Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
= 2017 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_January_2017|January]]
+
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_February_2017|February]]
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_March_2017|March]]
+
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_April_2017|April]]
+
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_May_2017|May]]
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_June_2017|June]]
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_July_2017|July]]
 
  
[[WormBase-Caltech_Weekly_Calls_August_2017|August]]
+
==March 14, 2024==
  
[[WormBase-Caltech_Weekly_Calls_September_2017|September]]
+
=== TAGC debrief ===
  
 +
==February 22, 2024==
  
== October 5, 2017 ==
+
===NER with LLMs===
  
=== NAR Paper ===
+
* 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%)
* Raymond will send around reviews
 
  
=== Mary Ann's transition ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
* Cecilia will take over laboratory curation
 
* Hinxton (Paul Davis) will take over nomenclature work
 
* Hinxton will take over strain info, Mitani (NBP) alleles, sequence features (large scale)
 
* Sequence feature curation (literature-based, small-scale) will move to Caltech
 
* Molecule curation may be split; Hinxton could coordinate with ChEBI; GO-CAM modeling molecules handled at Caltech?
 
* SOP? Karen wrote Wiki pages for molecule curation; she will look them over and can review with others
 
* Metabolomics was recent big push (biggest effort needed); need to discuss with Michael Witting
 
  
=== AGR Press Release ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
* Discussed briefly at AGR all-hands call yesterday
 
* No one on the call had much info
 
* Ranjana can post on WB blog on Oct 20th (or earlier?)
 
* Will ask Stacia
 
  
=== AGR momentum ===
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
* AGR disease working group
 
** Lots going on, a lot of progress, still have much to discuss
 
** Next need to work out how to pull in new data objects like alleles, strains, genotypes, etc.
 
** Will need to establish a basic, consensus AGR data model for these data types/objects
 
** How is AGR disease data display compared to WB/MODs? WB is generally (as are other MODs) ahead of AGR
 
* Site-visit
 
** PIs go to D.C. to discuss AGR
 
* Wen working on lab meeting presentations; will present AGR progress, give tutorial
 
* Raymond working on methods paper for SObA display
 
* Raymond will start working on neural functional units with phenotype
 
  
=== Sequence feature curation ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
* Really need to encourage authors to submit tables with specific sequence feature info
 
* Need to make the data submission process easy, user-friendly
 
* Karen looking into it
 
* Work study jobs for students to curate? May not be preferred job for students
 
* Temp jobs may be the way to go; but learning curve needs to be very short
 
  
=== WB Person curation/outreach ===
 
* Cecilia contacts 1-6 people per week by email
 
* She can ask for contact info: address, email address, phone #, etc.
 
* How many persons do we have email addresses for?
 
* Would be good to establish a 2-way communication with WBPersons
 
* Should some people be demoted if they don't respond to emails? If they are not worm people?
 
* We provide options to hide email addresses from WB person page
 
* What do other MODs do? How extensive is the outreach to the community?
 
* Cecilia reaches out when affiliations change
 
* Some journals require use of ORCID IDs; makes identifying authors less ambiguous
 
* Can ask people to update their intellectual lineage (can show lineage graph)
 
* Juancarlos will query to see how many people with an email address don't have lineage info
 
* One email from WB per month is OK
 
* Can use Twitter more, when we do site visits
 
  
  
== October 12, 2017 ==
+
==February 15, 2024==
  
=== Strain curation ===
+
=== Literature Migration to the Alliance ABC ===
* Paul Davis will take over strain curation
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
* Many strains important to disease curation may not have been submitted to CGC, and may not exist in WB
+
===== 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 =====
* Ranjana needs a way to create new strains for disease models
+
*Facet for topic
* Ranjana will talk to Paul, and will add documentation about the issue
+
*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
  
=== Phenotype data display proposal ===
+
===== Manually validate paper - topic flags without curating =====
* Chris has been working on a new way to display phenotype data
+
*Facet for topic
* This will largely depend on the new ?Phenotype_experiment model
+
*Facet for manual assertion
* Will hopefully solve a number of issues regarding how phenotype data is currently displayed
+
**professional biocurator assertion
* Mockups here: https://docs.google.com/presentation/d/1XvMN16B7RU2yPwjD5p9_TywMj0itln-djEWyGx2IxiQ/edit?usp=sharing
+
***ABC - no data
* Goals are:
 
** Clarify phenotype experiment meta data and provenance
 
** Indicate when multiple perturbations may be responsible for a phenotype
 
** Clarify when a non-coding gene is annotated to a phenotype whether the phenotype may actually result from disruption of a protein coding gene
 
