Difference between revisions of "WormBase-Caltech Weekly Calls"

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= Previous Years =
 +
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2009|2009 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2014|2014 Meetings]]
 +
 +
[[WormBase-Caltech_Weekly_Calls_2015|2015 Meetings]]
  
==2011 Meetings==
+
[[WormBase-Caltech_Weekly_Calls_2016|2016 Meetings]]
  
[[WormBase-Caltech_Weekly_Calls_February_2011|February]]
+
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
== March 3, 2011 ==
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
SUMMARY:
 
  
Every other month patch:
 
*We will try to generate an ACEDB patch every other month, starting with the Paper class data
 
*Need to coordinate with Juancarlos and Todd
 
  
Need to check .ACE patch files before upload:
 
*Will need to be vigilant about checking for errors and inconsistencies before sending to Todd to put up on website
 
*Curators need to check their own data for problems
 
*Wen will check for consistency between the different data types
 
  
Think about connecting website to Postgres:
+
= 2020 Meetings =
*Think about showing Postgres data "immediately" on site
 
  
 +
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
DETAILS:
+
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
Delayed release cycle:
+
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
*Will require more work to prepare for more frequent release of certain data types
 
*Aside from Kimberly's data, most data types are not urgent (e.g. Expression pattern)
 
*What are the users feeling?
 
**Having data faster will help users; they don't ask, because they don't see it
 
*On-the-fly updating of website? Like Postgres?
 
*Since we use ACEDB, we have to patch WS with .ACE file, or rebuild whole thing
 
*Flat file Postgres database, replaced every night?
 
*Website calls Postgres directly for certain data types?
 
*Performing build without sequence is easy? Do everything without sequence?
 
*How to integrate sequence data with other data once they're decoupled through the patching process?
 
*We need .ACE patch files
 
*Concise description separate from most else (but connected to papers)
 
*Do papers first?
 
*Website can show anything
 
*If we have a lot of patches, will not have check for data inconsistency/confliction
 
*Trial patch .ace files for papers first
 
*Juancarlos: Scripts that check differences between data dumps; scripts are data type specific
 
**Curators need to talk to Juancarlos about the importance of different data tags
 
*Paper .ACE file: Would include bibliographic info, journals, authors, genes associated from abstract or added manually
 
*One reason for more frequent releases: because we have first pass author forms; show them we add it quickly
 
**what will be added through the forms: expression patterns? RNAi (difficult?)?
 
*We should check patch before we send to Todd!!! Don't want to crash database
 
*How frequently to patch? Weekly? Daily? Check with Todd, how often he can load them?
 
*Chron job to create patch ACE files, send to curators to check for problems, then send to Todd
 
*Interdependency of data types; curators rely on other curators?
 
*Postgres directly to website? Todd would have to work it out
 
*New information flag on website? Toggle visibility?
 
*How do we know that the data do not conflict with each other?
 
*What are common problems? Dumper script goes bad, makes broken lines, empty fields
 
*Error catching mechanisms? More checks on postgres? Dump files?
 
*Data merging problems? What are the cases that are conflicts? Prevent them? Know beforehand?
 
*If we don't know, as long as it doesn't crash the database or fail to load, then OK
 
*Don't do -D stuff, maybe? No deletions? Skip typos?
 
*Always have to check ACE files anyway, but have to do every week (2 weeks?)
 
*We can try a patch every other month
 
*What can we do without the patch?
 
*Did SAB talk about changing to relational databases?
 
**Get website going as is first, and see if it matters?
 
**If people don't want to change data models, we can switch over to relational
 
**Separate panel on website directly from Postgres?
 
*Wen can check the data integration every other month for patch
 
  
 +
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
 +
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
== March 10th, 2011 ==
+
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
  
Release schedule and patches
+
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
*What is the appropriate frequency?
 
*Scheme: do what we're already doing, Wen merges into citace
 
*Excluding sequence related data
 
*Need to include Mary Ann's data (strains etc.)
 
