Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
 
  
  
= 2019 Meetings =
 
  
[[WormBase-Caltech_Weekly_Calls_January_2019|January]]
+
= 2020 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_February_2019|February]]
+
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
+
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
+
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
+
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
[[WormBase-Caltech_Weekly_Calls_August_2019|August]]
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
  
 +
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
  
== September 12, 2019 ==
 
  
=== Update on SVM pipeline ===
+
== September 3, 2020 ==
* New SVM pipeline: more analysis and more parameter tuning
 
* avoiding precision (and F-value) as a measure (dependent on ratio of positives and negatives in test set)
 
* For example shown, "dumb" machine starts out with precision above 0.6
 
* G-value (Michael's invention); does not depend on distribution of sets
 
* Applied to various data types
 
* Analysis: 10-fold cross validation
 
** Randomly select 10% pos and neg (without replacement) and repeat until all papers sampled
 
* F-value changes over different p/n values; G-value does not (essentially flat)
 
* Area Under the Curve (AUC): probability that a random positive scores higher than random negative
 
* AUC values for many WB data types upper 80%'s into 90%'s
 
* Ranjana: How many papers for a good training set? Michael: we don't know yet
 
* Can't reproduce old training sets (for old SVM); provide Michael better training sets if you want improved SVM
 
* If SVM still not good enough, Michael will work on deep neural networks (Tensor Flow)
 
* Michael can provide training sets he has used recently
 
  
=== Clarifying definitions of "defective" and "deficient" for phenotypes ===
+
=== WS279 Citace upload ===
* WB phenotype ontology has many "variant/abnormal" terms and distinct subclass terms for "defective/deficient"
+
* September 25
* Have tried to create a logical definition pattern for these terms, but the vagueness of the meaning of "defective" and how it is distinct from "abnormal" has stalled the process
+
* Local CIT upload (to Wen) Tuesday September 22 by 10am Pacific
* What do we mean exactly by "defective" and how, specifically, is this distinct from "abnormal"?
 
* Definitions include meanings or words:
 
** "Variations in the ability"
 
** "aberrant"
 
** "defect"
 
** "defective"
 
** "defects"
 
** "deficiency"
 
** "deficient"
 
** "disrupted"
 
** "impaired"
 
** "incompetent"
 
** "ineffective"
 
** "perturbation that disrupts"
 
** Failure to execute the characteristic response = abnormal?
 
** abnormal
 
** abnormality leading to specific outcomes
 
** fail to exhibit the same taxis behavior = abnormal?
 
** failure
 
** failure OR delayed
 
** failure, slower OR late
 
** failure/abnormal
 
** reduced
 
** slower
 
  
=== Citace upload ===
+
=== New AFP datatype for curation status form (CSF)? ===
** Tuesday, Sep 24th
+
* afp_othergenefunc (to capture gene function other than enzymatic activity)
 +
* Can wait a bit before adding to CSF; if there will be dedicated curation for that data type we may add later
  
=== Strain to ID mapping ===
+
=== GO annotation for description ===
* Waiting on Hinxton to send strain ID mapping file?
+
* Kimberly will look into 'male tail tip developement' terms for description
* Hopefully we can all get that well before the upload deadline
 
* Will do global replacement at time of citace upload (at least for now)
 
  
=== New name server ===
+
=== Migrate wobr1 server to AWS ===
* When will this officially go live?
+
* SOLR, WOBr, SObA, Enrichment analysis
* Will we now be able to request strain IDs through the server? Yes
+
* Working with Sibyl on the process
 +
* Will try migrating wobr1 first, as a test case
 +
* May eventually move, for example, Tazendra
 +
** Will there be drawbacks to doing this?
 +
** Can we regularly ssh into Tazendra on AWS without issue? Costs for transferring large files
 +
* Don't yet know the details of the costs, but we can try and keep track
 +
* We should move into WB or Alliance AWS instances (or Stanford)
  
=== SObA Graphs ===
+
=== WormBase talk at Boston Area Worm Meeting ===
* New graphs now live on site (Expression, Gene Ontology, Human Diseases, Phenotypes)
+
* https://www.umassmed.edu/ambroslab/meetings/bawm/
* A lot of whitespace padding above and below graph; maybe trim? trimming vertically would ultimately limit the view pane when user wants to zoom in, so we should leave as is for now
+
* Meeting will be virtual on Zoom
* Diff tool: Raymond and Juancarlos created a prototype diff tool (for comparing two genes, for example)
+
* Chris will give a talk September 23rd, 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
** Paul: compared two genes that should be very similar, but there are a lot of differences; may reflect annotation coverage rather than biology
+
* Send topic requests to Chris for the talk
 +
* Current topics:
 +
** Micropublications
 +
** Author First Pass
 +
** Automated Gene Descriptions
 +
** Community Curation
 +
** WB Query Tools
 +
* Chris will ask organizers if others can join: post on WormBase blog? May draw too large an audience for the zoom channel;
 +
* If the organizers record the talk, we can post it on the blog and WB YouTube channel
  
