Revision as of 17:30, 1 October 2020

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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.

@@ Line 42: / Line 42: @@
 [[WormBase-Caltech_Weekly_Calls_August_2020|August]]
+[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
-== 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)? ===
+== October 1, 2020 ==
-* 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 ===
+=== Gene association file formats on FTP ===
-* Kimberly will look into 'male tail tip developement' terms for description
+* 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
-=== Migrate wobr1 server to AWS ===
+=== Phenotype association file idiosyncrasy ===
-* SOLR, WOBr, SObA, Enrichment analysis
+* As we've discussed previously, there is an oddity to how the phenotype association file we provide lists, or doesn't, references
-* Working with Sibyl on the process
+* According to the GAF spec, column 6 is for reference and is required, whereas column 8 is "With (or) From" and is optional
-* Will try migrating wobr1 first, as a test case
+* 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
-* May eventually move, for example, Tazendra
+* 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.
-** Will there be drawbacks to doing this?
+** 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
-** Can we regularly ssh into Tazendra on AWS without issue? Costs for transferring large files
+* 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)?
-* Don't yet know the details of the costs, but we can try and keep track
+* 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
-* We should move into WB or Alliance AWS instances (or Stanford)
+* Proposal is to put WBPerson IDs in column 6 for personal communications. Chris & Karen will check if this will work.
-=== WormBase talk at Boston Area Worm Meeting ===
+=== Server space in Chen Building ===
-* https://www.umassmed.edu/ambroslab/meetings/bawm/
+* It looks like that we will not have a specific space for server computers.
-* 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
-* [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]
-* 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 ===
-* https://www.umassmed.edu/ambroslab/meetings/bawm/
-* Chris will give a talk September 23rd (< 2 weeks), 6pm Eastern, 3pm Pacific (probably first speaker but not sure)
-* 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
-=== 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 ===
-* 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.

Difference between revisions of "WormBase-Caltech Weekly Calls"

Revision as of 17:30, 1 October 2020

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October 1, 2020

Gene association file formats on FTP

Phenotype association file idiosyncrasy

Server space in Chen Building

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