Optimizing Our Data and Time

http://www.w3.org/2015/Talks/0922-rda-egp/

Eric Prud'hommeaux, <eric@w3.org>
- Sanitation Engineer, W3C

Data Value

Data utility depends on whether it

Directs our actions
- improves research
- saves money
- improves environment
- improves lives
- saves lives
Affects our confidence
Costs less than the value it provides

Data dimensions

Size of population
Coverage of population
Phenotypic breadth

Size/Structure (false) dichotomy

Data Availability

Permitted to see it -- license/policy
Physically reachable -- publication/distribution
Understandable -- published model/semantics
Machine-readable -- consistent, unambiguous representation
Temporally available -- use it before the sun burns out
Interconnectable -- consistent with other data

Lower barrier to investigation.
Data for far-sighted decisions.
Democratize innovation.

Data scale

Growing data size:

imaging: PET scans, CT scans, FMRI
molecular diagnostics
genome (3 billion base pairs)
biome (300 billion base pairs)

Growing data vectors:

next-generation (post-Sanger) sequencing. (name stuck to Moores law?)
online genomics services: Navigenics, 23andMe and Helix Health
online support communities: CureTogether, patientslikeme
virtual visits: American Well, Cisco HealthPresence, RelayHealth, Teladoc, Medfusion Virtual Office
remote clinical devices: RP-7i (robo-nurse), iPill
commodity clinics: minute clinic (CVS), take care clinic (Walgreens), RediClinic (H-E-B), Target Clinic, The Little Clinic
consumer devices: asthma-charter, USB chip for STDs, glucose meter, urinalysis

Three forms of standards:

syntactic standards:
fax-level interoperability shares data between humans.
HTML's ubiquitous rendering is a great success.
semantic standards:
code systems, data types and value sets.
human eyes not required.
Semantic Web-based standards:
use RDF, OWL, Web architecture etc. in definitions and data.
leverage growing body of standards and expertise.

Semantic standards:

Reduce the n² pressure.

hundreds of partially-overlapping formats.
no forum for collaborative mapping.
many mappings are use-case-dependent.
reduce risk to entrepreneurs.
foster interesting innovation.

Semantic Web standards:

further reduce the n² pressure.

homogeneous medium for different standards.
enable distributed, progressive standardization.
reduce cost of standards.
tools and conventions apply to al standards.
- query - SPARQL
- description logic - OWL
- rules - RIF, SWRL
- validation - ShEx/SHACL

Clinical Informatics: connected models

information model
(Concepts and Relationships)
- Observations
- AdverseEvents
- Substance Administrations
on patient Isabella Jones
terminology model
(Terms and Relationships)
- Pneumonia a Pulmonary Disease
- Serum Sodium a lab test
- Penicillin an antibiotic
value sets
- Pneumonia, SLE, CHF
- mild, medium, severe
datatypes
- dates
- times
- intervals

Lay pipes and conduit

invent models
record as schemas
socialize
socialize
socialize

... to provide homogeneous interfaces ...

:subjectspostOpDay3GFR a rrej:RenalFunctionObservation ;
    mm:observationTime "2013-07-08T14:50:00"^^xsd:dateTime ;
    rrej:gfrFlowRate [ data:value 12.0 ; data:units ucum:mL-per-minute ].

Would be in a table with codes in an EMR:

obs id	when	coding system	ObsCode	value	units	addressing…performer…
1234	2013-07-08T14:50:00	CPT	82565	12	mL-per-minute
5678	2013-07-08T14:50:00	SNOMED 2014-01-01	241374009	12	mL-per-minute
4321	2013-07-08T14:50:00	LOINC	48643-1	12	mL-per-minute

or C-CDA:

<observation classCode="OBS" moodCode="EVN">
  <code code="48643-1" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC"
        displayName="Glomerular filtration rate/1.73 sq M.predicted.black" />
  <effectiveTime value="201307081450"/>
  <value type="PQ" value="12.0" unit="mL/min"/>
  <interpretationCode/>
  <referenceRange />
</observation>

... so mashups become queries

SERVICE <http://uu3.org:8888/7tm_receptors>
  {
    ?iuphar  iface:family      ?family .
    ?iuphar  iface:code	       ?code .
    ?iuphar  iface:iupharName  ?iupharNm .
    ?human   iface:iuphar      ?iuphar .
    ?human   iface:geneName    "GABBR1" .
    ?human   iface:entrezGene  ?humanEntrez .
  }
SERVICE <http://dbpedia.org/sparql?default-graph-uri=http%3A%2F%2Fdbpedia.org&>

  {
     _:gene  dbp:entrezgene    ?humanEntrez ;
             rdfs:label        ?label ;
    FILTER (lang(?label) = "en")
  }
SERVICE <http://hcls.deri.org/atag/data/gabab_example.html>
  {
     ?topic  rdfs:label        ?label .
     ?post   sioc:topic        ?topic
  }

Don't have too much fun

	Learn	Invent
idiom	embrace	extend
costs	apparent	hidden

SemWeb makes invention too easy and safe.

Try stuff out, ask questions, fix other peoples' stuff.

When I understand a model well enough to criticize it,
only then do I understand it well enough to use it.

the Pain of Re-use

Portable BRIDG Representation

Motivations

?
?
!

Thank you

Come geek with us in the W3C Semantic Web in Health Care and Life Sciences IG