Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
 
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
  
 +
[[WormBase-Caltech_Weekly_Calls_October_2020|October]]
  
== October 1, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_November_2020|November]]
  
=== 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 ===
+
==Dec 3rd, 2020==
* 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 ===
+
=== Hench et al paper ===
* It looks like that we will not have a specific space for server computers.
+
* Thomas Burglin would like the data from paper 00046864 to be included in WB
 +
* They want to provide APT profiles (signal intensity along the  anterior-posterior axis over time) as images and movies (time lapse reporter expression)
 +
* They have recorded movies for 60 homeobox genes and over 85 genes in total.
 +
* If we decide to import the collection, movies, images, and description could be displayed as the collection from Murray: https://wormbase.org/species/all/expr_pattern/Expr10431#012--10
  
 +
=== WormBase Papers and Alliance ABC - What papers to add? ===
  
== October 8, 2020 ==
+
* PubMed keyword search 'elegans' (Approve, Reject, Remove)
 +
* Legacy papers from manual concise descriptions
  
=== 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 ===
+
{| border=1 cell-padding=5 cell-spacing=10
* One suggestion for the Alliance is to create a description based on a GO-CAM model
+
|-
* Could also micropublish some descriptions (semi-automated?)
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! PMID
* Can make curators authors of micropublications for GO-CAM models/pathways
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! Paper Editor Action
 +
! WBPaper ID
 +
! Paper Title
 +
! Species
 +
! Primary/Not Primary
 +
! Other Paper Editor Flags
 +
! Any SVM Positives
 +
! Add to ABC
 +
! Comments (1)
 +
! Comments (2)
 +
! Comments (3)
 +
|-
 +
| 31761535
 +
| Approve
 +
| 58971
 +
| The Hyaluronidase, TMEM2, Promotes ER Homeostasis and Longevity Independent of the UPR ER
 +
| Homo sapiens, Caenorhabditis elegans
 +
| Primary
 +
| Author-Person
 +
| Yes
 +
| Yes
 +
|
 +
|
 +
|
 +
|-
 +
| 31868179
 +
| Approve
 +
| 58999
 +
| Measuring the Effects of Bacteria and Chemicals on the Intestinal Permeability of Caenorhabditis elegans
 +
| Caenorhabditis elegans
 +
| Primary
 +
| Author-Person
 +
| None
 +
| Yes
 +
|
 +
|
 +
|
 +
|-
 +
| 16919905
 +
| Approve
 +
| 28426
 +
| The trifecta of aging in Caenorhabditis elegans.
 +
| Caenorhabditis elegans
 +
| Not-primary
 +
| Author-Person
 +
| N/A
 +
| Yes
 +
|
 +
|
 +
|
 +
|-
 +
| 28744338
 +
| Approve
 +
| 51561
 +
| Role of Kallistatin Treatment in Aging and Cancer by Modulating miR-34a and miR-21 Expression.
 +
| Caenorhabditis elegans, Homo sapiens (human, humans), Mus musculus (mice, mouse), Rattus norvegicus (rats)
 +
| Not-primary
 +
| Author-Person
 +
| N/A
 +
| Yes
 +
|
 +
|
 +
|
 +
|-
 +
| 31875562
 +
| Reject
 +
| None
 +
| Intracellular Vesicle Fusion Requires a Membrane-Destabilizing Peptide Located at the Juxtamembrane Region of the v-SNARE
 +
| Mus musculus (mouse), Rattus norvegicus (rat)
 +
| Primary
 +
| N/A
 +
| N/A
 +
| Not from WormBase, but if added from another group we'd want to indicate that it doesn't have C. elegans experimental data?
 +
| Paper shows partial sequence alignment including C. elegans snb-1 in Figure 1A; other species in alignment include M. musculus, H. sapiens, X. leavis, and D. melanogaster
 +
| PubMed indexes proteins and their respective species shown in sequence alignments
 +
|
 +
|-
 +
| 31569547
 +
| Reject
 +
| None
 +
| Mapping the Biotransformation of Coumarins through Filamentous Fungi
 +
| Cunninghamella elegans, Aspergillus brasiliensis
 +
| Primary
 +
| N/A
 +
| N/A
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
| 10625658
 +
| Entry into WB pre-dated current paper editor
 +
| 12789
 +
| Both PCE-1/RX and OTX/CRX interactions are necessary for photoreceptor-specific gene expression
 +
| Homo sapiens (human), Mus musculus (mouse, mice, murine), Rattus norvegicus (rat, rats), Bos taurus(bovine)
 +
| Primary
 +
| non-nematode; Author-Person (pre-dated current Author-Person curation criteria)
 +
| N/A
 +
| Yes??
 +
| Used in legacy manual ceh-8 gene description (how many of these papers were used)
 +
| Used in human manual GO curation (Protein2GO)
 +
| 492 non-nematode papers; not systematically associated with species
 +
|-
 +
|}
  
