using knowledge engineering to study the brain gully apc burns knowledge mechanics research group,...
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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.