WormBase-Caltech Weekly Calls

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

January

February 6, 2014

AGENDA

• Topic Curation
  • WS243,244: Innate immunity and response to pathogens
  • WS242: miRNA pathway
  • WS241: UPR pathways
  • using the caltech FTP site for storing topic page pathway images for the web team. Where is it, what information do we want to include, can we use this to track history of pathways?
  • model change to put topics in hierarchical structure.
• File cabinets in hallway?
• Variations that have lost a public_name due to Million Mutation processing in WS240.
  • What to do with ones that have phenotypes attached, should they have their public_names restored, so we can see them in our OA dropdown lists?

> WBVar00249046 former public-name sy5417
> WBVar00275318 former public-name y87
> WBVar00275321 former public_name y95
> WBVar00000714 former public_names cb107, cbs107
> WBVar00000718 former public_names cb111, cbs111
> WBVar00000716 former public_names cb109, cbs109
> WBVar00000720 former public_names cb113, cbs113
> e2518 is an other_name of WBVar0014462
> g320 is an other_name of WBVar00017601

• Models meeting in Toronto March 10-11

Gene Association files

• Life stage-gene associations
• Capturing relations (e.g. "involved_in") in GAF; how to do that for life stage?
• What search tool do we plan for e.g. "what genes are expressed in a particular neuron AND during dauer larval stage?"

we can use WormMine. Example query: http://www.wormbase.org/tools/wormmine/template.do?name=Anatomy_LS_Genes&scope=all

• Expression data model needs updating to capture BOTH place AND time of gene expression

Pathway images on topic pages

• Do we store/supply a flat image file for the web team?
• Store image files on the FTP site? Canopus, nightly mirroring
• Release-specific directories/images? OICR needs to know and handle
• Daniela's images are collected cumulatively; Wen's are overwritten
• May be an issue embedding iFrame interactive viewer

Variations losing public names

• Million Mutation project, variations getting renamed
• Distinguishing natural variants vs. lab-induced alleles
• Merging event (natural variants at same location merged), existing names become "Other_name"s
• Can we have a mechanism in place to decide one Public_name if there are multiple? Temporal precedence?
• First published name can be official Public_name?
• decided to leave things as they are

February 13, 2014

AGENDA

• Infection model
• Reminder: Alex Pico, Mary Ann Tuli, Xiaodong visiting Caltech Feb 24th
• Sequence Feature interactors
• Viewing list of topics in OA

Infection model

• Infection model discussion--Advantages/disadvantages to curating to the level of strain for pathogens like Bacteria, Fungi etc) (Ranjana)

Please see http://wiki.wormbase.org/index.php/Modeling_data_for_Infectious_agents

• Do we create non-nematode Strain objects here at Caltech? (Ranjana)
  • (Mary Ann) As far as I can see, no. But I don't see a reason why you can't if there is a need. We will simply need to make sure you know the right curation format, which for non-nematode strains is a bit vague. I am talking to Aric shortly about the Db11 strain you sent me earlier this week.
• Things to consider:
  • Creation of "?Infection" class
  • Species-species interactions versus more specific strain-strain interactions
  • Should we create topics that represent species-species interactions that can then be associated to relevant strain-strain interaction objects of an "?Infection" class?
• We would like to be able to create/manage new strains, nematode and non-nematode, for these annotations
• Strain OA?

WikiPathways meeting

• Feb 24th with Alex Pico
• Comments and requests for WikiPathways can be posted on Wiki page
• Alex Pico will present updates to viewer/editor (new JS viewer/editor)

Topic list in OA

• Xiaodong requesting Topic list viewer
• Best to just have a browser window/tab open with topics listed, either in Process Term OA or in the Curation Status form

Feature interactors

• Some interaction objects currently refer to multiple sequence feature objects in addition to a regulator gene and a regulated gene; this results in "hairballs" in interactions, Cytoscape view
• We probably want a separate widget/viewer for gene/protein-sequence feature interactions involving a GBrowse window, displaying the interacting sequence feature in the context of the genome (to infer relevant genes, for example)
• Need to consider options for display and annotation (e.g. should we only have binary interactions?)

February 20, 2014

AGENDA

• Pathways in general and WikiPathways
  

To plan for Alex's visit, it would be good to solidify our wants and needs for process and pathway visualization. Please add specific questions for Alex to the WikiPathways_Questions_&_Comments page.
Some global discussion points for our in-house Caltech meeting:

• • what do we want our pathways to show?
  • how do we want pathways displayed?
• Schedule your meeting with Mary Ann and or Alex. Either add yourself to the Calendar or let Karen know when you have time to chat.