*Daily update too frequent; maybe once per month/week
 
*Submit .ACE file to Todd with simple syntax; easily parsable; old description removed and new information added
 
*Make updates only in contrast to last WS, not previous patch/temporary upload
 
*ACEDB diff step only relative to WS
 
*Wen: Postgres can dump diff ace file; already have diff ace files for every data type at Caltech; integrate into citace;
 
*Raymond: integration is important; we need to talk about how much work needs to be done by each approach
 
*Wen: consistency checks, backups, store each version?
 
*Rayomnd: citace 224 to 225 (for example), display done on class level
 
**Example: Gene page; only update information relevant to gene class to be displayed
 
*Do once per month: faster than currently because it doesn't have to go through the dev site
 
*If we update Citace to Citace, missing a lot of cross-references?
 
*Mock citace with Mary Ann's data? Becomes diff base; Mary Ann submits (non-sequence related) data directly to WBCIT
 
*Build low-connectivity ace at WBCIT? Add Mary Ann's data, remove RNAi
 
*Todd: important consideration: things added won't be available for search until formal release; weird things about diff; new reference associations with genes; a lot of duplications?
 
**Raymond: will look at it
 
*Todd: WBGene00000846, example, see how fast it loads, go from there; would like a single ACE file (concatenation of all individual ace files); would not happen on development; would have to happen on production releases; would take production database off line, clone it, and upload it to all production nodes
 
*Individual curators need to check their individual ace files for errors
 
*Frequency: monthly
 
*Todd: we should just run some tests first, to check feasibility
 
*Raymond: WBGene1, example, concise description has typo, WS225 has typo fixed from WS224, diff file shows:
 
**-D old_description
 
**new_description
 
*Load diff ace into original database?
 
*parallel display; unrelated to resident WS?
 
*Todd: producing two web pages for each object?
 
*Raymond: No, only changing relevant tags, etc.
 
*Todd: Two databases running at same time inefficient; include timestamps?
 
*Raymond: No, cannot include timestamps
 
*Wen: Send patch ace files to Todd
 
*Raymond: In conflict with versioning; how to show new data
 
*Wen: Call it "WS225.1"
 
  
 +
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
  
Human Disease Relevance tag in Concise Description
+
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
*Ranjana: Sent out e-mail; human disease tag "Human Disease Relevance"; to clean up concise description form (old tags in form outdated); could be putting more information into concise description; OMIM human disease
 
*Raymond: make not just text field, but make entity field pointing to object; meant to be human readable, this may break up the concise description into OMIM-related and OMIM-non-related info; why parse the data into a tag?
 
*Paul S: OMIM descriptions as a separate tag
 
*Raymond: Rewrite concise description?
 
*Ranjana: No
 
*Paul S: Would you mention human disease relevance in concise description? yes, but if it's just a link out to OMIM, then separate out; OMIM may have changed since Erich wrote original script; check OMIM for new information and tags that may be able to get pulled out
 
*Ranjana: Michael Paulini can consolidate orthology information?
 
  
  
Karen: Transgene model
+
== October 1, 2020 ==
*A lot of changes to propose
 
*Deletions of tags; more coming
 
*Other things in database connected to transgenes
 
*Many things in transgene objects that may be able to be parsed into different tags (new job for someone?)
 
*Strict nomenclature for transgene descriptor
 
*Clones present need to be parsed into clone class?
 
*Todd made Clone page;
 
*Start with vectors/backbones and then work on specific plasmids
 
  
 +
=== Gene association file formats on FTP ===
 +
* For example, current production release ONTOLOGY directory: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/ONTOLOGY/
 +
* Our association files have format "*.wb"; is this useful or necessary?
 +
* Other than referring to GAF in the header, it isn't clear to users what the columns refer to or what the column headers should be
 +
* We could add a README file and/or convert to the new [https://github.com/geneontology/geneontology.github.io/blob/issue-go-annotation-2917-gaf-2_2-doc/_docs/go-annotation-file-gaf-format-22.md GAF 2.2 format] which would have a more expressive file header and possibly column headers(?)
 +
** File headers could possibly link to the format specification page
  
