Difference between revisions of "WormBase-Caltech Weekly Calls"
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*Daniela was proposing changes to the models | *Daniela was proposing changes to the models | ||
*Daniela can/should coordinate with Wen for microarray/tiling array data/quantitative expression data | *Daniela can/should coordinate with Wen for microarray/tiling array data/quantitative expression data | ||
| + | * For now Daniela will request only Tiling Array and Microarray tags. Wen will put in the additional model changes later on. | ||
*Does the text entry need to be indexed (?Text vs Text) for DB_info? | *Does the text entry need to be indexed (?Text vs Text) for DB_info? | ||
| − | |||
=== Cataloging controlled vocabularies used in OA and models === | === Cataloging controlled vocabularies used in OA and models === | ||
Revision as of 10:32, 11 October 2013
Previous Years
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
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/quantitative expression data
- For now Daniela will request only Tiling Array and Microarray tags. Wen will put in the additional model changes later on.
- Does the text entry need to be indexed (?Text vs Text) for DB_info?
Cataloging controlled vocabularies used in OA and models
- Karen generated Wiki page: http://wiki.wormbase.org/index.php/OA_forms,_tables,_scripts,_etc#OA_form_dropdown_lists
- Tables list Postgres tables and OA forms and the controlled vocabularies (drop down values that dump to Text fields in the .ACE file)
- Paul Davis wanted a list of all of the controlled vocabularies we use during curation
- We will want to create a Wiki page that clearly outlines a model-change protocol that people should follow when changing models and refer to this page
WikiPathways
- WormBase approval process needs to be flushed out
- We can annotate edges in a pathway with text: references/citations, text from article, WormBase object referenes, etc.
- We want to link all relevant WormBase objects to the pathway where possible
- We want to establish a graded spectrum of confidence for each pathway component/annotation/edge
- Confidence or rigor of annotation can span across evidence types: Review reference only (low score), review figure/table, primary research evidence article, primary research evidence figure/table within article, WormBase data object (e.g. interaction, etc.) (high score)
Topic curation: Unfolded Protein Response
- Mitochondrial UPR pathway an official WormBase topic
- WikiPathway curation would be best while curating a paper; update on WikiPathways site for other curators to see
- We can add annotations (papers, figures, tables, WB data objects) to edges in pathways
- While curating a data type, there are many more aspects of the biology from the paper that inform the curator of the pathway
- Regular editing and updating of WikiPathways will keep other curators updated on what still needs adding to the pathway
- We should continue to focus on how this pipeline can be improved for future curation