  
== September 19, 2019 ==
+
== September 10, 2020 ==
  
=== Strains ===
+
=== GO GAF Files ===
* Need to wait for new strain IDs from Hinxton before running dumping scripts
+
* WS278 GO GAF is using the new 2.2 file format
* Don't edit multi-ontology strain fields in OA for now!
+
* [https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md Specifications]
* Juancarlos will map free text and ontology-name strain entries to strain IDs once we have the complete mapping file
+
* GO will not be emitting GAF 2.2 until the end of the year (will try to get a fixed date)
* "Requested strain" field in Disease OA; not dumped, so don't need to worry about right now
+
* Implications for gene descriptions, but what about other tools, applications at WB?
 +
* Some errors in the current WS278 GAF, but will get fixed soon
 +
** Impacts gene descriptions for WS278, so using WS277 for now; will be OK once source GAF is fixed
  
=== Alliance literature curation ===
+
===Disease files on FTP===
* Working group will be formed soon
+
*No changes for WS278 FTP files, except an extra custom file that Hinxton is producing mostly for gene descriptions so that we don't get the wrong human diseases via poor orthology calls (see GitHub issue https://github.com/WormBase/website/issues/7839)
* Will work out general common pipelines for literature curation
+
*Will be some consolidation of disease data possibly for WS279 FTP files, implications for downstream tools--gene descriptions, WOBR, ??
  
=== SObA Graph relations ===
+
=== WormBase talk at Worcester Area Worm Meeting ===
* Currently only integrating over "is a", "part of" and "regulates"
+
* Chris set to give talk on December 1st, 2020, via Zoom, 4pm (or 4:30pm) EST / 1pm Pacific
* Maybe we could provide users an option to specify which relations to include, or maybe just exclude "regulates"
+
* 30 minute slot; complementary to BAWM talk?
 +
* WormBase members can attend
  
=== Author First Pass ===
+
=== WormBase talk at Boston Area Worm Meeting ===
* Putting together paper for AFP
+
* https://www.umassmed.edu/ambroslab/meetings/bawm/
* Reviewing all user input for paper
+
* Chris will give a talk September 23rd (< 2 weeks), 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
* Asking individual curators to check input
+
* WormBase members can attend; Zoom link will be sent next Monday
  
 +
=== Worm Anatomy Ontology Fixes ===
 +
* Raymond working on addressing warnings and errors (missing definitions, duplicate labels, duplicate definitions)
 +
* Assessing the best way to address them
 +
* Would be good to be able to automate some edits; options:
 +
** Use OWL API (need someone proficient in coding with OWL API)
 +
** Convert to OBO, programmatically edit, convert back to OWL?
 +
** Use Cellfie plugin for Protege?
 +
** Should discuss with Nico once we have a sense as to what changes need to be made
  
== September 26, 2019 ==
+
=== Dead Variations in Postgres ===
 +
* Currently pulling in variations/alleles from Postgres to populate "allele" and "genetic perturbation" categories in Textpresso
 +
* Noticed that many transgene names were being included, which can result in false positives for the categories
 +
* Looking at Postgres table "obo_data_variation", there are ~100,000 entries, ~40,000 with status "Dead" and ~60,000 with status "Live"
 +
* Trying to determine the history of the "Dead" variations, where most of the transgene names are coming from
 +
* May still want to include "Dead" variations/alleles in Textpresso category for historical reasons
 +
* We could use pattern matching to filter out transgene names
 +
* Possible to search C. elegans corpus for all "real" allele public names in the "Dead" set to see if they should still be included in categories
  
=== Data mining ===
+
=== WS279 Citace Upload ===
* Someone in Paul's lab asking to retrieve list of C. elegans orthologs from a list of human genes
+
* Local Caltech upload to Spica, Tuesday September 22, 10am Pacific
* Could we build a (simple) Alliance tool to do this?
 
* Could SimpleMine do this? Could we build a SimpleMine-like tool for Alliance?
 
