Communication between NIF and Resource Providers

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Communication between NIF and Resource Providers

• Overview of the Framework Components and their
  Interactions

Luis Marenco, M.D.
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Basic NIF Elements

• Resources Web accessible information/resources
  of Neuroscience content
• NIF Servers Applications integrating an specific
  type of resource in the framework
• NIF Integrators Applications leveraging NIF
  Servers to integrate several types of
  information
• Communication framework Set of protocols and
  practices to allow interactions between
  resources, servers and integrator applications

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1. Resources

• Some types of information to cover include
• Resource descriptions NIF registry
• Databases Database Mediator
• Semi structured free text - Journal articles
  Textpresso
• Vocabularies - Ontologies Bonfire
• Web pages - non derived from a DB Indexing
  engine Nutch
• Distributed applications or functions Web
  services Mediator
• Non-NIF Servers Proxy Services

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2. NIF Servers

• Initial set of applications consisted on
• Database Registry
• Ontology Services (Bonfire, TIS)
• Database Mediator
• Textpresso
• New NIF Servers
• Entrez LinkOut Broker

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3. NIF Integrators

• Concept Base Query Interfaces a) Structured
  (Prototype NIF Query Interfaces), b) Graphical
  (BIRN), and c) Free text (involving NLP)
• Ontological applications (plug-ins) to interact
  with the NIF ontology
• (e.g. Analyze the latest neuroscience knowledge
  map as perceived by the current integration of
  resources)
• Federated data-mining tools (?)
• Data crawlers (Tools to help indexing the
  hidden Web data)
• Alert systems Inform users of availability of
  new type of data

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4. Communication Framework

• Communication between NIF Elements.
• Resource to NIF Serves Use vendor/industry
  specific protocols (ODBC, XML, HTML, RDF etc)
• NIF Servers to NIF Integrators
• Currently use proprietary Web services
• Currently being cataloged and normalized to
  define the standard set of NIF Web Services
  (These will be required for new Resource
  Providers)

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4. Communication Framework (2)

• Interactions between the Concept Based Query
  Interface (NIF Integrator) and the underlying NIF
  Servers

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4. Communication Framework (3)

• Automated Registration
• Current prototype protocol (ndg.disco) It is a
  simple XML manifest file with explicit links to
  other type of self describing information
• Resource catalog Designed to auto populate DB
  registries
• Entrez Broker links Exports resources Entrez
  links to the NIF LinkOut repository DB
• Interoperability Describes Interoperable
  interfaces. Can be used to describe database
  Mediator registration parameters
• Terminology Exports database vocabularies .
  (Several uses)

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(NIF Entrez) LinkOut Broker

• Entrez LinkOut is a functionality provided by
  NCBI to allow links from objects in their
  databases (PubMed, ) to specific external Web
  pages (e.g. data related to a paper, protein,
  gene, etc)
• It is specific to each Web site in particular.
  Requires registration, data upload, and approval.

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(NIF Entrez) LinkOut Broker (2)

• SfN Interoperability subcommittee.
• Creating a repository for Entrez links of
  neuroscience content
• Moves registration and data upload to NIF
• Several programming steps are avoided.
• One single place to find all related neuroscience
  data (A level of data integration from multiple
  resources)
• Allows to further annotate each resources Entrez
  Links (e.g. Link categories)
• Minimizes the cluttering of new resources
  providers at NCBI

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Navigating to the LinkOut Broker
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Navigating to the LinkOut Broker (2)
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Navigating to the LinkOut Broker (3)

• http//128.36.123.938080/lb/linkoutToResources.do
  ?idPubMed16293591

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Navigating to the LinkOut Broker (4)
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Other LinkOut Broker Examples

• http//soma.med.yale.edu8080/lb/linkoutToResource
  s.do?idNucleotideNP_014085pacc

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Other LinkOut Broker Examples (2)

• http//soma.med.yale.edu8080/lb/linkoutToResource
  s.do?idPubMed9570789

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Entrez Broker Level II Registration
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Entrez Broker Interoperation at Level III Res.
Reg.