Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
  
 +
= 2021 Meetings =
 +
== January 14th, 2021 ==
  
= 2020 Meetings =
+
===PubMed LinkOut to WormBase Paper Pages (Kimberly) ===
 +
* Other databases [https://www.ncbi.nlm.nih.gov/projects/linkout/doc/nonbiblinkout.html link out from PubMed] to their respective paper pages
 +
* For example, https://pubmed.ncbi.nlm.nih.gov/20864032/ links out to GO and MGI paper pages
 +
* Would like to set this up for WormBase and ultimately for the Alliance, but this will require some developer help
 +
* Work on this next month (after AFP and GO grant submissions)?
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
+
===Update cycle for HGNC data in the OA (Ranjana) ===
 +
*Juancarlos had these questions for us:
 +
<pre style="white-space: pre-wrap;
 +
white-space: -moz-pre-wrap;
 +
white-space: -pre-wrap;
 +
white-space: -o-pre-wrap;
 +
word-wrap: break-word">
  
[[WormBase-Caltech_Weekly_Calls_February_2020|February]]
+
There's a script here that repopulates the postgres obo_*_hgnc tables
 +
based off of Chris and Wen's data
 +
/home/postgres/work/pgpopulation/obo_oa_ontologies/populate_obo_hgnc.pl
  
[[WormBase-Caltech_Weekly_Calls_March_2020|March]]
+
It's not on a cronjob, because I think the files are not updated that
 +
often.  Do we want to run this every night, or run it manually when
 +
the files get re-generated ?  Or run every night, and check if the
 +
files's timestamps have changed, then repopulate postgres ?
  
[[WormBase-Caltech_Weekly_Calls_April_2020|April]]
+
</pre>
  
[[WormBase-Caltech_Weekly_Calls_May_2020|May]]
+
===Minutes===
 +
====PubMed LinkOut to WormBase Paper Pages====
  
[[WormBase-Caltech_Weekly_Calls_June_2020|June]]
+
====Update cycle for HGNC data in the OA====
 +
*We will update when Alliance updates the data
 +
*Juancarlos will set it to check the timestamps and if they change will do an update for the OAs
  
[[WormBase-Caltech_Weekly_Calls_July_2020|July]]
+
====CENGEN====
 +
*Wen, Daniela, and Raymond will look at the datasets to work out how to incorporate. Start simple.
 +
*We will make links to pages on their site.
  
[[WormBase-Caltech_Weekly_Calls_August_2020|August]]
 
  
[[WormBase-Caltech_Weekly_Calls_September_2020|September]]
+
== January 21, 2021 ==
  
[[WormBase-Caltech_Weekly_Calls_October_2020|October]]
+
=== Neural Network (NN) Paper Classification Results ===
 +
* Linking to Paper Display tool (as opposed to Paper Editor) from Michael's webpage for NN results (Michael will make change)
 +
* NN results will be incorporated into the Curation Status Form
 +
* For AFP and VFP, there is now a table with mixed SVM and NN results ("blackbox" results); for a given paper, if NN results exist, they take priority over any SVM results
 +
* Decision: we will omit blackbox results (at least for now) from curation status form (just add the new NN results separately)
 +
* We have stopped running SVM on new papers
 +
* Interactions SVM has performed better than new NN results; would be worth attempting a retraining
  
[[WormBase-Caltech_Weekly_Calls_November_2020|November]]
+
=== Community Phenotype Curation ===
 +
* On hold for a few months to commit time to updating the phenotype annotation model to accommodate, e.g. double mutant phenotypes, multiple RNAi targets (intended or otherwise), mutant transgene products causing phenotypes, expressed human genes causing phenotypes, etc.
 +
* Changes made for WB phenotypes may carry over to Alliance phenotype work
 +
* [https://www.preprints.org/manuscript/202101.0169/v1 Paper out now] on undergrad community phenotype curation project with Lina Dahlberg; we may get more requests for trying this with other undergrad classes
  
 
+
=== AFP Anatomy Function flagging ===
==Dec 3rd, 2020==
+
* Sometimes it is difficult to assess whether an author flag is correct (often times can be wrong/absent)
 
+
* What about giving authors/users feedback on their flagging results?
=== Hench et al paper ===
+
* Would be good to provide content from paper where this data is said to exist (automatically from a Textpresso pipeline or manually from author identified data)
* Thomas Burglin would like the data from paper 00046864 to be included in WB
+
* We want to be careful about how we provide feedback; we should be proactive to make improvements/modifications on our end and bring those back to users for feedback to us
* 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
 
 
 
 
 
{| border=1 cell-padding=5 cell-spacing=10
 
|-
 
! 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?
 

Revision as of 17:52, 21 January 2021

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings


2021 Meetings

January 14th, 2021

PubMed LinkOut to WormBase Paper Pages (Kimberly)

  • Other databases link out from PubMed to their respective paper pages
  • For example, https://pubmed.ncbi.nlm.nih.gov/20864032/ links out to GO and MGI paper pages
  • Would like to set this up for WormBase and ultimately for the Alliance, but this will require some developer help
  • Work on this next month (after AFP and GO grant submissions)?

Update cycle for HGNC data in the OA (Ranjana)

  • Juancarlos had these questions for us:

There's a script here that repopulates the postgres obo_*_hgnc tables
based off of Chris and Wen's data
/home/postgres/work/pgpopulation/obo_oa_ontologies/populate_obo_hgnc.pl 

It's not on a cronjob, because I think the files are not updated that
often.  Do we want to run this every night, or run it manually when
the files get re-generated ?  Or run every night, and check if the
files's timestamps have changed, then repopulate postgres ?

Minutes

PubMed LinkOut to WormBase Paper Pages

Update cycle for HGNC data in the OA

  • We will update when Alliance updates the data
  • Juancarlos will set it to check the timestamps and if they change will do an update for the OAs

CENGEN

  • Wen, Daniela, and Raymond will look at the datasets to work out how to incorporate. Start simple.
  • We will make links to pages on their site.


January 21, 2021

Neural Network (NN) Paper Classification Results

  • Linking to Paper Display tool (as opposed to Paper Editor) from Michael's webpage for NN results (Michael will make change)
  • NN results will be incorporated into the Curation Status Form
  • For AFP and VFP, there is now a table with mixed SVM and NN results ("blackbox" results); for a given paper, if NN results exist, they take priority over any SVM results
  • Decision: we will omit blackbox results (at least for now) from curation status form (just add the new NN results separately)
  • We have stopped running SVM on new papers
  • Interactions SVM has performed better than new NN results; would be worth attempting a retraining

Community Phenotype Curation

  • On hold for a few months to commit time to updating the phenotype annotation model to accommodate, e.g. double mutant phenotypes, multiple RNAi targets (intended or otherwise), mutant transgene products causing phenotypes, expressed human genes causing phenotypes, etc.
  • Changes made for WB phenotypes may carry over to Alliance phenotype work
  • Paper out now on undergrad community phenotype curation project with Lina Dahlberg; we may get more requests for trying this with other undergrad classes

AFP Anatomy Function flagging

  • Sometimes it is difficult to assess whether an author flag is correct (often times can be wrong/absent)
  • What about giving authors/users feedback on their flagging results?
  • Would be good to provide content from paper where this data is said to exist (automatically from a Textpresso pipeline or manually from author identified data)
  • We want to be careful about how we provide feedback; we should be proactive to make improvements/modifications on our end and bring those back to users for feedback to us