=== Transcription Factors in WormBase ===
+
*/home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids - ~3300 papers
* WormBase has a ?Transcription_factor class that is currently underutilized
+
*/home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids - ~100 papers
* 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 ==
+
*What about WormBase Parasite papers?
 
 
=== 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
 

Latest revision as of 16:23, 3 December 2020

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Dec 3rd, 2020

Hench et al paper

  • Thomas Burglin would like the data from paper 00046864 to be included in WB
  • They want to provide APT profiles (signal intensity along the anterior-posterior axis over time) as images and movies (time lapse reporter expression)
  • They have recorded movies for 60 homeobox genes and over 85 genes in total.
  • If we decide to import the collection, movies, images, and description could be displayed as the collection from Murray: https://wormbase.org/species/all/expr_pattern/Expr10431#012--10

WormBase Papers and Alliance ABC - What papers to add?

  • PubMed keyword search 'elegans' (Approve, Reject, Remove)
  • Legacy papers from manual concise descriptions


PMID Paper Editor Action WBPaper ID Paper Title Species Primary/Not Primary Other Paper Editor Flags Any SVM Positives Add to ABC Comments (1) Comments (2) Comments (3)
31761535 Approve 58971 The Hyaluronidase, TMEM2, Promotes ER Homeostasis and Longevity Independent of the UPR ER Homo sapiens, Caenorhabditis elegans Primary Author-Person Yes Yes
31868179 Approve 58999 Measuring the Effects of Bacteria and Chemicals on the Intestinal Permeability of Caenorhabditis elegans Caenorhabditis elegans Primary Author-Person None Yes
16919905 Approve 28426 The trifecta of aging in Caenorhabditis elegans. Caenorhabditis elegans Not-primary Author-Person N/A Yes
28744338 Approve 51561 Role of Kallistatin Treatment in Aging and Cancer by Modulating miR-34a and miR-21 Expression. Caenorhabditis elegans, Homo sapiens (human, humans), Mus musculus (mice, mouse), Rattus norvegicus (rats) Not-primary Author-Person N/A Yes
31875562 Reject None Intracellular Vesicle Fusion Requires a Membrane-Destabilizing Peptide Located at the Juxtamembrane Region of the v-SNARE Mus musculus (mouse), Rattus norvegicus (rat) Primary N/A N/A Not from WormBase, but if added from another group we'd want to indicate that it doesn't have C. elegans experimental data? Paper shows partial sequence alignment including C. elegans snb-1 in Figure 1A; other species in alignment include M. musculus, H. sapiens, X. leavis, and D. melanogaster PubMed indexes proteins and their respective species shown in sequence alignments
31569547 Reject None Mapping the Biotransformation of Coumarins through Filamentous Fungi Cunninghamella elegans, Aspergillus brasiliensis Primary N/A N/A
10625658 Entry into WB pre-dated current paper editor 12789 Both PCE-1/RX and OTX/CRX interactions are necessary for photoreceptor-specific gene expression Homo sapiens (human), Mus musculus (mouse, mice, murine), Rattus norvegicus (rat, rats), Bos taurus(bovine) Primary non-nematode; Author-Person (pre-dated current Author-Person curation criteria) N/A Yes?? Used in legacy manual ceh-8 gene description (how many of these papers were used) Used in human manual GO curation (Protein2GO) 492 non-nematode papers; not systematically associated with species
  • /home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids - ~3300 papers
  • /home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids - ~100 papers
  • What about WormBase Parasite papers?