Gene class-phenotype connections and descriptions?
+
=== Phenotype association file idiosyncrasy ===
 +
* As we've discussed previously, there is an oddity to how the phenotype association file we provide lists, or doesn't, references
 +
* According to the GAF spec, column 6 is for reference and is required, whereas column 8 is "With (or) From" and is optional
 +
* When we have a reference, the WBPaper ID is provided in column 6 and the WBVar ID or RNAi ID is provided in column 8
 +
* However, when we have no reference (personal communication, e.g. from NBP allele submissions), the WBVar ID is instead put in column 6 (because we need something there), and column 8 is blank.
 +
** This results in (1) column 6 having a mix of paper/reference IDs (good) and WBVar IDs (not good) and (2) WBVar IDs split between column 6 and 8; thus making it tedious to parse this file
 +
* Proposed solution: Can we come up with some type of reference object ID to associate to the personal communications (or any annotations currently lacking a formal reference)?
 +
* With the proposed solution, we can always have a reference ID in column 6 (the intended purpose of the column) and WBVar IDs for alleles can always remain consistently in column 8
 +
* Proposal is to put WBPerson IDs in column 6 for personal communications. Chris & Karen will check if this will work.
  
 +
=== Server space in Chen Building ===
 +
* It looks like that we will not have a specific space for server computers.
  
GSA markup at Flybase
 
*Flybase is not willing to fully QC all papers
 
*Do we push Flybase and/or provide a better tool to QC?
 
*Are we worried about the GSA markup for flies not looking professional?
 
*People need to be willing to pay for the QC/curation; depends on database priorities
 
*CIT will spend more time on in-house development to make Fly GSA markup easier/more efficient
 
  
 +
== October 8, 2020 ==
  
Putting SPELL on Amazon cloud?
+
=== Webinar Announcement ===
 +
* Here is the live registration site: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/webinar.cgi
 +
* Caltech zoom allows 300 attendees.
  
 +
=== Descriptions from GO-CAM models ===
 +
* One suggestion for the Alliance is to create a description based on a GO-CAM model
 +
* Could also micropublish some descriptions (semi-automated?)
 +
* Can make curators authors of micropublications for GO-CAM models/pathways
  
 +
=== Transcription Factors in WormBase ===
 +
* WormBase has a ?Transcription_factor class that is currently underutilized
 +
* Chris spoke with Gary Williams about the status as he has done much of the work on the class
 +
* Because transcription factors can often be complexes, it was decided to create the ?Transcription_factor class rather than simply an extension of tags to the existing ?Gene class
 +
* The class seems reasonably complete; it's important to note that some TFs are general transcription factors, not necessarily gene-specific or sequence-specific DNA-binding TFs; it will be good to make that distinction clear to users
 +
* Chris has compiled a [https://docs.google.com/spreadsheets/d/1KdmvybWDWHXdlJwZgfleL4xHDoyPoYR13WAUcERF82g/edit?usp=sharing Google sheet] to assess the class before Gary W. leaves WB in the next couple of weeks
 +
* The Google sheet has several tabs/worksheets, including one for the ACEDB data model (and notes about usage of tags), a summary table of associated genes, bound sequence features, existence of other protein-DNA binding data, etc.
 +
* It would be good to make TF binding info (per gene and globally) more accessibly to our users, maybe via a new widget on gene pages (e.g. list incoming, regulating TFs and, for TF genes themselves, list potential target genes)
  
== March 17th, 2011 ==
+
== October 15, 2020 ==
  
Transgene Information was the only topic discussed.
+
=== BioGRID data sharing ===
 +
* Rose from BioGRID proposed that BioGRID curate high-throughput C. elegans interaction datasets, capturing confidence scores when available, and making those annotations available to WormBase for regular ingest
 +
* Will need to consider a few points:
 +
** BioGRID doesn't curate protein-DNA interactions
 +
** We don't yet know the turn-around timeline for BioGRID curation of worm datasets; WB may be able to curate them much sooner
 +
* Chris and Jae will work with Rose et al. to coordinate HTP curation
  
