Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
Line 1: Line 1:
 +
= Previous Years =
 +
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
 +
 +
 +
==March 14, 2024==
 +
 +
=== TAGC debrief ===
 +
 +
==February 22, 2024==
  
==2011 Meetings==
+
===NER with LLMs===
  
[[WormBase-Caltech_Weekly_Calls_February_2011|February]]
+
* 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
  
== March 3, 2011 ==
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  
SUMMARY:
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
  
Every other month patch:
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
*We will try to generate an ACEDB patch every other month, starting with the Paper class data
 
*Need to coordinate with Juancarlos and Todd
 
  
Need to check .ACE patch files before upload:
 
*Will need to be vigilant about checking for errors and inconsistencies before sending to Todd to put up on website
 
*Curators need to check their own data for problems
 
*Wen will check for consistency between the different data types
 
  
Think about connecting website to Postgres:
 
*Think about showing Postgres data "immediately" on site
 
  
 +
==February 15, 2024==
  
DETAILS:
+
=== 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
  
Delayed release cycle:
+
===== Manually validate paper - topic flags without curating =====
*Will require more work to prepare for more frequent release of certain data types
+
*Facet for topic
*Aside from Kimberly's data, most data types are not urgent (e.g. Expression pattern)
+
*Facet for manual assertion
*What are the users feeling?
+
**professional biocurator assertion
**Having data faster will help users; they don't ask, because they don't see it
+
***ABC - no data
*On-the-fly updating of website? Like Postgres?
 
*Since we use ACEDB, we have to patch WS with .ACE file, or rebuild whole thing
 
*Flat file Postgres database, replaced every night?
 
*Website calls Postgres directly for certain data types?
 
*Performing build without sequence is easy? Do everything without sequence?
 
*How to integrate sequence data with other data once they're decoupled through the patching process?
 
*We need .ACE patch files
 
*Concise description separate from most else (but connected to papers)
 
*Do papers first?
 
*Website can show anything
 
*If we have a lot of patches, will not have check for data inconsistency/confliction
 
*Trial patch .ace files for papers first
 
*Juancarlos: Scripts that check differences between data dumps; scripts are data type specific
 
**Curators need to talk to Juancarlos about the importance of different data tags
 
*Paper .ACE file: Would include bibliographic info, journals, authors, genes associated from abstract or added manually
 
*One reason for more frequent releases: because we have first pass author forms; show them we add it quickly
 
**what will be added through the forms: expression patterns? RNAi (difficult?)?
 
*We should check patch before we send to Todd!!! Don't want to crash database
 
*How frequently to patch? Weekly? Daily? Check with Todd, how often he can load them?
 
*Chron job to create patch ACE files, send to curators to check for problems, then send to Todd
 
*Interdependency of data types; curators rely on other curators?
 
*Postgres directly to website? Todd would have to work it out
 
*New information flag on website? Toggle visibility?
 
*How do we know that the data do not conflict with each other?
 
*What are common problems? Dumper script goes bad, makes broken lines, empty fields
 
*Error catching mechanisms? More checks on postgres? Dump files?
 
*Data merging problems? What are the cases that are conflicts? Prevent them? Know beforehand?
 
*If we don't know, as long as it doesn't crash the database or fail to load, then OK
 
*Don't do -D stuff, maybe? No deletions? Skip typos?
 
*Always have to check ACE files anyway, but have to do every week (2 weeks?)
 
*We can try a patch every other month
 
*What can we do without the patch?
 
*Did SAB talk about changing to relational databases?
 
**Get website going as is first, and see if it matters?
 
**If people don't want to change data models, we can switch over to relational
 
**Separate panel on website directly from Postgres?
 
*Wen can check the data integration every other month for patch
 
  
 +
===== 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?
  
== March 10th, 2011 ==
+
==February 8, 2024==
 +
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
Release schedule and patches
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
*What is the appropriate frequency?
 
*Scheme: do what we're already doing, Wen merges into citace
 
*Excluding sequence related data
 
*Need to include Mary Ann's data (strains etc.)
 
*Daily update too frequent; maybe once per month/week
 
*Submit .ACE file to Todd with simple syntax; easily parsable; old description removed and new information added
 
*Make updates only in contrast to last WS, not previous patch/temporary upload
 
*ACEDB diff step only relative to WS
 
*Wen: Postgres can dump diff ace file; already have diff ace files for every data type at Caltech; integrate into citace;
 
*Raymond: integration is important; we need to talk about how much work needs to be done by each approach
 
*Wen: consistency checks, backups, store each version?
 
