Presented at UNM Data2Knowledge (D2K) Day, Albuquerque, New Mexico, Feb. 20, 2015.

1. The Language Diversity
of Computing
Or, how to talk with a computer.
Jeremy Yang
(Mgr., Systems & Programming)
Translational Informatics Div.
Dept. of Internal Medicine
University of New Mexico
UNM D2K Day -- Feb. 20, 2015 1

2. Language Diversity Examples
Python Perl
Natural
Language
Icons Menus
C++ Java APIs SQL Sparql
XML XSD XPath URLs bash
HTML HTTP ASCII UTF-8 regex
TCP/IP
Controlled
Vocabularies REST OWL RDF 2

3. A Working Definition of “Language”
● Coherent symbology (symbolic system)
3

4. 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)
4

5. Language merit vs. elitism
5

6. Why do we care about languages?
● Compatibility
● Efficiency
● Usability
● Knowledge
representation
● Intelligence
● Evolution
Of course we care. Duh!
6

7. Q: So what is the problem?
A: Language gaps
CODE
JARGON
MEANING
“Interpretation”
MATH
7

8. Q: So what is the problem?
A: Standards (so many!)
“Why can’t my iPhone talk to my ...”
● TV
● Audio system
● Car
● Medical records
8

9. Domain study: Languages of
Biomedical Knowledge
Computers learning and talking medicine 9

10. Our project:
Illuminating the Druggable Genome (IDG)
$4.9M
10

11. Illuminating the Druggable Genome
Knowledge Management Center (IDG-KMC)
Translational Informatics Division
Chief: Tudor Oprea, MD, PhD
IDG-KMC Workflow
11

12. Slide ℅ Tudor Oprea12

13. IDG-KMC Collaborator Network
13

14. IDG-KMC
Language
Challenge:
Case #1:
Drug
Nomenclature
14

15. IDG-KMC
Language
Challenge:
Case #2:
Disease
Ontology
17k codes in ICD-9.
155k codes in ICD-10.
Medical “coding” a
huge $ item.
15

16. 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”:
16

17. Language Diversity of Computers
Final Thought:
“Can we talk?”*
℅ Joan Rivers, 1933-2014
17