Karen noticed that CGC strain information contains more detailed information about transgenes then what is found in the papers that describe the transgenes.  She would like to integrate the CGC strain information into the transgene curation pipeline.  This could potentially lead to some redundancy, but the consensus was that this was a good idea.  Going forward  - Initially Karen will go through all the CGC strains that have transgene info and add it to the transgene objects in WB.  Once that is accomplished we will institute some system (like the NBP allele info) to update as new strains w/transgene info are entered into the CGC.
+
=== Enriched genes ===
 +
* Some genes are considered "enriched" for an expression cluster data set even if the enrichment was in comparison to another cell or tissue (not whole animal)
 +
* We should reconsider the ?Expression_cluster model to make sure we can appropriately model and communicate enrichment or subtypes thereof

Latest revision as of 16:33, 15 October 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


October 1, 2020

Gene association file formats on FTP

  • For example, current production release ONTOLOGY directory: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/ONTOLOGY/
  • Our association files have format "*.wb"; is this useful or necessary?
  • Other than referring to GAF in the header, it isn't clear to users what the columns refer to or what the column headers should be
  • We could add a README file and/or convert to the new GAF 2.2 format which would have a more expressive file header and possibly column headers(?)
    • File headers could possibly link to the format specification page

Phenotype association file idiosyncrasy

  • As we've discussed previously, there is an oddity to how the phenotype association file we provide lists, or doesn't, references
  • According to the GAF spec, column 6 is for reference and is required, whereas column 8 is "With (or) From" and is optional
  • When we have a reference, the WBPaper ID is provided in column 6 and the WBVar ID or RNAi ID is provided in column 8
  • However, when we have no reference (personal communication, e.g. from NBP allele submissions), the WBVar ID is instead put in column 6 (because we need something there), and column 8 is blank.
    • This results in (1) column 6 having a mix of paper/reference IDs (good) and WBVar IDs (not good) and (2) WBVar IDs split between column 6 and 8; thus making it tedious to parse this file
  • Proposed solution: Can we come up with some type of reference object ID to associate to the personal communications (or any annotations currently lacking a formal reference)?
  • With the proposed solution, we can always have a reference ID in column 6 (the intended purpose of the column) and WBVar IDs for alleles can always remain consistently in column 8
  • Proposal is to put WBPerson IDs in column 6 for personal communications. Chris & Karen will check if this will work.

Server space in Chen Building

  • It looks like that we will not have a specific space for server computers.


October 8, 2020

Webinar Announcement

Descriptions from GO-CAM models

  • One suggestion for the Alliance is to create a description based on a GO-CAM model
  • Could also micropublish some descriptions (semi-automated?)
  • Can make curators authors of micropublications for GO-CAM models/pathways

Transcription Factors in WormBase

  • WormBase has a ?Transcription_factor class that is currently underutilized
  • Chris spoke with Gary Williams about the status as he has done much of the work on the class
  • Because transcription factors can often be complexes, it was decided to create the ?Transcription_factor class rather than simply an extension of tags to the existing ?Gene class
  • The class seems reasonably complete; it's important to note that some TFs are general transcription factors, not necessarily gene-specific or sequence-specific DNA-binding TFs; it will be good to make that distinction clear to users
  • Chris has compiled a Google sheet to assess the class before Gary W. leaves WB in the next couple of weeks
  • The Google sheet has several tabs/worksheets, including one for the ACEDB data model (and notes about usage of tags), a summary table of associated genes, bound sequence features, existence of other protein-DNA binding data, etc.
  • It would be good to make TF binding info (per gene and globally) more accessibly to our users, maybe via a new widget on gene pages (e.g. list incoming, regulating TFs and, for TF genes themselves, list potential target genes)

October 15, 2020

BioGRID data sharing

  • Rose from BioGRID proposed that BioGRID curate high-throughput C. elegans interaction datasets, capturing confidence scores when available, and making those annotations available to WormBase for regular ingest
  • Will need to consider a few points:
    • BioGRID doesn't curate protein-DNA interactions
    • We don't yet know the turn-around timeline for BioGRID curation of worm datasets; WB may be able to curate them much sooner
  • Chris and Jae will work with Rose et al. to coordinate HTP curation

Enriched genes

  • Some genes are considered "enriched" for an expression cluster data set even if the enrichment was in comparison to another cell or tissue (not whole animal)
  • We should reconsider the ?Expression_cluster model to make sure we can appropriately model and communicate enrichment or subtypes thereof