WormBase-Caltech Weekly Calls
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2013 Meetings
October 3, 2013
Development environment for Raymond
- Todd is working on it; will do today
NAR Manuscript
- Todd will send around for comments today
WormBase Ontology Browser (WOBr)
- We have a stable server for the information the browser queries: gene ontology associations, gene association files
- Raymond was trying to keep up with the AMIGO 2 development upgrades
- Raymond will soon be getting other ontology info into the browser
- Takes about an hour to load data into the browser
Movie objects stored as URLs
- There are 209 RNAi objects referencing 513 movies via URLs
- The URLs are for RNAi.org pages that have the movies; we don't have the movie files themselves
- Daniela will add a Database tag to the ?Movie class
- URL suffixes/endings will act as the RNAi.org Accession number that will go into the respective Movie objects
Movie curation
- Movie files are stored on Canopus
- Anyone importing new movies will need to get their movies into the appropriate directories on Canopus
- Currently movie files are all from three large scale movie datasets, so names are currently unique
- Daniela will now sort movies according to WBPaper ID or WBPerson ID (depending on the source) and place them in directories accordingly
- Movie files will then be organized according to these directories as ?Picture objects are already
Changing "Biological Process" to "Biological Topic"
- Changing the class name in the web code is laborious and not good practice
- We will keep the ?WBProcess class name, but only refer to them as "Biological Topics" on the website
- A comment will be added to the models.wrm file explaining the discrepancy
Database OA
- Karen and Juancarlos will construct a ?Database class OA
- Curators can enter new databases or edit existing databases there
- There is a static file for the web code that provides URL constructors for links out to those databases and their objects
- In the past, the file has been manually updated to accommodate new databases or updates to URLs, for example
- There needs to be a mechanism in place to edit or replace the file to correspond to the Database OA data
Unfolded Protein Response curation - Pilot topic curation
- Already an ER UPR Stress WikiPathway and a Mitochondrial UPR WIkiPathway
- Do we create one parent pathway/topic, or do we keep them separate?
- As we work on a topic, we will assess how much material there is to cover and whether or not we need to be more specific (or more broad) in topic