Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[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]]
 
  
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
+
==March 14, 2024==
  
 +
=== TAGC debrief ===
  
== May 3, 2018 ==
+
==February 22, 2024==
  
=== SimpleMine output ===
+
===NER with LLMs===
* Wen was working on simplification of SimpleMine output
 
* Considering removing general terms in an ontology when more specific terms exist
 
* Concern that we would be removing information; will keep terms
 
  
=== SPELL topics ===
+
* 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%)
* Topics in SPELL need some organization, possibly trimming
 
* We could create a graph (SObA) display of topics (based on GO process)
 
  
=== SPELL problem with WS265 ===
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
* Wen had to debug; SPELL has limit of how many genes can be processed per data set (46,340)
 
* Wen trying to accommodate, deleting some genes from data set that had no expression (kludge)
 
* Wen will write to Matt Hibbs to ask how to deal with
 
* Will Alliance work together on a system to analyze large scale expression data?
 
  
=== Curator candidate ===
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
* Will arrive at 10am
 
* Skype calls with remote curators
 
* Curators will send group Skype handle and requested time to talk
 
  
== May 10, 2018 ==
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
  
=== ECO terms for genome editing ===
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
* Asking group's feedback on ECO terms for genome editing (Daniela)
 
* What would be used for fly-enhancer trap experiment?
 
* Genomically encoded GFP, for example
 
* ECO: GFP localization
 
* ECO term, example: Fluorescent protein transcript localization evidence
 
* Single copy transgene? Endogenous locus?
 
* Whether it is CRISPR or not may not be relevant
 
* May request ECO terms that capture distinct types of transgenes evidence
 
* Will use generic term for now
 
* Do other MODs use ECO?
 
* May want to capture endogenous/non-endogenous, multi-copy/single-copy distinctions
 
* Many of these features are captured in the transgene and construct objects already; specific ECO code redundant?
 
  
=== ZFIN SAB ===
 
* Significant involvement in Alliance
 
* Interest in micropublications; will push a pilot
 
* June 19, moving from older DB to Postgres
 
* Investigating automation for some curation processes
 
* Students review which papers to include; acquire PDF
 
* Curate paper-by-paper
 
  
=== Alliance ===
 
* Supplement request for year 3, due soon (May 15)
 
* Formal report from NHGRI, 18-month plan looks good
 
* Further future plans (from NHGRI perspective) aren't quite clear
 
* Software infrastructure?
 
* Central- vs. MOD-control of resources questions
 
* Likely will have to write a NIH proposal in Fall or Winter
 
* How much is Alliance going to handle human variants?
 
* NHGRI interested in metabolomics; Alliance plans?
 
  
=== Genome-wide screens ===
+
==February 15, 2024==
* Had help desk question about phenotypic screens in organisms other than worms, flies, yeast, bacteria
 
* There have been human cell line phenotypic screens (e.g. siRNA/shRNA); who curates these, if anyone?
 
* Also, induced pluripotent stem cell experiments
 
  
=== Nameserver issues ===
+
=== Literature Migration to the Alliance ABC ===
* Issue came up about assigning unique WBStrain IDs
+
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
* Can use a nightly nameserver dump from Hinxton to populate Postgres/OA
+
===== 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 =====
* Will need to clean up existing strains in Postgres
+
*Facet for topic
* Also, considering unique IDs for genotypes
+
*Facet for automatic assertion
* Mechanics of naming and managing naming of objects
+
**neural network method
** Nightly syncing (cronjob) to nameserver
+
*Facet for confidence level
** Ideally, we would have instant updates; Hinxton firewall prevents direct access; Matt working on establishing a separate nameserver location to gain direct access
+
**High
** Strain names (at least historically) have been updated quarterly from CGC file
+
*Facet for manual assertion
** Curators need mechanism to create and use strain (and variation) names right away
+
**author assertion
** Current system requires manual denormalization step; has worked so far
+
***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
  
== May 17, 2018 ==
+
===== 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
  
=== Strains ===
+
=== PDF Storage ===
* Create a strain OA? Central curation tool for strain data?
+
* At the Alliance PDFs will be stored in Amazon s3
* Would need to maintain synchrony with CGC and Hinxton
+
* We are not planning to formally store back-up copies elsewhere
* Postgres/Tazendra variation adding CGI: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo
+
* Is this okay with everyone?
* Will add similar link for Strains, adding info to obo_name_strain and obo_data_strain as well as a tempfile, which will those objects in postgres when the nightly_geneace.pl updates the OA strain info
 
  
=== SAB 2018 ===
+
==February 8, 2024==
* Who will present? Present what?
+
* TAGC
* We can generate a central document with stats to give to SAB
+
** Prominent announcement on the Alliance home page?
* Ask SAB for opinions and guidance?
 
* Would be good to assess current efforts and priorities, ask if we should stay the course or make modifications to our approach
 
  
== May 24th, 2018 ==
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
  
=== Helpdesk ===
+
==February 1, 2024==
*[https://github.com/WormBase/website/issues/6423 Not sure if this falls under content....]
+
* 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.
  
=== Relations Ontology ===
+
==January 25, 2024==
*Working on new model for importing RO terms into WormBase
+
 
*Question: Do we need to import all of RO?
+
=== Curator Info on Curation Forms ===
**For example, RO also has terms from other ontologies:
+
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
    [Term]
+
 
    id: GO:0003674
+
=== ACKnowledge Author Request - WBPaper00066091 ===
    name: molecular_function
+
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
    is_a: BFO:0000015 ! process
+
 
    property_value: IAO:0000589 "molecular process" xsd:string
+
* 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.
*Question: How much term information do we want and/or need?
+
 
**For example:
+
* 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.
    [Typedef]
+
 
    id: BFO:0000050
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
    name: part of
+
 
    def: "a core relation that holds between a part and its whole" []
+
=== Update on NN Classification via the Alliance ===
    property_value: IAO:0000111 "is part of" xsd:string
+
* Use of primary/not primary/not designated flag to filter papers
    property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string
+
* Secondary filter on papers with at least C. elegans as species
    property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string
+
* Finalize sources (i.e. evidence) for entity and topic tags on papers
    property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string
+
* Next NN clasification scheduled for ~March
    property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string
+
 
    property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
    certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string
+
* NNC html pages will show NNC values together with species.
    property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an
+
* Show all C. elegans papers first and other species in a separate bin.
    independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically
+
 
    dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A
+
=== Travel Reimbursements ===
    material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent
+
* Still waiting on October travel reimbursement (Kimberly)
    continuant: use 'bearer of'." xsd:string
+
* Still waiting on September and October travel reimbursements (Wen)
    property_value: IAO:0000118 "part_of" xsd:string
+
 
    property_value: RO:0001900 RO:0001901
+
=== UniProt ===
    property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections
+
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
    property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf
+
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.  
    property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string
+
* Stavros escalates the issue on Hinxton Standup.
    is_transitive: true
+
* Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.
    is_a: RO:0002131 ! overlaps
+
 
    inverse_of: BFO:0000051 ! has part
+
==January 18, 2024==
*Proposal: WB ingests only the BFO and RO ID spaces of RO, and information in id, name, def, is_a parentage, domain, range, and inverse_of tags
+
* OA showing different names highlighted when logging in the OA, now fixed on staging
**We can always link out from WB to pages with more detail on RO terms
+
 
 +
 
 +
==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