Presentation for the open space session of TMRA 2008, International Conference on Topic Maps Research and Applications, Leipzig, Germany.

1. TMRA 2008: OpenSpace session: Dense Topic Maps
2008-10-17
Dense Topic Maps
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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
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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?
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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
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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
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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
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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
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