  
=== Strains ===
 
* Paul D generated WBStrains for the missing TransgeneOme objects
 
* Working on a pipeline to identify new TransgeneOme strains at each upload
 
* One TransgeneOme object had 2 strains. Possible solutions: dump 2 expression objects that differ only in the Strain or remove the UNIQUE tag in the data model
 
** Probably best to keep UNIQUE tag
 
* Raymond: concerned about automatically generating strains based on imports from the group
 
* Many odd strain names are coming from the TransgeneOme group; maybe we ought to have more discussions about generating official (following nomenclature standards) strain names from their imports
 
* Quarantine strains on initial import; review and accept if pass standards
 
  
=== Community phenotype requests August 2019 ===
+
== September 17, 2020 ==
* Sent out new round of phenotype requests on August 20, 21, and 22, 2019
+
 
* 2,626 emails/papers requested
+
=== Species errors in CITace ===
* 114 emails bounced; 5 resent to new addresses
+
* Wen is reviewing species coming from CIT and will send individual curators lists of species that need correction
* 460 Phenotype OA community annotations; 181 RNAi OA annotations (641 annotations total)
+
 
* From 94 papers (83 for Phenotype OA; 33 for RNAi; 22 for both)
+
=== Webinars ===
* By 81 distinct community curators (70 for Phenotype OA; 32 for RNAi OA; 21 for both)
+
* We could perform a general WormBase webinar to cover all of WormBase, maybe one hour long
* 50 papers flagged as not having phenotypes (40 papers DO have phenotypes; 10 marked as negative; 80% failure rate!)
+
* Allow 20-30 minutes for discussion? Can allow interruptions but plan for one hour
** Email states: "If there are no nematode phenotypes in this paper click the following link :"
+
* Follow up with more specific webinars in following months: JBrowse, WormMine, Micropublication, AFP, Textpresso Central, Ontology browser & Enrichment tools, SPELL, ParaSite BioMart
* 4 papers flagged for phenotypes (only 2 had curatable phenotypes; 1 had honey-induced phenotypes)
+
* Chris and Wen can discuss how to setup
* 115 papers with responses (5% response); 24 papers with input that were not main focus of request
+
* Should we have people register? Maybe
 +
* AFP probably doesn't need an hour; maybe split an hour across micropublications and AFP?
 +
 
 +
=== Transcription factors and regulatory networks ===
 +
* Had another question about TFs, asking for common TFs for a list of genes
 +
* An issue is that the TF binding data we have is in disparate forms, trying to reconcile
 +
* We have a ?Transcription_factor class; it would be good to update and integrate with other related data types
 +
 
 +
=== Alzheimer's disease portal ===
 +
* Funding has been awarded for Alzheimer's research
 +
* Ranjana: should the disease working group consider more about an Alliance Alzheimer's disease portal?
 +
* Paul S: Alliance SAB tomorrow; we'll see what the SAB says
 +
* Can look at other resources like RGD disease portals and Reactome disease-related pathway models
 +
* Ruth Lovering is doing some work in this regard
 +
 
 +
=== GO meeting ===
 +
* All are welcome to attend
 +
* Will discuss GAF format changes, etc.
 +
* Ranjana: should she and Valerio attend to learn about GO changes that affect the gene descriptions pipeline?
 +
** Kimberly: there could be a particular breakout group that Ranjana and Valerio could attend to discuss
 +
 
 +
=== New GAF 2.2 file ===
 +
* Kimberly has reviewed and sent feedback to Michael P
 +
* Valerio would like to stay in the loop to test the new files
 +
 
 +
=== Data mining tool comparison sheet ===
 +
* https://docs.google.com/spreadsheets/d/1vBTDBOKfXn9GcdpF1bXI62VEJ7hwyz2hOyAZcoV1_ng/edit?usp=sharing
 +
* Needs an update
 +
* Could we make this available to users? A link in the Tools menu?
 +
* Is this useful to users? Would they understand it? Maybe be better as a curator resource
 +
* Could this be micropublished?
 +
** Possible; may want to consider a series of publications with videos of webinars, etc.

Revision as of 16:39, 17 September 2020

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings



2020 Meetings

January

February

March

April

May

June

July

August


September 3, 2020

WS279 Citace upload

  • September 25
  • Local CIT upload (to Wen) Tuesday September 22 by 10am Pacific

New AFP datatype for curation status form (CSF)?

  • afp_othergenefunc (to capture gene function other than enzymatic activity)
  • Can wait a bit before adding to CSF; if there will be dedicated curation for that data type we may add later

GO annotation for description

  • Kimberly will look into 'male tail tip developement' terms for description

Migrate wobr1 server to AWS

  • SOLR, WOBr, SObA, Enrichment analysis
  • Working with Sibyl on the process
  • Will try migrating wobr1 first, as a test case
  • May eventually move, for example, Tazendra
    • Will there be drawbacks to doing this?
    • Can we regularly ssh into Tazendra on AWS without issue? Costs for transferring large files
  • Don't yet know the details of the costs, but we can try and keep track
  • We should move into WB or Alliance AWS instances (or Stanford)

