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Who will be the users of NIF?
NIF is intended to aid neuroscientists and other
biomedical and biobehavioral scientists in finding resources relevant
to neuroscience research. It also will aid students, and scientists and
experts in other fields in understanding the state of neuroscience research
with respect to available data and the tools for generating and analyzing
that data.
Is NIF a resource repository?
No, NIF itself is not a repository for resources. It is a means for publishing
information about the availability of those resources, and then enabling
their discovery via the web.
What types of resources are included in
NIF?
Through NIF, users can find data, software and experimental resources
(such as specialized cell lines and tissues) as well as textual and educational
resources, and links to other specialized portals, repositories and registries.
How many entities are in the NIF inventory?
Approximately 400 resources are identified, but many of these represent
large data bases with many entries, or large coordinated efforts that
provide multiple data sets and suites of analytical tools.
How do I include my resource in the NIF
inventory?
The amount of information about your resource, and the extent
of public availability to it, depends upon which of three levels of interoperability
you wish to register the resource. "Level 1" provides only very
basic information, such as name, type of resource, URL for the resource,
and contact information. "Level 2" interoperability uses NIF
related vocabularies to more fully descibe the resource and to interact
automatically with NIF. "Level 3" interoperability also uses
NIF vocabularies to enable their content to be searched simultaneoulsy
with other resources also registered at "Level 3" interoperability.
During the NIF beta test, you include your resource in the NIF inventory
in one of three ways:
- During the NIF beta test, first contact one
of the NIH staff listed under "contacts" on this website,
who already is registered with NIF and can help you publish information
about your resource. (Registration is requested in order to prevent
malicious or senseless entries into NIF.) Manual addition of a resource
to the catalogue involves making appropriate selections from drop down
menus of controlled vocabulary terms, using a registration entry interface
provided by NIR. For certain catetoriges of information, free text may
also be entered into this interface.
- Alternatively, you may submit an XML version
of your catalog entry Click here
for more information on this process. This approach already has been
implemented by the Internet Analysis Tools Registry as discussed on
that Registry's website, here.
- To more fully expose the contents and availability
of your resource, you may also register with the "Mediator"
component of NIF, known as "Level III Interoperabilit" registratyon.
This first involves establishing connection between NIF and your resource.
You may provide detailed connection information, or you may use an interoperability
tool NIF will provide for installation on your local machine. The next
steps involve deciding which data you actually wish to make available.
Finally, in consultation with the NIF administrator, you register your
local export schema with NIF, and map your terminology to one of the
NIF terminologies, if you have not already used one of the standard
terminologies on the NIF vocabulary server.
What resources have been registered at Level 3 interoperabilty?
Three data bases are registered at "Level 3" interoperability:
Neuron DB, the Cell Centered Database, and Neuromorpho.org. Members of
the NIF consortium are in the process of registering additional resources.
Other resource providers, such as those having catalogs of research materials,
and other databases, also are interested exploring the registration of
their resources more deeply than "Level 1" or "Level 2"
and will be attending a meeting in October at the NIH to learn more about
the system and participating in the beta test.
Where can I find the vocabulary terms used
to describe a resource at "Level 2?"
These terms can be seen in the interface for registration with the NIF
database, and also here.
in the box titled "vocabulary terms."The highest level descriptors
for "resource type" can also be found at this link. These vocabulary
terms also are available in XML format here.
What do you mean by saying NIF will enable "concept based queries?"
What are the building blocks of NIF that enable it to function?
What vocabularies are available on the NIF server and how are
they expressed?
The server contains "NIF.owl"(also known as NIFSTD) which contains
BIRNLex1.3,
NIF Cell Types, NIF Molecules. More information about Birnlex can be found
here.
The domains covered by Birnlex include:
Anatomy
Imaging , e.g., imaging devices, imaging modes and parameters
Experimental design
Protocols
Project administration, e.g., project, experiment
Organism taxonomy – e.g., species and strain (for mouse)
Data types and data provenance
Phenotypes:
Behavioral, cognitive, anatomical, biochemical, molecular
Environment
The server also contains"NIF" vocabularies which consists
of domain related, undefined terminolgies expressed in a hierarchy, and
derived through meetings of experts. A list of workshops thus far held
or planned can be found here.
What is Textpresso, and why is it included in NIF?
How do I find a resource using NIF?
How do I find documents and other resources available from the
U.S. Government, such as patents and public biomedically related scientific
reports within the bibilographic repositories of government agencies?
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