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]]
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[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
  
[[WormBase-Caltech_Weekly_Calls_March_2019|March]]
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[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
  
[[WormBase-Caltech_Weekly_Calls_April_2019|April]]
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[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
  
[[WormBase-Caltech_Weekly_Calls_May_2019|May]]
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[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
  
[[WormBase-Caltech_Weekly_Calls_June_2019|June]]
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[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
  
[[WormBase-Caltech_Weekly_Calls_July_2019|July]]
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[[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_September_2019|September]]
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[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
  
 +
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
  
== October 3, 2019 ==
+
[[WormBase-Caltech_Weekly_Calls_October_2020|October]]
  
=== SObA comparison graphs ===
+
[[WormBase-Caltech_Weekly_Calls_November_2020|November]]
* Raymond and Juancarlos have worked on a SObA-graph based comparison tool to compare two genes for ontology-based annotations
 
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 1]
 
** [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=annotSummaryCytoscape&filterForLcaFlag=1&filterLongestFlag=1&showControlsFlag=0&datatype=phenotype&geneOneValue=lin-3%20(Caenorhabditis%20elegans,%20WB:WBGene00002992,%20-,%20F36H1.4)&autocompleteValue=let-23%20(Caenorhabditis%20elegans,%20WB:WBGene00002299,%20-,%20ZK1067.1 Example comparison between lin-3 and let-23]
 
* [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 2]
 
** [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=annotSummaryCytoscape&filterForLcaFlag=1&filterLongestFlag=1&showControlsFlag=0&datatype=phenotype&geneOneValue=lin-3%20(Caenorhabditis%20elegans,%20WB:WBGene00002992,%20-,%20F36H1.4)&autocompleteValue=let-23%20(Caenorhabditis%20elegans,%20WB:WBGene00002299,%20-,%20ZK1067.1) Example comparison between lin-3 and let-23]
 
* What information does a user most care about?
 
# What terms (nodes) are annotated to gene 1 and what terms to gene 2
 
# For a given term, what is the relative number of annotations between gene 1 and gene 2.
 
# For a given node, what is the relative number of annotations each gene has to the total annotations of that gene.
 
* # 3 is actually what we applied to size the nodes in the single-gene version of SObA. Thus, not surprisingly, I think it is important.
 
* Generally people like Prototype 2 as a default view; we could possibly have a toggle to see the other view
 
* In either case users need a good legend and/or documentation
 
* Jae, it would be good if a user could specifically highlight nodes specific to each gene and gray-out or de-emphasize the common nodes
 
  
=== Germ line discussion ===
 
* Currently, the anatomy ontology has "germ line" as a type of "Cell" and a type of "Tissue", and "germ cell" as a type of "germ line"
 
* Chris would like to (1) remove "germ line" from under "Cell" and leave it under "Tissue" and (2) move "germ cell" out from under "germ line" and place directly under "Cell"
 
** [https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/pull/23 Made pull request]
 
* Chris will update pull request to include a change to move "germline precursor cell" out from under "germ line" and place it under "Cell" (done)
 
  
=== Script to remove blank entries from Postgres ===
+
==Dec 3rd, 2020==
* Chris stumbled across several entries in the OA that were blank (empty strings) or consisted of only whitespace, some of which were causing errors upon upload to ACEDB
 
* Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
 
* Does anyone object to removing these entries throughout Postgres?
 
* Juancarlos will remove all the empty fields identified by his script
 
  
 +
=== 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
  
== October 10, 2019 ==
+
=== WormBase Papers and Alliance ABC - What papers to add? ===
  
=== Biocuration 2020 ===
+
* PubMed keyword search 'elegans' (Approve, Reject, Remove)
* Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
+
* Legacy papers from manual concise descriptions
* Dates: Sunday May 17th to Wednesday May 20th, 2020
 
* Will have 3rd POTATO workshop
 
* [https://www.jax.org/education-and-learning/education-calendar/2020/05-may/biocuration-2020-conference Meeting website]
 
* Key Dates
 
** October 31, 2019 - Paper Submission Deadline
 
** January 24, 2020 - Abstract  and Workshop Submission Deadline
 
** March 6, 2020 - Notification of Acceptance
 
** April 6, 2020 - Early Bird Registration Ends
 
** May 8, 2020 - Registration Deadline
 
* Academic ISB Member, early bird registration fee is $250
 
* Author First Pass form paper, submitting to Database, biocuration issue (managed by biocuration group); authors have an opportunity to present at Biocuration conference
 
  
=== ICBO 2020 ===
 
* International Conference on Biomedical Ontologies
 
* [https://icbo2020.inf.unibz.it/ Meeting website]
 
* Held in Bozen-Bolzano, Italy
 
* 16 - 19 September 2020
 
  
=== SObA comparison tool ===
+
{| border=1 cell-padding=5 cell-spacing=10
* [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype #1] updated
+
|-
 +
! 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
 +
|-
 +
|}
  
=== Textpresso derived paper connections ===
+
*/home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids - ~3300 papers
* For example for strains and constructs, maybe anatomy terms?
+
*/home/postgres/work/pgpopulation/wpa_papers/pmid_downloads/rejected_pmids - ~100 papers
* May want to flag Textpresso predictions (as opposed to manually connected)
 
* Couple of options:
 
** 1) At time of build, populate the papers (in ACEDB/Datomic) into a 'Putative_reference' tag and display in a distinct 'Putative references' widget
 
** 2) Not part of database build, but make associations live (using RESTful API to link out to Textpresso and submit search with URL) using Textpresso with links to Textpresso and Textpresso results, giving users chance to see context of matches in sentences at the Textpresso site
 
*** A link to Textpresso could be done regardless of other approaches; low-hanging fruit?
 
*** Do a diff so that Textpresso pulls up only additional papers (not already associated)?
 
** 3) Could populate WB page with connections made through a Textpresso API call (could cache results? maybe, but might as well choose 1st option?)
 
* Transgene pipeline:
 
** Arun wrote script, matching transgene names (using regex; Is and Si transgenes) to papers, automatically populate OA
 
** Another script, captures Ex transgenes as well, automatically connects to construct objects
 
** WB only displays verified papers; unverified (predicted) associations are not dumped
 
* Could integrate author verification as part of AFP pipeline, even for older papers? Would we want to re-request AFP results for authors that have already replied in the past? Probably not
 
* Could embed AFP predictions in WB display with link to AFP form for authors (and others?) to verify, via logged-in users? Or via a validation token sent via email?
 
* Chris will make GitHub ticket to ask WB web team to add a link to Textpresso search from References widget on respective page; will require a Textpresso URL constructor
 
* Can apply to: genes, transgenes, constructs, strains, alleles, AFP-vetted entities
 
  
 
+
*What about WormBase Parasite papers?
== October 17, 2019 ==
 
 
 
=== Alliance All Hands Face-to-Face ===
 
* Flights: has everyone already booked? No, not yet
 
* Any coordination of flights from Pasadena/LA?
 
** Ranjana and Valerio got a direct flight from Burbank to Boston on Sunday for premeetings
 
 
 
=== SObA Comparison Tool ===
 
* http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph
 
* Prototype discussed last week, updated with feedback from prior discussions
 
* Would this be a stand-alone tool discoverable under the Tools menu?
 
** Possibly; could be a gene page widget, but may be out of place
 
** Stand-alone tool probably makes more sense
 
* Life stage graph doesn't specify expression pattern vs. expression cluster; pretty much only expression patterns (no clusters)
 

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?