** Clarify when a phenotype results from a mutation that affects the exon(s) of one gene and only an intron of another
 
** Clarify when a phenotype is a double mutant (or other complex perturbation) phenotype
 
  
=== How we handle/display multiple supporting interactions ===
+
===== View all topic and entity flags for a given paper and validate, if needed =====
* As pointed out by Jae, some interactions appear very strange in the Interactions widget Cytoscape view when there are very many "independent" interactions/observations for a pair of genes
+
* Search ABC with paper identifier
* Example, tax-6 and rcan-1: http://www.wormbase.org/species/c_elegans/gene/WBGene00006527#0-8-10
+
* Migrate to Topic and Entity Editor
* We've tried to represent the "confidence" of interactions with thicker edges on the graph, but maybe this needs revisiting
+
* View all associated data
* Should there be a log-based increase in edge thickness, instead of a linear one?
+
* Manually validate flags, if needed
* Maybe evidence from the same paper should be considered as one observation?
 
  
=== Collecting person info ===
+
=== PDF Storage ===
* Could we request personal info when we ask for other info, like author first pass, community curation
+
* At the Alliance PDFs will be stored in Amazon s3
* Cecilia can manage feedback/input, and triage/defer issues to relevant curators etc.
+
* We are not planning to formally store back-up copies elsewhere
* Ask people to confirm current institution, lineage information
+
* Is this okay with everyone?
* Probably need to keep the request minimal (a single line), so as not to overburden people
 
* We need to point people to person update form
 
* We could also do more through the website
 
  
 +
==February 8, 2024==
 +
* TAGC
 +
** Prominent announcement on the Alliance home page?
  
== October 19, 2017 ==
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
=== Site visits, area meetings ===
+
==February 1, 2024==
* About a 12-15 area and topic meetings next year
+
* Paul will ask Natalia to take care of pending reimbursements
* Chris will present at Baltimore Worm Meeting on March 16, 2018
+
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
* Many meetings are annual (Topic, Seattle, New York), some bimonthly
 
* Many of these arrange speakers well ahead of time, 6 months ahead for example
 
* We should reach out to organizers soon, especially for annual meetings
 
* We can combine WB, Textpresso, and micropublications
 
* We can/should customize our talks to research areas of each audience
 
* Many of the talks are about 40 minutes to 1 hour
 
  
=== Micropublication forms vs. WB data submission forms ===
+
==January 25, 2024==
* Managing discrepancies still need to be worked out
 
* Looking at differences of output formats
 
* Customizable forms? Forms built by curator?
 
* Karen: aside from paper details/meta data, forms can be the same
 
  
=== Phenotype data display proposal ===
+
=== Curator Info on Curation Forms ===
* Chris has been working on a new way to display phenotype data
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
* This will largely depend on the new ?Phenotype_experiment model
 
* Will hopefully solve a number of issues regarding how phenotype data is currently displayed
 
* Mockups here: https://docs.google.com/presentation/d/1XvMN16B7RU2yPwjD5p9_TywMj0itln-djEWyGx2IxiQ/edit?usp=sharing
 
* Goals are:
 
** Clarify phenotype experiment meta data and provenance
 
** Indicate when multiple perturbations may be responsible for a phenotype
 
** Clarify when a non-coding gene is annotated to a phenotype whether the phenotype may actually result from disruption of a protein coding gene
 
** Clarify when a phenotype results from a mutation that affects the exon(s) of one gene and only an intron of another
 
** Clarify when a phenotype is a double mutant (or other complex perturbation) phenotype
 
  
 +
=== ACKnowledge Author Request - WBPaper00066091 ===
 +
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  
== October 26, 2017 ==
+
* 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.
  
=== GO CAM ===
+
* 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.
* GO CAM models do not go into ACEDB, yet
 
* Kimberly is working on it
 
* First, Berkeley group is working on producing correct GPAD files as output
 
* Work is ongoing for a Cytoscape view of pathways
 
* Noctua calls on 2nd and 4th Wednesdays of the month; anyone can sit in (ask Kimberly)
 
* Noctua call minutes on Wiki (Kimberly will send around link)
 
  
=== Site visits ===
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
* Wen setup Wiki page: http://wiki.wormbase.org/index.php/Meetings#Upcoming_Meetings
 
* What's the strategy overall? Are we trying to make all meetings?
 
* About 15 meetings to go to; would be good if we could make all of these, if possible
 
* Kimberly will go to New York meeting
 
* Chris will go to Baltimore meeting
 
* Boulder, CO meeting; interested in having WB talk; sometime in May
 
* San Diego meeting in January (Wen out of town); volunteers?
 
