Why, in the future, all Why, in the future, all sciences will be sciences will be

computer sciencescomputer sciences

Barry SmithBarry Smith

PythagoreanismPythagoreanism

Analogue vs. digitalAnalogue vs. digital Quantum physics: The world is a Quantum physics: The world is a

digital objectdigital object The science of digital objects as The science of digital objects as

Master ScienceMaster Science

All science is computer All science is computer sciencescience

~ All science is laboratory science~ All science is laboratory science All intellectual disciplines are All intellectual disciplines are

computer sciencecomputer science

ClassicsClassics

Thesaurus Linguae GraecaeThesaurus Linguae Graecae

digitised versions of all extant Greek digitised versions of all extant Greek texts from Homer to 600 ADtexts from Homer to 600 AD

Computer as (indisensable tool)Computer as (indisensable tool)

ArcheologyArcheology

Registry of all extant pre-historical Registry of all extant pre-historical artefactsartefacts

HistoryHistory

Cavalli-Sforza (languages, dialects, Cavalli-Sforza (languages, dialects, mapped to DNA) mapped to DNA)

HistoryHistory

How far can we document every How far can we document every single human being in the entire single human being in the entire history of the planet?history of the planet?

The Sykes’ shared Y chromosomeThe Sykes’ shared Y chromosome Scientific geneaology: The promise of Scientific geneaology: The promise of

MormonismMormonism How far can we document every How far can we document every

single historical event in the entire single historical event in the entire history of the planet?history of the planet?

Increasingly, both Increasingly, both linguistics and history linguistics and history overlap with biologyoverlap with biology

Medicine, too, increasingly overlaps Medicine, too, increasingly overlaps with biology (becomes biomedicine)with biology (becomes biomedicine)

and with chemistry (the legacy of and with chemistry (the legacy of the Human Genome Project)the Human Genome Project)

(knowledge intensive vs. theory (knowledge intensive vs. theory intensive disciplines)intensive disciplines)

increasingly, all these disciplines increasingly, all these disciplines become like astronomybecome like astronomy

Part I: The Human Genome Part I: The Human Genome ProjectProject

Completed in 2003Completed in 2003 Goals:Goals:

identify all the approximately 20,000-identify all the approximately 20,000-25,000 genes in human DNA, 25,000 genes in human DNA,

determine the sequences of the 3 billion determine the sequences of the 3 billion chemical base pairs that make up human chemical base pairs that make up human DNA, DNA,

store this information in databases, store this information in databases, improve tools for compuational data improve tools for compuational data

analysis analysis

ComplexityComplexity

About 25,000 genes in a humanAbout 25,000 genes in a human 100-200,000 proteins100-200,000 proteins Individual variation in most Individual variation in most

genesgenes 100s of cell types100s of cell types 100,000s of disease types 100,000s of disease types

From Gene to DiseaseFrom Gene to Disease

Biochemical Disease Biochemical Disease PathwaysPathways

Alzheimer Pathway

Electronic Health Electronic Health RecordsRecords

Personalized medicinePersonalized medicine

gene therapy / manipulationgene therapy / manipulation the addition of new genes to existing the addition of new genes to existing

humanshumans the creation of new types of humansthe creation of new types of humans

drugs tailored to your genetic make-drugs tailored to your genetic make-upup improved efficacy improved efficacy reduced side-effectsreduced side-effects

based on home genetic testing (the based on home genetic testing (the $1000 genome)$1000 genome)

genomicsgenomics proteomicsproteomics reactomics reactomics metabonomics metabonomics phenomicsphenomics behavioromicsbehavioromics connectomicsconnectomics toxicopharmacogenomicstoxicopharmacogenomics

Terabytes of dataTerabytes of data

-omics data-omics data biochemical disease pathway databiochemical disease pathway data biomedical image databiomedical image data electronic health record dataelectronic health record data hospital management datahospital management data hospital insurance datahospital insurance data public health datapublic health data Chinese chicken dataChinese chicken data

Terabytes of dataTerabytes of data

TheThe ideal ideal of seamless of seamless communicationcommunication

Electronic Health Record

(EHR) Data

Hospital Process Ontology

(+billing services)

SNOMED

GALENGO

a vast new a vast new problem of problem of communicationcommunication

medical researchers, clinical medical researchers, clinical practitioners, first responders, practitioners, first responders, customs agencies, customs agencies, pharmaceutical companies, pharmaceutical companies, disease control centers need to disease control centers need to communicate in ways which communicate in ways which involve huge amounts of datainvolve huge amounts of data

... have created a vast new ... have created a vast new problem of communicationproblem of communication

What happens when medical What happens when medical researchers, or pharmaceutical researchers, or pharmaceutical companies, or government companies, or government healthcare agencies, work healthcare agencies, work primarily with data inside primarily with data inside computers?computers?

How can we overcome the How can we overcome the incompatibilities which arise incompatibilities which arise when data from distinct sources when data from distinct sources need to be combined, if each need to be combined, if each information system uses its own information system uses its own classification ?classification ?

Answer from Tim Answer from Tim Berners-Lee:Berners-Lee:

The Semantic The Semantic WebWeb

National Center for National Center for Biomedical OntologyBiomedical Ontology

Stanford University Medical Stanford University Medical InformaticsInformatics

Mayo ClinicMayo Clinic Berkeley Fly Genome ProjectBerkeley Fly Genome Project Cambridge University Department of Cambridge University Department of

GeneticsGenetics University at Buffalo Department of University at Buffalo Department of

PhilosophyPhilosophy