WormBase-Caltech Weekly Calls

From WormBaseWiki
Jump to navigationJump to search

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings



March 6, 2014


  • ?Construct model


  • WS242 started to have miRNA datasets; very short probes, not uniquely mapped
  • Wen made modifications to SPELL to accommodate
  • Wen has started separating datasets from papers
  • miRNA analyses have used completely different platforms than protein-coding genes, so requires a different dataset for each
  • Wen started loading WB topics into SPELL
  • Wen would like assign ~100 papers in SPELL to WB topics
  • Wen also modified SPELL script to annotate datasets applicable to specific tissues or cells
  • Wen may/will co-opt Juancarlos' SPELL instance for testing

?Construct model

  • New ?Construct model will be vetted and approved for early in the WS244 curation cycle
  • Some changes to the ?Construct model proposed over last week
  • Still discussing how to handle plasmids/vectors, whether they should go in the ?Clone class (there is precedence)
  • We should defer to the Sequence Ontology, wherever possible, for definitions and relationships
  • We will go ahead with considering including all plasmids and vectors (e.g. AddGene & Fire vectors) to the ?Clone class which can then be referenced within the ?Construct class
  • Will change the "Identical_transgene"/"Identical_variation" tags to "Corresponding_transgene"/"Corresponding_variation"
  • If necessary, we will consider adding a ?Construct tag to the ?Interaction model to accommodate annotation of constructs used in in vitro physical interaction experiments; this is pending curation of (sufficient amounts of) the relevant data

March 13, 2014


Database Meeting Summary

  • Write up <https://www.dropbox.com/s/fr9qrsbup9djx4z/DatabaseFutureMeetingatOICR.pdf>.
  • Working group from three sites will test candidate technologies against metrics, considerations and requirements and report by Oct 2014.
  • Not clear yet whether everyone (in WormBase) will use one universal database technology, or if each site might use different databases
  • Site requirements: web speed & performance, model flexibility with regular updates, understandability of modeling language/structure
  • Different options: relational, row, column, NoSQL, SQL, object-oriented, graph database (Neo4J), DynamoDB (Amazon NoSQL DB)
  • Central database for everyone? Real-time editing and updating, or regular updating/synchronization
  • Process will take ~2 years or so

Data visualization with Santiago Lombeyda

  • Will play with some potentially straight-forward display options
  • Virtual worm renderings made into SVGs for layering and clicking/linking

?Infection_assay model

  • Broaden scope to include all types of species-species interaction (?Interspecies_interaction class ???)
  • Remove "Modifying_influence" tag and "Required*" tags in favor of "Resistance" and "Hypersensitivity" sets of tags
  • If we are going to include many types of species-species interactions, we need to consider how to make tag names that are unambiguous with respect to which species is playing a particular role
  • We will talk to parasite curators to see what we want to include in the model
  • Ranjana would like to add a concise-description-like text description to genes describing their role in infection
    • Will require retroactively making database connections once the ?Infection_assay (or equivalent) model is finalized and implemented (not this upcoming release)

WormBase Topic/Process hierarchy/ontology relationships

  • Karen will send around a working OBO file
  • Curators can look at which topics should be related to others (via parent-child relationships)
  • Also, we can look at trying to tie in to existing GO terms