Satellite meeting for Use-cases development and documentation

Topics

Participants

• Raoul JP Bonnal
• Toshiaki Katayama
• Vachiranee Limviphuvadh
• Tobias Gattermayer
• Shuichi Kawashima
• Takeshi Kawashima
• Arek Kasprzyk
• Syed Haider
• Oswaldo Trelles
• José M. Fernández
• Paul Gordon
• Keun-Joon Park
• Yunsun Nam
• Young Joo Kim
• Tatsuya Nishizawa
• Riu Yamashita
• Fumikazu Konishi

Targets

Date

• 2009/3/19 15:00-18:00

Room

• 3F

Notes

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 can save result in xml format

Results

TODOs