* Chris could do Boston and Worcester meetings
 
  
=== Strains ===
+
=== Update on NN Classification via the Alliance ===
* Are strains in the nameserver? No, and Hinxton is likely retiring the nameserver soon
+
* Use of primary/not primary/not designated flag to filter papers
* Can curators get access to a tool to request a strain object?
+
* Secondary filter on papers with at least C. elegans as species
* Juancarlos and Ranjana are working on tool (cronjob) that will automatically transfer the strain in the 'Requested Strain' field in the disease OA to the 'Strain' field once Paul Davis approves the strain. 
+
* Finalize sources (i.e. evidence) for entity and topic tags on papers
* Once a strain is entered in the 'Requested strain' field, it also shows up in the the new_objects.cgi form, for Paul D. to approve or not, but he still needs to be alerted to this.
+
* Next NN clasification scheduled for ~March
  
=== Changes to phenotype form ===
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
* We need a mechanism to clarify if multiple perturbations entered in the phenotype form represent multiple single experiments or a single complex genotype experiment
+
* NNC html pages will show NNC values together with species.
* Will give users the option to indicate which of these two scenarios is the case
+
* Show all C. elegans papers first and other species in a separate bin.
* We discussed ways of managing this in a previous WB CIT meeting
+
 
* Produced mockups of proposal: https://docs.google.com/presentation/d/1HFVn1anbdCu8pHJW0g27a5AvYLFVMyBy4nnrEdA1wKQ/edit?usp=sharing
+
=== Travel Reimbursements ===
 +
* Still waiting on October travel reimbursement (Kimberly)
 +
* Still waiting on September and October travel reimbursements (Wen)
 +
 
 +
=== UniProt ===
 +
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
 +
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
 +
* Stavros escalates the issue on Hinxton Standup.
 +
* Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.
 +
 
 +
==January 18, 2024==
 +
* OA showing different names highlighted when logging in the OA, now fixed on staging
 +
 
 +
 
 +
==January 11, 2024==
 +
* Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
 +
** Curators should make sure that, when pasting special characters, the duplicate function works
 +
* OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
 +
** If you want to bookmark an OA url for your datatype and user, log on once, and bookmark that page (separately for prod and dev)
 +
* Chris tested on staging and production the phenotype form and the data are still going to tazendra
 +
** Chris will check with Paulo. Once it is resolved we need to take everything that is on tazendra and put it on the cloud with different PGIDs
 +
** Raymond: simply set up forwarding at our end?
 +
* AI working group: Valerio is setting up a new account for open AI -paid membership for ChatGPT4. We can also use Microsoft Edge copilot (temporary?)
 +
* Chris getting ready to deploy a 7.0.0. public release - February 7th. Carol wanted to push out monthly releases. This will include WS291. For subsequent releases the next several releases will be WS 291 until WS292 is available.
 +
* Valerio would like to use an alliancegenome.org email address for the openAI account
 +
* New alliance drive: https://drive.google.com/drive/folders/0AFkMHZOEQxolUk9PVA
 +
** note: please move shared files that you own to new Alliance Google Drive.  Here is the link to the information that Chris Mungall sent:  For more instructions see the video and SOP here:https://agr-jira.atlassian.net/browse/SCRUM-925?focusedCommentId=40674
 +
* Alliance logo and 50 word description for TAGC> Wen will talk to the outreach WG
 +
* Name server. Manuel working on this, Daniela and Karen will reach out to him and let him know that down the road micropublication would like to use the name server API to generate IDs in bulk
 +
* Karen asking about some erroneous IDs used in the name server. Stavros says that this is not a big deal because the "reason" is not populating the name server
 +
* It would be good to be able to have a form to capture additional fields for strains and alleles (see meeting minutes August 31st 2023. https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls_2023#August_31st.2C_2023). This may happen after Manuel is done with the authentication.
 +
* Michael: primary flag with Alliance. Kimberly talked about this with the blue team. They will start bringing that over all papers and fix the remaining 271 items later.
 +
 
 +
==January 4, 2024==
 +
* ACKnowlegde pipeline help desk question:
 +
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
 +
* Citace upload, current deadline: Tuesday January 9th
 +
** All processes (dumps, etc.) will happen on the cloud machine
 +
** Curators need to deposit their files in the appropriate locations for Wen
 +
* Micropublication pipeline
 +
** Ticketing system confusion
 +
** Karen and Kimberly paper ID pipeline; may need sorting out of logistics

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