The Language Diversity of Computing

Or, how to talk with a computer.

Jeremy Yang(Mgr., Systems & Programming)

Translational Informatics Div.Dept. of Internal MedicineUniversity of New Mexico

UNM D2K Day -- Feb. 20, 2015 1

Language Diversity Examples

Python Perl NaturalLanguage Icons Menus

C++ Java APIs SQL Sparql

XML XSD XPath URLs bash

HTML HTTP ASCII UTF-8 regex

TCP/IP ControlledVocabularies REST OWL RDF 2

A Working Definition of “Language”

● Coherent symbology (symbolic system)

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Languages: Some major advances

● FORTRAN (1953)

● COBOL (1960)

● C (1969)● SQL (1979)

● WWW (~1990)

● Semantic Web (~2000)○ RDF○ Sparql○ OWL

● C++ (1979)● Perl (1987)● Python (1989)● Java (1995)

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Language merit vs. elitism

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Why do we care about languages?

● Compatibility● Efficiency● Usability

● Knowledge representation

● Intelligence● Evolution

Of course we care. Duh!6

Q: So what is the problem?A: Language gaps

CODE

JARGON

MEANING

“Interpretation”

MATH

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Q: So what is the problem?A: Standards (so many!)

“Why can’t my iPhone talk to my ...”

● TV● Audio system● Car● Medical records

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Domain study: Languages of Biomedical Knowledge

Computers learning and talking medicine9

Our project:Illuminating the Druggable Genome (IDG)

$4.9M10

Illuminating the Druggable GenomeKnowledge Management Center (IDG-KMC)

Translational Informatics DivisionChief: Tudor Oprea, MD, PhD

IDG-KMC Workflow

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Slide ℅ Tudor Oprea12

IDG-KMC Collaborator Network

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IDG-KMC Language Challenge:Case #1: Drug Nomenclature

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IDG-KMC Language Challenge:Case #2:Disease Ontology

17k codes in ICD-9.155k codes in ICD-10.Medical “coding” a huge $ item.

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TCRD - Target Central Research Db+------------+------------+--------+------+--------------------------------------------------------------------+--------+--------+| doid | Disease | zscore | conf | Protein | idgfam | tdl |+------------+------------+--------+------+--------------------------------------------------------------------+--------+--------+| DOID:13189 | Gout | 3.512 | 1.8 | alpha-kinase 1 | Kinase | Tmacro || DOID:13189 | Gout | 3.214 | 1.6 | salt-inducible kinase 1 | Kinase | Tclin || DOID:13189 | Gout | 2.922 | 1.5 | melanocortin 3 receptor | GPCR | Tclin || DOID:13189 | Gout | 3.036 | 1.5 | olfactory receptor, family 2, subfamily M, member 3 | GPCR | Tdark || DOID:13189 | Gout | 2.797 | 1.4 | taste receptor, type 2, member 30 | GPCR | Tdark || DOID:13189 | Gout | 2.576 | 1.3 | taste receptor, type 2, member 16 | GPCR | Tmacro || DOID:13189 | Gout | 2.379 | 1.2 | hepatocyte nuclear factor 4, gamma | NR | Tgray || DOID:13189 | Gout | 2.441 | 1.2 | spleen tyrosine kinase | Kinase | Tclin || DOID:13189 | Gout | 1.948 | 1.0 | protein kinase, cGMP-dependent, type II | Kinase | Tclin || DOID:13189 | Gout | 1.798 | 0.9 | pannexin 1 | IC | Tmacro || DOID:13189 | Gout | 1.531 | 0.8 | transient receptor potential cation channel, subfamily V, member 1 | IC | Tclin+ || DOID:13189 | Gout | 1.517 | 0.8 | taste receptor, type 2, member 38 | GPCR | Tmacro || DOID:13189 | Gout | 1.565 | 0.8 | transient receptor potential cation channel, subfamily A, member 1 | IC | Tclin+ || DOID:13189 | Gout | 1.375 | 0.7 | transient receptor potential cation channel, subfamily M, member 3 | IC | Tmacro || DOID:13189 | Gout | 1.427 | 0.7 | interleukin-1 receptor-associated kinase 1 | Kinase | Tclin || DOID:13189 | Gout | 1.388 | 0.7 | adenosine kinase | Kinase | Tclin || DOID:1156 | Pseudogout | 2.410 | 1.2 | chloride channel, voltage-sensitive Kb | IC | Tmacro || DOID:1156 | Pseudogout | 2.423 | 1.2 | purinergic receptor P2Y, G-protein coupled, 11 | GPCR | Tchem || DOID:1156 | Pseudogout | 1.742 | 0.9 | calcium-sensing receptor | GPCR | Tclin+ || DOID:1156 | Pseudogout | 1.767 | 0.9 | activin A receptor, type I | Kinase | Tclin || DOID:1156 | Pseudogout | 1.454 | 0.7 | purinergic receptor P2Y, G-protein coupled, 2 | GPCR | Tclin+ |+------------+------------+--------+------+--------------------------------------------------------------------+--------+--------+

Sample query for disease substring “gout”:

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Language Diversity of Computers

Final Thought:

“Can we talk?”*

℅ Joan Rivers, 1933-201417