WBConfCall 2016.07.07-Agenda and Minutes

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Agenda

TransgeneOme import

From Daniela and Karen: We are importing in WormBase expression data generated by the TransgeneOme project. They worked on updating their fosmid sequences to the current WS release -previously mapped to WS184. Should we also import their coordinates and have a TransgeneOme track on JBrowse? Other than having the fosmids just connected to the construct class? In this way we will also have 'fresh' mappings on our end? What do we need to have to generate a new track?

Variation Viewer Prototype

Parasite update

Alliance updates

Call for WB release notes

Minutes

TransgeneOme import

To present the transgenes generated by the TransgeneOme project (sequences from fosmids driving GFP) on JBrowse we will create sequence objects that can be mapped and then associate these objects with a clone and then a construct (the latter 2 having metadata and connectivity). To begin Hinxton needs a GFF and IDs. They will check with Karen to see if the data she already has is enough to do this and if not speak with TransgeneOme . These can then be presented on JBrowse and linked to the construct and/or expression pattern pages.

Variation Viewer Prototype

- http://dev.wormbase.org:9015/

Here is the github issue for comments and feedback: https://github.com/WormBase/website/issues/4687

Parasite update

The group is getting the next release ready and it will include variations from different species.

Alliance updates

  • infrastructure: Currently at the “show and tell” stage. There are discussions among the MODs on their architecture and database builds.
  • Curation: There have been regular conference calls about different topics to share how different curation tasks are done by the different MODs. There has also been discussion about getting everyone to use some sort of Textpresso triage system to identify papers/datatypes. This will involve digitizing all "corpuses". Curation forms can also be through textpresso central. Discussion of the use of Noctua for curation is underway, but Noctua is still under beta testing. Noctua is a GO curation tool that “allows curators to connect together multiple annotations to give a cohesive picture of a biological process or mechanism”
  • Datatypes curated by MOD’s: Currently the following exists describing mgi and flybase datatypes

https://drive.google.com/open?id=1X0U5ph66yGaX36AoKFA3qJeYuSGguDuQmVeey9dv3bY

  • Orthologs: Discussions are very much in flux and there is no official working group, but there needs to be discussions of standard formats for data. Major questions include “how to aggregate the different types of orthology calls” and “what is the appropriate balance between stability and updates”. Perhaps the best place to start is to determine what WB needs and go from there.


Call for WB release notes

Please make sure to get any notes to Hinxton for WB255.