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TMRA 2008: OpenSpace session: Dense Topic Maps
2008-10-17




                  Dense Topic Maps




                     Xuân Baldauf <xuan--dtm--2008--tmra.de@baldauf.org>   1 of 7
TMRA 2008: OpenSpace session: Dense Topic Maps
2008-10-17




             Use Case: Annotate DNA
  Lifescience analyzes DNA
  produces multiple gigabytes per day
  for each base, following information is produced:
       type:         Is it A,C,G,T?
       probability: How probable is that it is what we believe it is?
  Current custom format:                       5 bytes per DNA base
       type:         1 byte
       probability: 4 bytes
                     Xuân Baldauf <xuan--dtm--2008--tmra.de@baldauf.org>   2 of 7
TMRA 2008: OpenSpace session: Dense Topic Maps
2008-10-17




                       as Topic Maps
    How to represent a DNA base which
         is a Thymine base
             with a probability of 99.6710%
         is at offset 938457
    as
         XTM?
         CTM?



                     Xuân Baldauf <xuan--dtm--2008--tmra.de@baldauf.org>   3 of 7
TMRA 2008: OpenSpace session: Dense Topic Maps
2008-10-17




                                as XTM 2.0
<topic id=quot;base938457quot;>
  <occurrence>
    <type><topicRef href=quot;#offsetquot;/></type>
    <resourceData datatype=quot;http://www.w3.org/2001/XMLSchema#integerquot;>938457</resourceData>
  </occurrence>
</topic>
<association reifier=quot;#base938457isaTquot;>
  <type><topicRef href=quot;#type-instancequot;/></type>
  <role>
    <type><topicRef href=quot;#typequot;/></type>
    <topicRef href=quot;#Tquot;/>
  </role>
  <role>
    <type><topicRef href=quot;#instancequot;/></type>
    <topicRef href=quot;#base938457quot;/>
  </role>
</association>
<topic id=quot;base938457isaTquot;>
  <occurrence>
    <type><topicRef href=quot;#probabilityquot;/></type>
    <resourceData datatype=quot;http://www.w3.org/2001/XMLSchema#decimalquot;>0.996710</resourceData>
  </occurrence>
</topic>


683 bytes per DNA base                                                bloat factor: 136.6
                         Xuân Baldauf <xuan--dtm--2008--tmra.de@baldauf.org>                    4 of 7
TMRA 2008: OpenSpace session: Dense Topic Maps
2008-10-17




                                  as CTM
base938457
  base_info(T,0.996710,938457).

42 bytes per DNA base                                                  bloat factor: 8.4
FYI: CTM template
    def base_info($base,$basetype,$probability,$offset)
      $base
        offset: $offset.
      type-instance(type: $basetype,instance: $base) ~ [
        probability: $probability
      ]
    end


                     Xuân Baldauf <xuan--dtm--2008--tmra.de@baldauf.org>             5 of 7
TMRA 2008: OpenSpace session: Dense Topic Maps
2008-10-17




                                  as DTM
0x543f7f2863
     0x54 = quot;Tquot;
     0x3f7f2863 = 0.996710

5 bytes per DNA base                                                  bloat factor: 1.0
How is this a Topic Map?
     Define a Dense Topic Map Format specification for a
      particular dense format



                     Xuân Baldauf <xuan--dtm--2008--tmra.de@baldauf.org>             6 of 7
TMRA 2008: OpenSpace session: Dense Topic Maps
2008-10-17




                                     Why?
    good-to-perfect compression
    allows a migration path from many custom data
    formats to Topic Maps
    allows a (limited) migration path to many custom
    data formats from Topic Maps




                     Xuân Baldauf <xuan--dtm--2008--tmra.de@baldauf.org>   7 of 7

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Dense Topic Maps

  • 1. TMRA 2008: OpenSpace session: Dense Topic Maps 2008-10-17 Dense Topic Maps Xuân Baldauf <xuan--dtm--2008--tmra.de@baldauf.org> 1 of 7
  • 2. TMRA 2008: OpenSpace session: Dense Topic Maps 2008-10-17 Use Case: Annotate DNA Lifescience analyzes DNA produces multiple gigabytes per day for each base, following information is produced: type: Is it A,C,G,T? probability: How probable is that it is what we believe it is? Current custom format: 5 bytes per DNA base type: 1 byte probability: 4 bytes Xuân Baldauf <xuan--dtm--2008--tmra.de@baldauf.org> 2 of 7
  • 3. TMRA 2008: OpenSpace session: Dense Topic Maps 2008-10-17 as Topic Maps How to represent a DNA base which is a Thymine base with a probability of 99.6710% is at offset 938457 as XTM? CTM? Xuân Baldauf <xuan--dtm--2008--tmra.de@baldauf.org> 3 of 7
  • 4. TMRA 2008: OpenSpace session: Dense Topic Maps 2008-10-17 as XTM 2.0 <topic id=quot;base938457quot;> <occurrence> <type><topicRef href=quot;#offsetquot;/></type> <resourceData datatype=quot;http://www.w3.org/2001/XMLSchema#integerquot;>938457</resourceData> </occurrence> </topic> <association reifier=quot;#base938457isaTquot;> <type><topicRef href=quot;#type-instancequot;/></type> <role> <type><topicRef href=quot;#typequot;/></type> <topicRef href=quot;#Tquot;/> </role> <role> <type><topicRef href=quot;#instancequot;/></type> <topicRef href=quot;#base938457quot;/> </role> </association> <topic id=quot;base938457isaTquot;> <occurrence> <type><topicRef href=quot;#probabilityquot;/></type> <resourceData datatype=quot;http://www.w3.org/2001/XMLSchema#decimalquot;>0.996710</resourceData> </occurrence> </topic> 683 bytes per DNA base bloat factor: 136.6 Xuân Baldauf <xuan--dtm--2008--tmra.de@baldauf.org> 4 of 7
  • 5. TMRA 2008: OpenSpace session: Dense Topic Maps 2008-10-17 as CTM base938457 base_info(T,0.996710,938457). 42 bytes per DNA base bloat factor: 8.4 FYI: CTM template def base_info($base,$basetype,$probability,$offset) $base offset: $offset. type-instance(type: $basetype,instance: $base) ~ [ probability: $probability ] end Xuân Baldauf <xuan--dtm--2008--tmra.de@baldauf.org> 5 of 7
  • 6. TMRA 2008: OpenSpace session: Dense Topic Maps 2008-10-17 as DTM 0x543f7f2863 0x54 = quot;Tquot; 0x3f7f2863 = 0.996710 5 bytes per DNA base bloat factor: 1.0 How is this a Topic Map? Define a Dense Topic Map Format specification for a particular dense format Xuân Baldauf <xuan--dtm--2008--tmra.de@baldauf.org> 6 of 7
  • 7. TMRA 2008: OpenSpace session: Dense Topic Maps 2008-10-17 Why? good-to-perfect compression allows a migration path from many custom data formats to Topic Maps allows a (limited) migration path to many custom data formats from Topic Maps Xuân Baldauf <xuan--dtm--2008--tmra.de@baldauf.org> 7 of 7