WormBase-Caltech Weekly Calls

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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

October 10, 2013

?Expr_pattern and ?Movie model changes

• Daniela was proposing changes to the models
• Daniela can/should coordinate with Wen for microarray/tiling array data
• Does the text entry need to be indexed (?Text vs Text) for DB_info?