*Karen will visit Pasadena 1/13-15
 
−
 
 
−
= December 8th, 2022 =
 
−
== Data Type Flagging Pipelines and Alliance Infrastructure ==
 
−
*We currently run the neural network algorithms at Caltech
 
−
*What will we need to do to transition this to run on Alliance infrastructure?
 
−
*Can we start to run the neural networks on a more frequent basis, e.g. monthly? Could that be automated?
 
−
 
 
−
== WB PDF Migration ==
 
−
* Daniel, Juancarlos, Kimberly continue some clean up of redundant files before moving things over to the Alliance
 
−
 
 
−
= November 17th, 2022 =
 
−
*TEC_RED meeting. Meeting with Nikita Jahveri, Wouter Van de Berg (Gupta's lab). Participants, Valerio, Daniela, Kimberly, Magda, Stavros.
 
−
identified a large number of operons in C Briggsae. Baghwathi Gupta's lab. 4200 Briggsae genes identified with SL influencers. Want to contribute the information in WormBase.
 
−
* Used WS279 for the annotations
 
−
* they have excel  documents with the location in the supplementary files
 
−
* Magda: are the tag sequences unique? Nikita: yes. If they bind to 2 ore more genes that have classified as paralogs
 
−
* Also  identified isoforms (multiple transcripts tab in the spreadsheet)
 
−
 
 
−
** Steps forward: need to update the gene models and the operon models on WormBase.
 
−
* Can bring in data in different tracks.
 
−
* Need to update gene models based on this new evidence
 
−
* Nikita will send the data to Magda and Stavros (3 spreadsheets). Need to write out the categories.
 
−
* they did not produce  the GFF file, all in excel sheets.
 
−
* Material used: mixed stage worm population
 
−
 
 
−
they have excel  documents with the location
 
−
 
 
−
= November 3rd, 2022 =
 
−
* Booth at IWM
 
−
** ACKnowledge will be showcased at the WB booth
 
−
** Will also advertise Alliance
 
−
 
 
−
= October 27, 2022 =
 
−
 
 
−
= October 6th, 2022 =
 
−
 
 
−
== Mangolassi ==
 
−
* Mangolassi is down (network only?); Michael will be in the office in an hour
 
−
** Start a cronjob to check for network connections? Already set up (Raymond)
 
−
** Michael can log into his machine; Tazendra is OK (so, not network issue?)
 
−
** Michael fixed it by unplugging and reconnecting ethernet cable (network card issue)
 
−
 
 
−
== GO meeting next week ==
 
−
* 7am - 11am PDT
 
−
* Zoom channel? Available on GO meeting agenda page:
 
−
** https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M
 
−
 
 
−
== Alliance Literature working group ==
 
−
* Subgroups; Ranjana interested in joining the search subgroup
 
−
* Can sign up on the lit group page
 
−
** https://docs.google.com/document/d/1hB6cft0J_DaapQ9uHUGXwbqrnsZs7wORoepQicLdhTk/edit?pli=1#bookmark=id.butj0rfl4zh1
 
−
 
 
−
== Persons ==
 
−
* Are there more use cases to collect?
 
−
* Some existing use cases:
 
−
** ACKnowledge attribution
 
−
** Community phenotype curators
 
−
** When do people need person IDs? When accessing/using some forms
 
−
* Content of earlier email
 
−
** When someone asks for a CGC Lab code, they must have a WBPerson ID.  To fill out some tazendra forms, I think they need a WBPerson ID.  To connect Persons to Laboratories for their WB lab page.  To track who is a PI for which Lab.  To connect to other Persons for Intellectual Lineage.  Connect authors to Persons so Papers have a list of authors in publication order, each author linked to the Person (ZFIN has two lists, sorted for authors, separate for persons).  Our users tell us they use the WB Person page for their cv.
 
−
** Use of Person Contact information: I think our use case for person information is mostly to have current emails for community outreach (ACKnowledge, community phenotype forms).  It's been used in the past to send letters to PIs, so we could prioritize maintaining more information just for PIs.  Some analysis is sometimes done by region / country, but this is rare.  If anyone can think of other use cases for person data, please let us know. While we mostly only use the email addresses, Cecilia uses address / webpage / ORCID to connect authors to Persons, so having that data is important to make more connections.
 
−
* Knowing address and affiliation can help disambiguate similarly named persons/authors
 
−
* Questions about ethics of tracking information and person lineage?
 
−
** Not really a new issue; people present CVs on grants and other contexts
 
−
** Can be problematic to display people's email address and physical address, from a security perspective
 
−
** Email addresses: if someone has a strain/reagent not in a repository, can be helpful to connect to access materials
 
−
** We and others provide email addresses in publications
 
−
** We don't currently ask for permission to display the information (email, address, etc.); maybe we should?
 
−
** Should we have a survey to ask users' opinions about displaying this information? Is it worthwhile? Concerning?
 
−
** Should we provide a waiver that people agree their information will be in the public domain?
 
−
** Person form disclaimer: "Note: Phone and fax information won't show in your Person report for privacy reasons, but we are collecting the information in case we need to contact you. We keep old email, old institution, and old registered_lab data for history, please don't remove it when updating your information."
 
−
** Person form is available to public and displays personal information, e.g.: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person.cgi?action=Display&number=WBPerson51134
 
−
*** Could someone scrape this information? Yes, person information is available from WB database dumps
 
−
** Could institute a login; we had wanted to keep the barrier to participate low
 
−
** Have 3 forms of privacy, where people can opt out of emails, hide their email address, or hide more information.  If hidden it stays in Caltech postgres, and doesn't go to acedb.
 
