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Interactions with other BRCs

Interactions with other BRCs. Scott Emrich “ all hands” meeting VectorBase. Interoperability with other BRCs. Three mechanisms are in use: Portal (minimal) IOWG (delivered: ontologies) BRC-GSC metadata group . IOWG. Rebecca Will (portal) is chair Two groups:

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Interactions with other BRCs

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  1. Interactions with other BRCs Scott Emrich “all hands” meeting VectorBase

  2. Interoperability with other BRCs • Three mechanisms are in use: • Portal (minimal) • IOWG (delivered: ontologies) • BRC-GSC metadata group

  3. IOWG • Rebecca Will (portal) is chair • Two groups: • RNAseq (Dan Lawson co-chair) • Metadata (Scott Emrich co-chair)

  4. BRC-based ideas? • PATHOGEN / VECTORWe started out by discussing what we could do to facilitate pathogen / vector interactions.   One thing noted was some GEO data sets that seemed applicable • Microarray analysis of Wolbachia (bacteria) infected Anopheles gambiae Sua5B cells http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE23215 • Expression profiling of hemocytes from Anopheles gambiae after malaria parasite infection http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17866 • Induction of a peptide with activity against a broad spectrum of pathogens in the Aedesaegypti salivary gland, following infection with dengue virus http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21528 I don’t think that we had any good ideas for exactly what we could do with these data sets or what we might do either AT the Portal or MEDIATED by the Portal with these data sets.  I had written that we shoudl all just look at the data sets to look for ideas for something that we could do.SOMETHING WITH MAPSI wrote down (after the fact) “put host / vector / pathogen data sets on a map”. This could deal with presenting data where overlap exists between host/vector/pathogen records contained in more than one BRC.

  5. HOST RESPONSEPut up a list of all host response data sets at GEO using specific chips (mouse and human)?  Or simply all host response data sets at GEO.Step 1 was simply a list with pointers to the data sets at GEO Step 2 was to expand to include “gene lists”, presumably host genes variably expressed, presumably starting w/ culling such lists from associated pubs and not applying any analysis ourselves. GALAXYPut up an instance of Galaxy at Portal that could be used for BRC specific workflows (as distinguished from integrating w/ the PSU instance of Galaxy).    1st step is that Becky will set up a concall between Portal folks working with Galaxy and the EuPathDB folks working with Galaxy for Portal folks to see what EuPathDB folks have implemented so far.

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