WormBase-Caltech Weekly Calls
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- 1 Previous Years
- 2 2021 Meetings
- 2.1 January 14th, 2021
- 2.2 January 21, 2021
- 2.3 January 21, 2021
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 ?
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
- 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
January 21, 2021
String Matching Pipelines
- Old pipelines on textpresso-dev are not compatible with the new TPC system
- New TPC API does not support string matching
- New Python library (wbtools) - used by variation pipeline - supports batch processing of WB literature and regex matching