Difference between revisions of "WormBase-Caltech Weekly Calls"

From WormBaseWiki
Jump to navigationJump to search
 
Line 17: Line 17:
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
= 2018 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
 
  
 +
==March 14, 2024==
  
== April 5, 2018 ==
+
=== TAGC debrief ===
  
=== GoToMeeting ===
+
==February 22, 2024==
* Todd would like access to run GoToMeetings
 
* Chris can send access credentials and GoToMeeting calendar details
 
  
=== Data Mining Tool comparison ===
+
===NER with LLMs===
* https://docs.google.com/spreadsheets/d/1vBTDBOKfXn9GcdpF1bXI62VEJ7hwyz2hOyAZcoV1_ng/edit?usp=sharing
 
* Chris and Ranjana will work on summarized blog post with link to table
 
  
=== Neuro Topic Meeting ===
+
* 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%)
* Submitting abstract for meeting, due April 13
 
* Wen will submit an abstract
 
  
=== Rutgers worm meeting ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
* We spoke to Andrew Singson; mentioned Rutgers meeting
 
* Kimberly will look into joining/speaking
 
  
=== Andy Golden disease and phenotype submission ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
* Andy had sent a sample file of alleles with disease and phenotype data
 
* Chris discussed phenotype details with Andy
 
* Andy will eventually send bulk data submission
 
  
=== Chen Institute furniture meeting ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
* Today at new building; reviewing office furniture
 
* Ranjana and Valerio will go
 
  
=== Alliance curation ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
* Paul needs to present on 5-year Alliance plan
 
* Maybe could discuss curation plan
 
  
=== Seek/modSeek ===
 
* Troyanskaya lab; have we been in touch?
 
* They may have new version that can be used
 
* Paul S. will see her soon; will ask about it
 
  
=== Alliance Entity Summaries ===
 
* Have been working on gene summaries
 
* Do we want to start working on summaries for other entities, like variations?
 
* Ranjana can put together some proposal
 
  
=== Alliance Tutorial ===
+
==February 15, 2024==
* For reverse-site SAB meeting (April 23), need a sample query/tutorial
 
* April has worked on a script for a tutorial; maybe we can use
 
  
 +
=== 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
  
== April 12, 2018 ==
+
===== Manually validate paper - topic flags without curating =====
 +
*Facet for topic
 +
*Facet for manual assertion
 +
**professional biocurator assertion
 +
***ABC - no data
  
=== Preliminary AGR Tutorial ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
* https://docs.google.com/document/d/1iwKs7K87DgbDopIzg9uRlZ9eoxbza2Gd05eaEPjpxn8/edit?usp=sharing
+
* Search ABC with paper identifier
* Document includes screenshots and text, which is subject to change.  Voiceover/basic video should be ready by the end of this week.  Additional video editing will be added later, including captions, an intro with footage of scientists, and visual aids (eg. arrows, boxes etc.)
+
* Migrate to Topic and Entity Editor
 +
* View all associated data
 +
* Manually validate flags, if needed
  
=== Alliance data refresh ===
+
=== PDF Storage ===
* Data refresh for 1.4 release
+
* At the Alliance PDFs will be stored in Amazon s3
* Is this for databases that have more frequent updates, such as daily updates? Does this apply to WB at all? Have to ask Kevin Howe if WB will have a data refresh.
+
* We are not planning to formally store back-up copies elsewhere
** Kevin responded: There is a WB refresh for Alliance 1.4 release based on WS264
+
* Is this okay with everyone?
  
=== Phenotype graph bug ===
+
==February 8, 2024==
* Maybe related to https issues
+
* TAGC
* May need to update server to serve https requests
+
** Prominent announcement on the Alliance home page?
* GitHub ticket: https://github.com/WormBase/website/issues/6326
 
* Juancarlos and Raymond working on
 
  
=== Essential gene lists ===
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
* Several requests for the essential gene list over the years
 
* Difficult to query this out of ACEDB
 
* Chris generated a Postgres query to pull out all allele-phenotype annotations with "lethal", "sterile" or descendant phenotypes, including meta data including penetrance, background genotype, etc.
 
  
=== Acquiring list of ontology term descendants ===
+
==February 1, 2024==
* Raymond has URL constructor, for private/internal use; will share internally
+
* Paul will ask Natalia to take care of pending reimbursements
* URL will return all ontological descendants, including all "is_a", "part_of", and "regulates"
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
* Phenotypes only have "is_a" relationships anyway, so not an issue
 
  
=== Gene set enrichment analysis: duplicate genes ===
+
==January 25, 2024==
* GitHub ticket: https://github.com/WormBase/website/issues/6300
 
* Issue where duplicate genes are not removed from input and are displayed in output
 
* We want to make clear to users that the duplicates are not counted multiple times in analysis
 
  
=== Gene names existing as secondary names for different genes ===
+
=== Curator Info on Curation Forms ===
* Many genes (120+) have primary names that are also secondary names of other genes
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
* Causes confusion in terms of data attribution
 
* e.g. mdh-1 and mdh-2: mdh-2 has "mdh-1" as an other name even though these are distinct genes
 
* May be good for curators to make sure, for their data type, the correct genes are annotated to the correct data
 
* Jae will send around list of problematic gene names
 
  
== April 19, 2018 ==
+
=== ACKnowledge Author Request - WBPaper00066091 ===
 +
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  
=== Genotype class ===
+
* 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.
* Need for number of use cases
 