*Rayomnd: citace 224 to 225 (for example), display done on class level
 
**Example: Gene page; only update information relevant to gene class to be displayed
 
*Do once per month: faster than currently because it doesn't have to go through the dev site
 
*If we update Citace to Citace, missing a lot of cross-references?
 
*Mock citace with Mary Ann's data? Becomes diff base; Mary Ann submits (non-sequence related) data directly to WBCIT
 
*Build low-connectivity ace at WBCIT? Add Mary Ann's data, remove RNAi
 
*Todd: important consideration: things added won't be available for search until formal release; weird things about diff; new reference associations with genes; a lot of duplications?
 
**Raymond: will look at it
 
*Todd: WBGene00000846, example, see how fast it loads, go from there; would like a single ACE file (concatenation of all individual ace files); would not happen on development; would have to happen on production releases; would take production database off line, clone it, and upload it to all production nodes
 
*Individual curators need to check their individual ace files for errors
 
*Frequency: monthly
 
*Todd: we should just run some tests first, to check feasibility
 
*Raymond: WBGene1, example, concise description has typo, WS225 has typo fixed from WS224, diff file shows:
 
**-D old_description
 
**new_description
 
*Load diff ace into original database?
 
*parallel display; unrelated to resident WS?
 
*Todd: producing two web pages for each object?
 
*Raymond: No, only changing relevant tags, etc.
 
*Todd: Two databases running at same time inefficient; include timestamps?
 
*Raymond: No, cannot include timestamps
 
*Wen: Send patch ace files to Todd
 
*Raymond: In conflict with versioning; how to show new data
 
*Wen: Call it "WS225.1"
 
  
 +
==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.
  
Human Disease Relevance tag in Concise Description
+
==January 25, 2024==
*Ranjana: Sent out e-mail; human disease tag "Human Disease Relevance"; to clean up concise description form (old tags in form outdated); could be putting more information into concise description; OMIM human disease
 
*Raymond: make not just text field, but make entity field pointing to object; meant to be human readable, this may break up the concise description into OMIM-related and OMIM-non-related info; why parse the data into a tag?
 
*Paul S: OMIM descriptions as a separate tag
 
*Raymond: Rewrite concise description?
 
*Ranjana: No
 
*Paul S: Would you mention human disease relevance in concise description? yes, but if it's just a link out to OMIM, then separate out; OMIM may have changed since Erich wrote original script; check OMIM for new information and tags that may be able to get pulled out
 
*Ranjana: Michael Paulini can consolidate orthology information?
 
  
 +
=== Curator Info on Curation Forms ===
 +
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
  
Karen: Transgene model
+
=== ACKnowledge Author Request - WBPaper00066091 ===
*A lot of changes to propose
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
*Deletions of tags; more coming
 
*Other things in database connected to transgenes
 
*Many things in transgene objects that may be able to be parsed into different tags (new job for someone?)
 
*Strict nomenclature for transgene descriptor
 
*Clones present need to be parsed into clone class?
 
*Todd made Clone page;  
 
*Start with vectors/backbones and then work on specific plasmids
 
  
 +
* 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.
  
Gene class-phenotype connections and descriptions?
+
* 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.
  
GSA markup at Flybase
+
=== Update on NN Classification via the Alliance ===
*Flybase is not willing to fully QC all papers
+
* Use of primary/not primary/not designated flag to filter papers
*Do we push Flybase and/or provide a better tool to QC?
+
* Secondary filter on papers with at least C. elegans as species
*Are we worried about the GSA markup for flies not looking professional?
+
* Finalize sources (i.e. evidence) for entity and topic tags on papers
*People need to be willing to pay for the QC/curation; depends on database priorities
+
* Next NN clasification scheduled for ~March
*CIT will spend more time on in-house development to make Fly GSA markup easier/more efficient
 
  
 +
* 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.
  
Putting SPELL on Amazon cloud?
+
=== 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
  
== March 17th, 2011 ==
 
  
Transgene Information was the only topic discussed.
+
==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.
  
Karen noticed that CGC strain information contains more detailed information about transgenes then what is found in the papers that describe the transgenes.  She would like to integrate the CGC strain information into the transgene curation pipeline.  This could potentially lead to some redundancy, but the consensus was that this was a good idea. Going forward  - Initially Karen will go through all the CGC strains that have transgene info and add it to the transgene objects in WB.  Once that is accomplished we will institute some system (like the NBP allele info) to update as new strains w/transgene info are entered into the CGC.
+
==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

Latest revision as of 18:18, 14 March 2024

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

2022 Meetings

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