translational research with the

farmpaintlickInternet and Web Development

Oct 21, 2013 (3 years and 7 months ago)

64 views

Advancing
translational
research with the
Semantic Web

Ruttenberg
, Clark, Bug,
Samwald
,
Bodenreider
, Chen, Doherty,
Forsberg,
Gao
,
Kashyap
, Kinoshita, Luciano, Marshall,
Ogbuji
,
Rees, Stephens, Wong, Wu,
Zaccagnini
,
Hongsermeier
,
Neumann, Herman, Cheung

Author Background


Many authors with diverse backgrounds:


Senior
s
cientist at pharmaceutical company (
Ruttenberg
)


Director of Bioinformatics at Harvard Univ. (Clark)


Neuroscientist and
informaticist

at Drexel Univ. (Bug)


Developer for Science Commons at MIT (
Samwald
)


Scientist at National Library of Medicine (
Bodenreider
)


Principal investigator at healthcare company (Chen)


Developer of ‘Semantic
Wb
’ iPhone app (Doherty)


Informatics scientist at pharmaceutical company (Forsberg)


Clinical instructor in neurology (
Gao
)


Senior Medical
Informatician

at healthcare company (
Kashyap
)


Alzheimer researcher (Kinoshita)





Author Background (Cont’d)


Lecturer on Genetics at Harvard Univ. (Luciano
)


Co
-
chair of HCLSIG (we’ll get to that later) (Marshall
)


Computer engineer at Case Western Univ. (
Ogbuji
)


Lead software engineer at pharmaceutical company (Rees
)


Director of Bioinformatics at Johnson & Johnson (Stephens
)


Alzheimer researcher (Wong)


Alzheimer researcher (Wu
)


VP of healthcare technology company (
Zaccagnini
)


Principle
Informatician

at healthcare company (
Hongsermeier
)


Senior Director of scientific data management co. (Neumann
)


Semantic Web Activity Lead at W3C (Herman
)


Associate Prof. of Computer Science & Genetics (Cheung
)


Definitions


Translational Research


the movement of discoveries in basic
research (the Bench) to application at the clinical level (the
Bedside)


Evidence
-
based medicine → solutions for public health problems


Information ecosystem


scientific literature, experimental
data, summaries of knowledge of gene products, diseases,
and compounds, and informal scientific discourse and
commentary in a variety of forums


The Semantic Web


an extension of the current Web that
enables navigation and meaningful use of digital resources by
automatic processes


Based on common formats supporting aggregation and
integration of data from diverse sources


Problems with the existing
Information Ecosystem


Lack of uniformly structured data


Often not interoperable; data can’t be used in combination with
data in other formats


“Data silos” concept


disconnected databases not used in
conjunction with one another


Data synthesis is necessary to cure and prevent diseases


Example: Parkinson’s Disease, Huntington’s Disease, and
Alzheimer’s Disease share clinical, neural, cellular, and molecular
traits

but specialists in each disease are often unaware of
important literature on the other diseases which could be related

Criteria for Solutions


Web
-
based


Queries across experimental data from different communities
of interest


Practicality


Linking and discovery of data interpretations need to be
supported


Tied to the scientific publication process and culture


Tied to both current and
evolving

processes

The Semantic Web


Triples



c
onsist of subject, predicate, and object


Subject: human TP53 gene


P
age describing the gene


Predicate:
hasGeneProduct


Page describing the relationship between them with a human
-
readable definition


Object: human TP53 MRNA


Page describing the object


Uniform Resource Identifier (URI)


string of characters used
to identify a name or a resource


Web URLs (Universal Resource Locators) are URIs


Networked computers are able to follow these, locate identical
(related) data references, and integrate knowledge

Semantic Web Technologies


Uniform naming of elements of discourse by URIs


Resource Description Framework (RDF)


gives formal
specification of the syntax and semantics of statements (triples)


Shared standards and technologies around these methods of
organization


SPARQL


standard query language for retrieving RDF
-
format
answers


Gleaning
Resource Descriptions from Dialects of Language
(GRDDL)


tool used to turn
XML data
into
RDF


Shared practices in using these standards and technologies

Applications to Biomedical
Research


Faster movement of innovation from research laboratory to clinic or
hospital


Utilizes the World Wide Web, the most successful information
dissemination and sharing apparatus in existence


URIs are global in scope


less effort will be spent developing
services to map gene identifiers to information about the gene


Common schema languages simplify management and
comprehension of complicated and rapidly
-
evolving relationships
among data


The subject, predicate, object structure itself can guide users towards
correct use of the data


Flexible, extendable, decentralized databases allow room for future
expansion of scientific knowledge


Ability to extend others’ work and build upon their data


Ability to check for consistency, classify, and inference


Less errors in diagnosis/treatment (clinical) and data analysis
(research)


Health Care and Life Sciences
Interest Group (HCLSIG)


How did you conceptualize the
medical examples?


How does HCLSIG hope to address
informaticians
’ potential
lack of specialized medical knowledge?


How did you conceptualize the
database syntax?


Again, I’m no expert

does anyone care to elaborate about
the parts of (SQL) syntax such as:


Will HCLSIG be able to utilize the resources of non
-
informatics
medical practitioners?