Satellite meeting for use-cases

Topics ¶

Participants¶
 * 




Date ¶

    * 2009/3/19 15:00-18:00 

Room ¶

    * Chura Hall (3F)


Presentations ¶

Fill:

    * Name of the presenter
          o Title of the talk
          o Attachments (PPT or PDF slides etc.) 

Notes ¶

   

    Log of use-case workgroup

Data
-SNPs, Affy provided by Prof.Kim
    SNPs data come from Affymatrix chip of stroke patients and normal people (contain 262,338 SNPs)
  
    - ANNOTATOR currently cannot analyse on SNPs data directly
    - Galaxy (http://galaxy.esphealth.org/) RGenetics
        quality control, ancestry and case-control analysis
    - BioMart

BioMart
- have to know dataset, filter, attribute
- can use Perl API,..
- Martview
- DAS access
- Martview
- can set up server and use in-house

Question
- Takeshi asked about how to annoate in-house data with comparing with public genome data using BioMart.
- For example, how to annotate Halocynthia roretzi or Molgula tectiformis ESTs comparing with Ciona intestinalis and Ciona savigni using BioMart.
Answer
- Convert Halocynthia data into BioMart format. Install BioMart server locally. Then merge public DB and local data together.
- BioMart format is simple.


Takeshi present
- minor animal (closet animal Ciona)
- how can analyze Halocynthia roretzi and M.tectiformis which are rare annotation.
- type of data is ESTs, assembled EST cluster,,,etc,,
- potential flow: BioMart -> ANNOTATOR -> TogoDB

DL ESTs of Halocynthia roretzi from NCBI/Taxonomy

TogoDB by Toshiaki
- upload table format  (table services for uploading data will be able to access using WS)


jORCA by Oswaldo

-mapped WABI services
- jORCA: WABI WSDL application can run in local machine after installation
- jORCA can tell which kind of analysis can do with our multifasta format file or anykind of format. For example, using Magallanes: INB*,
if put "FASTA" in Find box, the result come up with 23 tools that can use for analysis. For analysis use myexperiment.org
*Magallanes: INB (Services discovering that discover what kind of analysis can provide for your data format)


ANNOTATOR

- how different between ANNOTATOR and InterProscan
- how can I know the version of each DB use in Prim-seq-algorithm
- it would be nice if user


Results ¶


TODOs ¶