Difference between revisions of "WormBase-Caltech Weekly Calls"
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= 2020 Meetings = | = 2020 Meetings = | ||
| − | == | + | [[WormBase-Caltech_Weekly_Calls_January_2020|January]] |
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| + | [[WormBase-Caltech_Weekly_Calls_February_2020|February]] | ||
| + | |||
| + | [[WormBase-Caltech_Weekly_Calls_March_2020|March]] | ||
| + | |||
| + | [[WormBase-Caltech_Weekly_Calls_April_2020|April]] | ||
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| + | [[WormBase-Caltech_Weekly_Calls_May_2020|May]] | ||
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| + | [[WormBase-Caltech_Weekly_Calls_June_2020|June]] | ||
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| + | [[WormBase-Caltech_Weekly_Calls_July_2020|July]] | ||
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| + | [[WormBase-Caltech_Weekly_Calls_August_2020|August]] | ||
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| + | [[WormBase-Caltech_Weekly_Calls_September_2020|September]] | ||
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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 [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 | ||
| + | |||
| + | === 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 === | ||
| + | * 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) | ||
| − | == | + | == October 15, 2020 == |
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| − | === | + | === 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 | + | * 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 | |
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| − | == | + | == October 22, 2020 == |
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| − | === | + | === CHEBI === |
| − | * | + | * Karen spoke to CHEBI personnel on Tuesday |
| − | * | + | * CHEBI only has ~2 curators to create new entities |
| − | * | + | * CHEBI had submitted a proposal to establish pipelines to process requests from MODs |
| − | * | + | * Chemical Translation Service (CTS) |
| − | + | * OxO = https://www.ebi.ac.uk/spot/oxo/search | |
| − | === | + | === Training Webinar === |
| − | * | + | * Scheduled for tomorrow at 1pm Pacific/4pm Eastern |
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Latest revision as of 18:40, 22 October 2020
Contents
Previous Years
2020 Meetings
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
- 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 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
October 22, 2020
CHEBI
- Karen spoke to CHEBI personnel on Tuesday
- CHEBI only has ~2 curators to create new entities
- CHEBI had submitted a proposal to establish pipelines to process requests from MODs
- Chemical Translation Service (CTS)
- OxO = https://www.ebi.ac.uk/spot/oxo/search
Training Webinar
- Scheduled for tomorrow at 1pm Pacific/4pm Eastern
