Overview
• Brief overview of NIF philosophy• Examples of data about addiction• Why you should never use google to
answer any scientific question• How can we make google better?
Power!
• How many subject/patients do we need to be relatively certain that we are correct?
• More than you can afford?
• If YFGM gave each of you 1B dollars, would that solve the problem?
• But, what if:– Big data from small data?
Solving the large problems of science?
• Observation• Experimentation• Modeling• Cooperative data
intensive science
• NIF is an initiative of the NIH Blueprint consortium of institutes– What types of resources (data, tools, materials, services) are available to the
neuroscience community?– How many are there?– What domains do they cover? What domains do they not cover?– Where are they?
• Web sites• Databases• Literature• Supplementary material
– Who uses them?– Who creates them?– How can we find them?– How can we make them better in the future?
http://neuinfo.org
• PDF files
• Desk drawers
NIF: A New Type of Entity for New Modes of Scientific Dissemination
• NIF’s mission is to maximize the awareness of, access to and utility of digital resources produced worldwide to enable better science and promote efficient use– NIF unites neuroscience information without respect to domain, funding
agency, institute or community– NIF is a library for scholarly output that is a web enabled resource and
not a paper– Aggregates all the different databases, tools and resources now
produced by the scientific community– Makes them searchable from a single interface– A practical approach to the data deluge– Educate neuroscientists and students about effective data sharing
Surveying the resource landscape
NIF resource registry: listing of > 6000 databases, tools, materials, services, websites (> 2500 databases)
NIF data federation: Pub Med Central for data
NIF was designed to accommodate the multiplicity of heterogeneous and distributed data resources, providing deep query of the contents and unified views
200 sources> 360 M records
NIF Semantic Framework: NIFSTD ontology
• NIF covers multiple structural scales and domains of relevance to neuroscience• Aggregate of community ontologies with some extensions for neuroscience, e.g., Gene
Ontology, Chebi, Protein Ontology
NIFSTD
Organism
NS FunctionMolecule InvestigationSubcellular structure
Macromolecule Gene
Molecule Descriptors
Techniques
Reagent Protocols
Cell
Resource Instrument
Dysfunction QualityAnatomical Structure
Ontologies provide the universals for integrating across disparate data by linking them to human knowledge models
Neurolex: Machine-processable concepts for neuroscience
• Machine-processable lexical units
• Connected via relationships• Identified by a unique
identifier (URL)• Computable index for
neuroscience• Framework for linking
knowledge, claims and data
Built using a semantic wiki
NIF Analytics: The Neuroscience Landscape
Ontologies provide a semantic framework for understanding data/resource landscape
Where are the data?
StriatumHypothalamusOlfactory bulb
Cerebral cortex
Brain
Brai
n re
gion
Data source
Vadim Astakhov, Kepler Workflow Engine
Genetics of addiction?GeneProteinSubcellular componentsCellsCell microcircuitsCell macrocircuitsNetworksBrain regionsPNSWhole organismBehaving organism (environment)Networks of organismsPopulations
Genetics of addiction?GeneProteinSubcellular componentsCellsCell microcircuitsCell macrocircuitsNetworksBrain regionsPNSWhole organismBehaving organism (environment)Networks of organismsPopulations
Genetics of addiction?• Addiction is a disease of subpopulations of humans who take
sociologically undesirable drugs or sociologically desirable drugs at undesirable concentrations
• Drug is a molecule that does not exist in the body, an environmental factor
• Drugs are metabolized by the digestive system and act after crossing the BBB
• Drugs modify the activity of existing proteins on vastly different time scales
• Drugs modify behaviors that depend on the actions of an orchestra of neurons acting within circuits that all have a purpose that is not to take drugs
The ecosystem is diverse and messy (and that’s OK)
NIF favors a hybrid, tiered, federated system
• Domain knowledge– Ontologies
• Claims and observations– Virtuoso RDF triples
• Data– Data federation– Spatial data– Workflows
• Narrative– Full text access
Neuron Brain part DiseaseOrganism Gene
Caudate projects to Snpc Grm1 is upregulated in
chronic cocaineBetz cells
degenerate in ALS
Data Knowledge
Wish list: Cooperative science• A mission that will engage the entire neuroscience community
and beyond• An active community contribution model where everyone is
expected to contribute their outputs, not just a selected few– Diverse contributions are tracked and recognized– Spatial-semantic-genetic-temporal frameworks make data
discoverable-usable-integratable and help fill in the gaps
• A platform that moves neuroscience into the web– Networking data, knowledge, tools, models, efforts, people, compute
resources, simulation– Supports digital research objects as first order contributions, not just
narrative– Works through and with existing platforms to improve them where
possible
Cooperative system: “...individual components that appear to be “selfish” and independent work together to create a highly complex, greater-than-the-sum-of-its-parts system.”
20
neurolex.org
•INCF Community encyclopedia•Standardize vocabulary•Define all vocabulary, terms, protocols, brain structures, diseases, etc•Living review articles•Build and maintain working ontologiesLinks to data, models and literature•Semantic organization, search, analysis and integration•Global directory of all shared vocabularies, CDEs, etc
Slide courtesy of Sean Hill