# Presentation: 030514

## Communication between NIF and Resource Providers

*Overview of the Framework Components and their Interactions*

- Luis Marenco, M.D.

## 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

## 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]*
*...*

## 2. NIF Servers

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

## 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

## 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)

## 4. Communication Framework (2)

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

## 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 resource’s 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)

## (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.

## (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 resource’s Entrez Links (e.g.: Link categories)
- Minimizes the cluttering of new resources providers at NCBI

## Navigating to the LinkOut Broker

## Navigating to the LinkOut Broker (2)

## Navigating to the LinkOut Broker (3)

- _[http://128.36.123.93:8080/lb/linkoutToResources.do?id=PubMed|16293591|](http://128.36.123.93:8080/lb/linkoutToResources.do?id=PubMed|16293591|)_

## Navigating to the LinkOut Broker (4)

## Other LinkOut Broker Examples

- _[http://soma.med.yale.edu:8080/lb/linkoutToResources.do?id=Nucleotide||NP_014085[pacc](http://soma.med.yale.edu:8080/lb/linkoutToResources.do?id=Nucleotide||NP_014085[pacc)_]

## Other LinkOut Broker Examples (2)

- _[http://soma.med.yale.edu:8080/lb/linkoutToResources.do?id=PubMed|9570789|](http://soma.med.yale.edu:8080/lb/linkoutToResources.do?id=PubMed|9570789|)_

## Entrez Broker – Level II Registration

## Entrez Broker – Interoperation at Level III Res. Reg.