WormBase talk at Boston Area Worm Meeting

  • https://www.umassmed.edu/ambroslab/meetings/bawm/
  • Meeting will be virtual on Zoom
  • Chris will give a talk September 23rd, 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
  • Send topic requests to Chris for the talk
  • Current topics:
    • Micropublications
    • Author First Pass
    • Automated Gene Descriptions
    • Community Curation
    • WB Query Tools
  • Chris will ask organizers if others can join: post on WormBase blog? May draw too large an audience for the zoom channel;
  • If the organizers record the talk, we can post it on the blog and WB YouTube channel


September 10, 2020

GO GAF Files

  • WS278 GO GAF is using the new 2.2 file format
  • Specifications
  • GO will not be emitting GAF 2.2 until the end of the year (will try to get a fixed date)
  • Implications for gene descriptions, but what about other tools, applications at WB?
  • Some errors in the current WS278 GAF, but will get fixed soon
    • Impacts gene descriptions for WS278, so using WS277 for now; will be OK once source GAF is fixed

Disease files on FTP

  • No changes for WS278 FTP files, except an extra custom file that Hinxton is producing mostly for gene descriptions so that we don't get the wrong human diseases via poor orthology calls (see GitHub issue https://github.com/WormBase/website/issues/7839)
  • Will be some consolidation of disease data possibly for WS279 FTP files, implications for downstream tools--gene descriptions, WOBR, ??

WormBase talk at Worcester Area Worm Meeting

  • Chris set to give talk on December 1st, 2020, via Zoom, 4pm (or 4:30pm) EST / 1pm Pacific
  • 30 minute slot; complementary to BAWM talk?
  • WormBase members can attend

WormBase talk at Boston Area Worm Meeting

Worm Anatomy Ontology Fixes

  • Raymond working on addressing warnings and errors (missing definitions, duplicate labels, duplicate definitions)
  • Assessing the best way to address them
  • Would be good to be able to automate some edits; options:
    • Use OWL API (need someone proficient in coding with OWL API)
    • Convert to OBO, programmatically edit, convert back to OWL?
    • Use Cellfie plugin for Protege?
    • Should discuss with Nico once we have a sense as to what changes need to be made

Dead Variations in Postgres

  • Currently pulling in variations/alleles from Postgres to populate "allele" and "genetic perturbation" categories in Textpresso
  • Noticed that many transgene names were being included, which can result in false positives for the categories
  • Looking at Postgres table "obo_data_variation", there are ~100,000 entries, ~40,000 with status "Dead" and ~60,000 with status "Live"
  • Trying to determine the history of the "Dead" variations, where most of the transgene names are coming from
  • May still want to include "Dead" variations/alleles in Textpresso category for historical reasons
  • We could use pattern matching to filter out transgene names
  • Possible to search C. elegans corpus for all "real" allele public names in the "Dead" set to see if they should still be included in categories

WS279 Citace Upload

  • Local Caltech upload to Spica, Tuesday September 22, 10am Pacific


September 17, 2020

Species errors in CITace

  • Wen is reviewing species coming from CIT and will send individual curators lists of species that need correction

Webinars

  • We could perform a general WormBase webinar to cover all of WormBase, maybe one hour long
  • Allow 20-30 minutes for discussion? Can allow interruptions but plan for one hour
  • Follow up with more specific webinars in following months: JBrowse, WormMine, Micropublication, AFP, Textpresso Central, Ontology browser & Enrichment tools, SPELL, ParaSite BioMart
  • Chris and Wen can discuss how to setup
  • Should we have people register? Maybe
  • AFP probably doesn't need an hour; maybe split an hour across micropublications and AFP?

Transcription factors and regulatory networks

  • Had another question about TFs, asking for common TFs for a list of genes
  • An issue is that the TF binding data we have is in disparate forms, trying to reconcile
  • We have a ?Transcription_factor class; it would be good to update and integrate with other related data types

Alzheimer's disease portal

  • Funding has been awarded for Alzheimer's research
  • Ranjana: should the disease working group consider more about an Alliance Alzheimer's disease portal?
  • Paul S: Alliance SAB tomorrow; we'll see what the SAB says
  • Can look at other resources like RGD disease portals and Reactome disease-related pathway models
  • Ruth Lovering is doing some work in this regard

GO meeting

  • All are welcome to attend
  • Will discuss GAF format changes, etc.
  • Ranjana: should she and Valerio attend to learn about GO changes that affect the gene descriptions pipeline?
    • Kimberly: there could be a particular breakout group that Ranjana and Valerio could attend to discuss

New GAF 2.2 file

  • Kimberly has reviewed and sent feedback to Michael P
  • Valerio would like to stay in the loop to test the new files

Data mining tool comparison sheet