| 1 | |
| 2 | Satellite meeting for use-cases |
| 3 | Topics ¶ |
| 4 | |
| 5 | Participants¶ |
| 6 | * |
| 7 | |
| 8 | |
| 9 | |
| 10 | |
| 11 | Date ¶ |
| 12 | |
| 13 | * 2009/3/19 15:00-18:00 |
| 14 | |
| 15 | Room ¶ |
| 16 | |
| 17 | * Chura Hall (3F) |
| 18 | |
| 19 | |
| 20 | Presentations ¶ |
| 21 | |
| 22 | Fill: |
| 23 | |
| 24 | * Name of the presenter |
| 25 | o Title of the talk |
| 26 | o Attachments (PPT or PDF slides etc.) |
| 27 | |
| 28 | Notes ¶ |
| 29 | |
| 30 | |
| 31 | |
| 32 | Log of use-case workgroup |
| 33 | |
| 34 | Data |
| 35 | -SNPs, Affy provided by Prof.Kim |
| 36 | SNPs data come from Affymatrix chip of stroke patients and normal people (contain 262,338 SNPs) |
| 37 | |
| 38 | - ANNOTATOR currently cannot analyse on SNPs data directly |
| 39 | - Galaxy (http://galaxy.esphealth.org/) RGenetics |
| 40 | quality control, ancestry and case-control analysis |
| 41 | - BioMart |
| 42 | |
| 43 | BioMart |
| 44 | - have to know dataset, filter, attribute |
| 45 | - can use Perl API,.. |
| 46 | - Martview |
| 47 | - DAS access |
| 48 | - Martview |
| 49 | - can set up server and use in-house |
| 50 | |
| 51 | Question |
| 52 | - Takeshi asked about how to annoate in-house data with comparing with public genome data using BioMart. |
| 53 | - For example, how to annotate Halocynthia roretzi or Molgula tectiformis ESTs comparing with Ciona intestinalis and Ciona savigni using BioMart. |
| 54 | Answer |
| 55 | - Convert Halocynthia data into BioMart format. Install BioMart server locally. Then merge public DB and local data together. |
| 56 | - BioMart format is simple. |
| 57 | |
| 58 | |
| 59 | Takeshi present |
| 60 | - minor animal (closet animal Ciona) |
| 61 | - how can analyze Halocynthia roretzi and M.tectiformis which are rare annotation. |
| 62 | - type of data is ESTs, assembled EST cluster,,,etc,, |
| 63 | - potential flow: BioMart -> ANNOTATOR -> TogoDB |
| 64 | |
| 65 | DL ESTs of Halocynthia roretzi from NCBI/Taxonomy |
| 66 | |
| 67 | TogoDB by Toshiaki |
| 68 | - upload table format (table services for uploading data will be able to access using WS) |
| 69 | |
| 70 | |
| 71 | jORCA by Oswaldo |
| 72 | |
| 73 | -mapped WABI services |
| 74 | - jORCA: WABI WSDL application can run in local machine after installation |
| 75 | - jORCA can tell which kind of analysis can do with our multifasta format file or anykind of format. For example, using Magallanes: INB*, |
| 76 | if put "FASTA" in Find box, the result come up with 23 tools that can use for analysis. For analysis use myexperiment.org |
| 77 | *Magallanes: INB (Services discovering that discover what kind of analysis can provide for your data format) |
| 78 | |
| 79 | |
| 80 | ANNOTATOR |
| 81 | |
| 82 | - how different between ANNOTATOR and InterProscan |
| 83 | - how can I know the version of each DB use in Prim-seq-algorithm |
| 84 | - it would be nice if user |
| 85 | |
| 86 | |
| 87 | Results ¶ |
| 88 | |
| 89 | |
| 90 | TODOs ¶ |
| 91 | |
| 92 | |