* Also good to be compliant with other MODs/Alliance members
 
  
=== Biocuration ===
+
* 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.
* Meeting minutes [https://docs.google.com/document/d/1U4prvuSfhWp8D9GWAjIepZL4kE0W206o5YVwkse-pcU/edit?usp=sharing]
 
* Attn Wen: GEO data interface
 
** May be of more use to Alliance than WormBase; fewer GEO submissions these days
 
** GEO often omits relevant biological background information
 
** Any GEO data sets that are unpublished? Some, not many (6-7 data sets); some have lagged publications
 
* Text mining tools
 
** iTextmine
 
*** Highly experimental (PhD project)
 
** Pubtator
 
*** Similar to Textpresso
 
*** Only index (or allow annotations of) abstracts
 
*** Solid project; using state-of-the-art technology and techniques
 
* Mike Cherry introduced Alliance
 
* Not much with community curation
 
* OntoChina: ontologies translated to Chinese
 
* Pathway icons (Reactome)
 
* Technique to identify the most relevant ontology common ancestor
 
** Accounts for information content of each node
 
** Valerio will send publication to Raymond
 
* Automated descriptions
 
** We should talk to GO about which data sources should be used to construct statements
 
** Similarly, work with relevant data/curation groups for the respective data types
 
** GO data coming directly from Alliance; may need to come directly from GO
 
  
=== Postgres reading access ===
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
* Coko will start generating submission forms as part of the platform build, can we have read access to postgres for them to get WB entities?
 
* Juancarlos: Can make dumps specifically for the data objects you need, instead of giving full read access
 
** Can create URL that points to all of the needed data
 
* Transgenes don't come from name server; from Postgres
 
* Current Postgres architecture is not setup for public access
 
** Could accommodate, but need to look into what that entails
 
** Probably need a server and a sys admin
 
** How would it impact our other work/curation?
 
** Security? Passwords?
 
** How much time would we then need to devote to answering user questions, usability, user interface?
 
  
=== AFP ===
+
=== Update on NN Classification via the Alliance ===
* AFP mock http://textpressocentral.org:5000/overview
+
* Use of primary/not primary/not designated flag to filter papers
* Update to AFP form to allow authors to confirm/validate predicted entities and data types
+
* Secondary filter on papers with at least C. elegans as species
* Steer authors towards data submission forms
+
* Finalize sources (i.e. evidence) for entity and topic tags on papers
* Form layout tries to mirror gene page
+
* Next NN clasification scheduled for ~March
* Can confirm gene references, add new ones
 
* Can report gene corrections and gene-sequence connections
 
* Would be good to make clear to users what are the validated/accepted entities when confirming entity recognition
 
* May be good to have common interface for each section; maybe one interface for data types and another for entity recognition
 
* Need to make clear that the "Next" button marks the section as complete
 
* Do we offer text fields for authors to indicate where the data is in the paper? May be asking too much and difficult to implement
 
* Do we specify species for data types to verify it is relevant to C. elegans (e.g. physical interactions)? Again, may be asking too much; issue with what the flagging criteria are
 
  
 +
* 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.
  
== April 26, 2018 ==
+
=== Travel Reimbursements ===
 +
* Still waiting on October travel reimbursement (Kimberly)
 +
* Still waiting on September and October travel reimbursements (Wen)
  
=== Alliance reverse site visit ===
+
=== UniProt ===
* Went well, positive response
+
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
* Good feedback on automated gene descriptions
+
* 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.
  
=== Automated gene descriptions ===
+
==January 18, 2024==
* Where is data coming from? GO data, from Alliance or GO?
+
* OA showing different names highlighted when logging in the OA, now fixed on staging
** Part_of relationships not loaded into Alliance GO data
 
** Federated data vs. centralized data issues
 
* Involves architecture discussions and decisions
 
* Using same lowest-common-ancestor algorithm as GO
 
* Newer WB descriptions are a big improvement
 
  
=== WormBase Grant ===
 
* There may be a separation of effort/support for tools vs. database
 
* Knowledgebase vs. database: which are we?
 
  
=== Data Commons ===
+
==January 11, 2024==
* WB rep? Ask Mike Cherry (cc Kevin)
+
* 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.
  
=== WB SAB ===
+
==January 4, 2024==
* Lincoln needs head count for SAB
+
* ACKnowlegde pipeline help desk question:
* http://wiki.wormbase.org/index.php/2018_Advisory_Board_Meeting
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
 
+
* Citace upload, current deadline: Tuesday January 9th
=== Noctua 1.0 release ===
+
** All processes (dumps, etc.) will happen on the cloud machine
* Noctua 1.0 release coming soon
+
** Curators need to deposit their files in the appropriate locations for Wen
* Worm Anatomy ontology; issue with being incorporated into the Uberon ontology
+
* Micropublication pipeline
* Worm anatomy terms not available in Noctua table annotator
+
** Ticketing system confusion
* Kimberly will send relevant GitHub ticket to Raymond
+
** Karen and Kimberly paper ID pipeline; may need sorting out of logistics
* Raymond will follow up with Chris Mungall
 
 
 
=== Alliance phenotype face-to-face ===
 
* June 13-14 in Eugene, Oregon
 
* Working group will discuss initial and long term plans
 
* Chris & Ranjana plan to go
 
* Discuss travel with Sarah Torres
 
 
 
=== Datomic widgets ===
 
* Juancarlos discussed person_lineage widget with Adam at length on Monday.
 
* Adam says about 90% complete, about 20 to go.
 
 
 
=== WS266 Citace upload ===
 
* Deposit files for Wen by May 15th, 10am Pacific time
 
 
 
=== WormBase curator candidate ===
 
* Meet with her next Thursday
 

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