Using knowledge engineering to study the brain

Using knowledge engineering to study the brain

Gully APC BurnsKnowledge Mechanics Research Group,

University of Southern California

Gully APC BurnsKnowledge Mechanics Research Group,

University of Southern California

Using knowledge engineering to study the brain

Using knowledge engineering to study the brain

Gully APC BurnsKnowledge Mechanics Research Group,

University of Southern California

Gully APC BurnsKnowledge Mechanics Research Group,

University of Southern California

“…most complex thing we have yet discovered in our universe”

James Watson

“…most complex thing we have yet discovered in our universe”

James Watson

Neuroscience traverses several spatial orders of magnitude

Neuroscience traverses several spatial orders of magnitude

Whole animal

‘System’ (e.g. visual system)Brain region

Cell population

Whole cell

Organelles

Molecular signaling

GeneticsG. Shepherd (1994) Neurobiology

The number of components in the brain is literally astronomical

The number of components in the brain is literally astronomical

Whole animal‘System’ (e.g. visual system)Brain region

Cell population

Whole cell

Organelles

Molecular signaling

Genetics

In Rat~ 103 regions~ 104 neuronal cell-types~ 250,000 projections between neuronal cell types

~ 108 neurons~ 1011 synapses

~ ??? proteins~ ??? pathways

Rat genome has 2.75 Gb

It involves a large number of sub-disciplines

It involves a large number of sub-disciplines

Whole animal‘System’ (e.g. visual system)Brain region

Cell population

Whole cell

Organelles

Molecular signaling

Genetics

Anatomy

Physiology Ethology

Molecular BiologyMolecular Biology

Neurochemistry

Biophysics

The neuroscience communityThe neuroscience community

Society for Neuroscience ~34,000 members.

Mostly non-computational

Neuroscience Database Gateway (NDG) has 73 separate ‘neuroinformatics’ projects in different fields (http://big.sfn.org/NDG)

Community is hungry for informatics solutions but knowledge acquisition still a prime concern

Neuroinformatics is…Neuroinformatics is…

… ‘the information science infrastructure of neuroscience’

( editorial from inaugural issue of the Journal ‘Neuroinformatics’ )

… hold on a sec! Doesn’t neuroscience already have an ‘information science infrastructure’ already?

The Neuroscientific LiteratureThe Neuroscientific Literature

… is the end-product of scientific research

… forms the basis for human understanding of the subject

… is structured

… is interpretable

… is phenomenally expensive to produce

… is difficult to track and use

… is terse

Image taken from U.S. Geological Survey Energy Resource Surveys Program

Unpublished knowledge forms a huge resource within a laboratory

Unpublished knowledge forms a huge resource within a laboratory

Notes Laboratory notebooks Data files In-house documentation Powerpoint presentations Word-of-mouth / conversation

NeuroScholar’s approach to the literature

NeuroScholar’s approach to the literature

‘Fact A’

‘Fact B’

‘Fact C’

‘Interpretation A*’

‘Interpretation B*’

‘Interpretation C*’

‘Relation BC*’

This approach may be generalizedThis approach may be generalized

‘Fact A’

‘Fact B’

‘Fact C’

‘Interpretation A*’

‘Interpretation B*’

‘Interpretation C*’

‘Relation BC*’

All design work built in UMLAll design work built in UML

CV

name : string(10)context : string(255)description : string(-)

(from persistantData)

authorOrder

order : int32(from bibliography)

Excerpt

bl_x : int32 = 0bl_y : int32 = 0tr_x : int32 = 0tr_y : int32 = 0li_x : int32 = 0li_y : int32 = 0ri_x : int32 = 0ri_y : int32 = 0annotation : stringpagenumber : int32

enclose_excerpt()enclose_corner_area()

(from bibliography)

Author

FirstName : StringMiddleName : StringLastName : StringCollecttiveName : StringSuffix : StringAffiliation : String

(from bibliography)

Journal

PublisherName : StringJournalTitle : StringIssn : String

(from bibliography)

Article

ArticleTitle : string(255)VernacularTitle : string(-)

FirstPage : int32LastPage : int32Language : object(CV)Volume : int32Issue : int32PubDate : datePublicationType : object(CV)ArticleID : StringPMID : int32Abstract : Stringsize : int32checksum : String

(from bibliography)

1..n

1..n

+authorList1..n

+publishedW...

1..n

1

0..*

+journal

1

0..*

Fragment

fragment_type : object(CV)annotation : Stringkeywords : String

(from bibliography)

1

1..n +fragment

1+excerpts

1..n

0..n

1

+fragments0..n

+publication 1

UML packages & classes…

Knowledge sharing architectureKnowledge sharing architecture

PubMed & the literaturePubMed & the literature

Accessing the contents of pdfsAccessing the contents of pdfs

Diagrams in NeuroScholarDiagrams in NeuroScholar

Other systems: ‘NeuroAtlas’Other systems: ‘NeuroAtlas’

Not currently available pending resolution of copyright issues with atlas publishers

www.neuroscholar.orgwww.neuroscholar.org

www.sourceforge.net/projects/neuroscholarwww.sourceforge.net/projects/neuroscholar

Open QuestionsOpen Questions

Build better, faster, larger plumbing help!

Seeking access to (and building our own) analysis techniques for knowledge base contents help!

AcknowledgementsAcknowledgements

This work is funded by the National Library of Medicine (LM07061)Arshad KhanLori HowardKim RappJoel HahnMihail Bota

Alan WattsLarry Swanson

Wei Cheng ChenShyam KapadiaYi-Shin Chen

Shahram Ghandehanderazdeh Cyrus Shahabi

Mark O’Neill

“It is easy to impose a pattern

less easy to make it

stickless still

to discover one there.”

“It is easy to impose a pattern

less easy to make it

stickless still

to discover one there.”

‘Building a snowman’. Richard Burns.

‘Building a snowman’. Richard Burns.