Bespoke	  data	  integra/on	  using	  open	    source	  &	  seman/c	  technologies    	           Nadia	  Anwar,	  Mar/jn	...
What	  do	  we	  do?	  Direct	  support	  of	  scien.sts	  in	  research	  Data	  Acquisi.on,	  Management	  and	  Steward...
Goals                                                  	      Integrate	  data	       -    Typically,	  using	  linked	  ...
You	  have	  data,	  I	  have	  data...now	  what?	             * Adapted from http://xkcd.com/208/ (CC-BY-NC)            ...
hVp://fly.cloud.generalbioinforma/cs.com	    FlyAtlas    FlyCyc                         1) Transform	  into	  triples	     ...
1st	  you	  need	  some	  triples	                     Expert	  Bioinforma/cs	  from	  Bioinforma/cs	  Experts	  
Then,	  you	  need	  some	  magic                                                      	      Transi/ve	  Proper/es	     ...
Next,	  the	  preVy	  bit:	  Visualisa/on	      PathVisio	                                        Cytoscape	            ...
Finally...                          	  Expert	  Bioinforma/cs	  from	  Bioinforma/cs	  Experts	  
<Posi/on	  about:Flexiblilty/>	      Flexible	  data	  integra/on	        -    Use	  Linked	  Data	        -    Use	  Ide...
We	  are	  hiring!                          	  www.generalbioinforma/cs.com   	      Nadia	  Anwar,	  Mar/jn	  van	  Ierse...
Upcoming SlideShare
Loading in …5
×

Swat4 ls2012

199 views

Published on

0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
199
On SlideShare
0
From Embeds
0
Number of Embeds
7
Actions
Shares
0
Downloads
0
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Swat4 ls2012

  1. 1. Bespoke  data  integra/on  using  open   source  &  seman/c  technologies   Nadia  Anwar,  Mar/jn  van  Iersel  
  2. 2. What  do  we  do?  Direct  support  of  scien.sts  in  research  Data  Acquisi.on,  Management  and  Stewardship  Data  Integra.on  Answering  specific  and  complex  Bioinforma.cs  ques.ons  Tool  kit  deployment  and  maintenance  for  use  in-­‐house  
  3. 3. Goals    Integrate  data   -  Typically,  using  linked  data    Answer  biological  ques/ons   -  Through  useful  visualisa/ons      Reproducible   -  Everything  is  scripted,  version  controlled  and  tracked    Flexible   -  Using  Mul/ple  Specialized  Tools   Expert  Bioinforma/cs  from  Bioinforma/cs  Experts  
  4. 4. You  have  data,  I  have  data...now  what?   * Adapted from http://xkcd.com/208/ (CC-BY-NC) Expert  Bioinforma/cs  from  Bioinforma/cs  Experts  
  5. 5. hVp://fly.cloud.generalbioinforma/cs.com   FlyAtlas FlyCyc 1) Transform  into  triples     Fly  Expression  Data     Fly  Pathway  Data   2)   Infer  some  more  triples   3)   Visualize  triples      Pathways      Networks   Expert  Bioinforma/cs  from  Bioinforma/cs  Experts  
  6. 6. 1st  you  need  some  triples   Expert  Bioinforma/cs  from  Bioinforma/cs  Experts  
  7. 7. Then,  you  need  some  magic    Transi/ve  Proper/es     flyatlas:ProbeData   -  A-­‐B-­‐C  →  A-­‐C   subclass  BP:DNAregion    Class  Subsump/on   -  FlyAtlas  to  BioPAX     flyatlas:1234_at  is  a   flyatlas:ProbeData,      Node  Integra/on   -  iden/fiers.org  URIs     flatlas:1234_at  is  a   BP:DNARegion     Expert  Bioinforma/cs  from  Bioinforma/cs  Experts  
  8. 8. Next,  the  preVy  bit:  Visualisa/on    PathVisio     Cytoscape     And  other  views  ….   Expert  Bioinforma/cs  from  Bioinforma/cs  Experts  
  9. 9. Finally...  Expert  Bioinforma/cs  from  Bioinforma/cs  Experts  
  10. 10. <Posi/on  about:Flexiblilty/>    Flexible  data  integra/on   -  Use  Linked  Data   -  Use  Iden/fiers.org   -  Don’t  be  afraid  to  extend  Ontologies,  that’s  the  point     -  Be  reasonable  with  what  you  integrate,  you  can  always   add  more  later...    Use  tools  that  best  answers  the  biological  ques/ons    Script  everything,  you  will  probably  have  to  redo  it!    It  needs  to  be  flexible,  this  is  research  and  is  not   about  building  the  best  Enterprise  like  “one  fits  all”   solu/on.     Expert  Bioinforma/cs  from  Bioinforma/cs  Experts  
  11. 11. We  are  hiring!  www.generalbioinforma/cs.com   Nadia  Anwar,  Mar/jn  van  Iersel   Expert  Bioinforma/cs  from  Bioinforma/cs  Experts  

×