The Entrez linkOut broker (ELB) like its name indicates, is an application that provides Entrez-linkOut brokering services to NIF resources. Entrez has a public linkOut service, that allows linkage of external information to any of their objects (Publications, genes, proteins, etc). For this to be possible, external resources must provide that information in a specifc XML format uploaded via FTP.
NIF provides a service by which individual resources can provide their Entrez related information in XML as defined by the ndg.disco protocol ( Used as one of the NIF Level 2 registration implementation). Using this information, the ELB will be able to extract the information from each reource and collect it in a database repository. Whenever this information changes, ELB will update Entrez with the latest data. Having a repository of Entrez data provides an added value to the NIF community. The same object identifiers in Entrez can be used to link relevant data between NIF resources.
This document presents ELB from the regular user, ELB administrator and resource implementer perspective.
There are two ways the regular user will benefit from the ELB funcitonality: By finding and following the links sent by ELB to Entrez sites such as PubMed, or by data integration to the lnkOut broker sites, provided from any Web site (not restringed to those in NIF). See the next two case - figures.
In this page follow first the "links" URL, that brings up a "Links" menu. In that menu clich the LinkOut URL to get to the next page...
In this page select any of the links under the "Neuroscience Information Framework" to be directed to external data related to that publication. In this case, following the "ModelDB: Computational model (Squid axon (Hodgkin, Huxley 1952) (NEURON))" link will lead to the "Neuron" simulator implementation of this experiment in the ModelDB Web site.
Similar Links:
The other way to leverage the ELB is by calling its "linkoutToResources" page with some parameters.
The next link /lb/linkoutToResources.do?id=PubMed|11731556|
shows all NIF data linked via the PubMed id 9570789.
ELB displays all NIF resources having data related to this publication: The image shows one link to ModelDB and another in NeuronDB. As more databases start sending their Entrez links to NIF, related information will grow.
Linking to related information on ELB:
Owners of other Web sites, not exclusively restricted to NIF, can point to related
Neuroscience information on NIF by following these guidelines:
Asumming the ELB root directory is located at http://soma.med.yale.edu:8080/lb
use the following path to construct your URL
http://soma.med.yale.edu:8080/lb/linkoutToResources.do?id={entrez_db}|{entrez_object_id}|{entrez_query}
Either {entrez_id} or {entrez_query} must be present. If both are present, the second one is ignored. Details how to construct an entrez_query can be found at the Entez site.
Similar links:
ELB has a Web based management console. The main page is located at tge relative path /lb . The first screen shows links to the main administrative console and several sample links. Follow first the Login link and provide the adminstrator credentials provided during installation; then follow the [Administration] link
The administrative interface contains several controls to populate and curate the ELB database. The first time that you use the system the database will be empty. Use the[Update] button to interactively load (updates) all information in the ELB system. Internally the system will:
This process can take several minutes.
Once the Update process is completed, a screen similar to the next one is displayed. In this page you can choose to:
1. Display/edit resource information by clicking on the resource name (e.g.: NeuronDB)
1.1. The INTEROPERABILITY_URL's [details]
link shows disco implementation by NeuronDB. Note the entrez_oid's url attribute
pointing to the entrez links source.
1.2 The DISCO_ENTREZ_OBJECTS_URL's [details]
link shows the NeuronDB Entrez information
1.3 The Data in DB link shows the
information that has been imported into the ELB repository for this database. You
can scroll to see more inforamtion. Including live Web links to the source database
1.4 The [Import] button will only update the Entrez linkOut data for this resource
1.5 The [Edit] button is used to change the local registration information for testing
Back in the Administrative console, use:
2. [New Source] button to manualy add an entry (This process is used for testing
a Level 2 implementations
with new ELB providers), and
3. Export link to generate the information
to upload to Entrez via FTP (user/password and URL are provided by Entrez linkOut
team on request). In the case of NeuronDB the following information is generated
For those resources interested on sharing their Entrez data on NIF, they need to implement the NIF Level 2 registration. The current version of NIF uses the current ndg.disco protocol to acomplish this task. Here is a simplyfied description of this protocol.
What is basically needed are two files / streams: disco, and disco.entrez_oid
disco file: To be automatically discoverable, this file must be placed at the root directory of the Website and be named disco.xml. Assumming a NIF Level 2 complaiant site has a Web root located at http://ccdb.ucsd.edu, the disco file should be at http://ccdb.ucsd.edu/disco.xml
Here is a sample file. The important parts for the ELB are highlighted.
Besides this file, you need to implement an Entrez Web feed. Currently ELB only supports the disco.entrez_oid.1 format. Its location in this sample resource can be generated by following the value in the url atribute of the entrez_oid node in the disco file. For this example that will be http://ccdb.ucsd.edu/./disco_entrez_objects.xml
This file / stream(in case you prefer to use a Web program that generates this information from the database) has basically one node with the information. The oid node. This node repeats as many times as needed to export all your links. The node contains the following attributes
You can find the XML schemas of these messages at disco.xsd and disco.entrez_oid.1.xsd.