−
* Going forward, the Alliance can implement better security for person information
 
−
 
 
−
= Aug 25th, 2022=
 
−
* Phosphoproteomic dataset
 
−
* WB grant - the new and radically different format for a “Biomedical Knowledgebase (U24 - Clinical Trials Not Allowed)” application
 
−
*
 
−
*
 
−
 
 
−
 
 
−
 
 
−
 
 
−
 
 
−
= Aug 18th, 2022=
 
−
* Raymond reporting on meeting with Scott Emmons and neural connectivity data
 
−
 
 
−
= Aug 11th, 2022 =
 
−
 
 
−
Secondary species information content.
 
−
* Gone through and counted number of objects in different data classes for all species
 
−
* https://docs.google.com/spreadsheets/d/1Q1FE7Miz0IJxultBtEq-VFoAcdz1UpxM3wfER4-qQGg/edit?usp=sharing
 
−
* Pristionchus: Talk to Ralf Sommer and see if wee can take some of the pristionchus.org data into WB -> Ranjana; Decision: after more discussion, decided to hold off on this as the plan is to focus on C. elegans for the grant. Perhaps in the future, we can seek finding and collaboration with the Pritionchus community (such as Sommer lab, etc).
 
−
 
 
−
* Brainstorm on how wee can utilize other species data -> may be a separate grant
 
−
* remanei (4 genome versions) and briggsae (3 genome versions) problem -> several versions of the genome. Same problem in parasite. Will need to address in the future. Want to have multiple sequence alignments so researchers can compare different versions.
 
−
* Address c elegans version assemblies in the grant. LoS from authors?
 
−
* Parasite has a new RNAseq analysis pipeline (not single cells yet)
 
−
 
 
−
= July 28th, 2022 =
 
−
 
 
−
Global Core Biodata Resource application
 
−
https://docs.google.com/document/d/1juJ4mm1evay32lNt3OOsbKL36RY4_3cW/edit?usp=sharing&ouid=106019143058337411488&rtpof=true&sd=true
 
−
 
 
−
 
 
−
 
 
−
= July 14th, 2022 =
 
−
== Reference and Person Evidence ==
 
−
* We need to know how best to move forward with ?Reference and ?Person evidence in the context of data exchange between WB and the Alliance
 
−
* Does A-team need to connect those WB Persons to be able to populate data in the Alliance curation db ? 
 
−
** If so, can it wait until we have proper persons ? 
 
−
** If not, when we have persons later will the data be reconnected to Person objects ?
 
−
* Where does data come from, which we call Person_evidence ?  Some forms ?  Direct emails ?  Other sources ? 
 
−
* For author curation/verification, what evidence do we want to use?
 
−
* Can we create Paper objects for the actual emails or other forms of communication (figure out details of when and what requirements), but keep Person_evidence for form submissions ?
 
−
* How much will it muddy things to create Paper objects for emails, e.g. how will it affect NLP downstream, do we need PDFs ?
 
−
* If we create personal communication References at Alliance only do we also want them as WBPapers, or will we just keep ?Person evidence at WB?
 
−
* Are we okay with conflating Person data and Paper data in Reference at the Alliance.  That is, duplicating the same data as a Person and as a Reference.
 
−
 
 
−
== How to look up balancers (Df / Dp) in WB (PWS/Ryan Baugh) ==
 
−
 
 
−
= June 30, 2022 =
 
−
 
 
−
= June 23, 2022 =
 
−
 
 
−
Helpdesk tickets
 
−
 
 
−
SOba in Alliance
 
−
 
 
−
GCBR application due 8th Aug
 
−
 
 
−
Prepare for grant; nice pics for metrics eg https://pharos.nih.gov
 
−
 
 
−
Should Alliance gene & allele model have Clone/Sequence name as an attribute?
 
−
 
 
−
 
 
−
= May 26, 2022 =
 
−
 
 
−
WormBase user survey
 
−
 
 
−
 
 
−
 
 
−
 
 
−
= May 12, 2022 =
 
−
 
 
−
==Subcellular localization field==
 
−
* WB has 2 separate free text fields to capture anatomical and subcellular localization statements but obviously the boundaries are fuzzy, see the example below where the statement belongs to both- there are many examples.
 
−
“miR-228 is expressed in the germline and preferentially localizes to the nuclear periphery.”
 
−
 
 
−
* Other MODs do not make such distinction.
 
−
* Daniela is asking the group advice to see if there is any objection in merging the 2 fields and slot the paragraph descriptions in the  ExpressionExperimentStatement in LinkML.
 
−
 
 
−
* Decision: Keep just one field that will take care of both anatomical expression and subcellular localization
 
−
 
 
−
<pre>
 
−
ExpressionExperimentStatement:
 
−
 
 
−
    is_a: EntityStatement
 
−
 
 
−
    description: >-
 
−
 
 
−
      Free-text describing some aspect(s) of a gene's expression, particularly
 
−
 
 
−
      nuanced information that is not readily captured in annotations.
 
−
 
 
−
      This statement's scope is limited to the associated ExpressionExperiment.
 
−
 
 
−
    notes: >-
 
−
 
 
−
      Inherits: statement_subject, statement_type, statement_text, references.
 
−
 
 
−
    slot_usage:
 
−
 
 
−
      statement_subject:
 
−
 
 
−
        range: ExpressionExperiment
 
−
</pre>
 

Revision as of 18:18, 14 March 2024

Previous Years

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2014 Meetings

2015 Meetings

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2023 Meetings


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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