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A guided tutorial of the Neuroscience Information Framework
NIF Registry and Data FederationGenetics of Addiction Workshop
Jackson LaboratoriesAug 28-Sept 1 2014
This tutorial will go over...
• Finding resources in the NIF Registry*:– A catalog of data, tools, materials, services and
organizations available to biomedical researchers– Descriptions, keywords, organisms, resource type
• Exploring the NIF Data Federation:– Contents of > 200 databases registered to the NIF
Data Federation
*Now sometimes referred to as the SciCrunch Registry
EXPLORING THE NIF RESOURCE REGISTRY
Part 1
Use case: What resources are available for the genetics of addiction?
• Go to: http://neuinfo.org
• Type in: Addiction• Select: Registry: a
catalog of tools, materials, services and data
Explore the Registry
• Use facets on the side– Select:
Organism– Select:
Mouse• To return to
browsing, remove filter
Optogenetics data set
reinforcement learning
Many ways to explore the Registry
• Select: Table view
• Select: Facet graph
Use facets to explore resources available
NIF connects you to resources
EXPLORING THE NIF DATA FEDERATION
Part 2
Exploring the data space
• Select: Data
• Click: Type of data
Looking for a specific database?:
-Select:Sort by:
alphabetically
Facet graph works here too!
• Only it’s called:– Category graph at
this level• But it works the
same way• Select:– Gene– Select: Gemma
Exploration of NIF Data Space: Progressive refinement of search
More effective to start with a general query and use the navigation to refine search
Exploring a source• The same tools
work for exploring an individual source
• For Gemma, there are ~30,000 results
• But they come from 2 sources
• Facet graph shows that too
Additional filters• Sometimes facets
aren’t very useful– Description
fields– Free text– Poorly
controlled vocabulary
• NIF provides additional filters
Filter 1: Add an additional search term
• If you are in a source already, the filter will be applied to the source
Filter 2: In column filter
• NIF lets you search within columns
3. Search filter• If you are getting a lot of
results that aren’t relevant, there are things you can do
• Filters and facets help• But you can also restrict
your search to certain columns, e.g., those containing anatomical structures
• In the example shown, the search term “cerebellum” returns results on a gene “zinc finger protein of cerebellum”
• Searching for Anatomy:Cerebellum restricts search to columns containing anatomical structures
Available search filters
NIF has designated special categories to help narrow down your search even further.
• Anatomy (Anatomy:"pulvinar nucleus")• Cell (Cell:purkinje)• Disease (Disease:parkinsons)• Molecule (Molecule:grm1)• Organism (Organism:mouse)• Phenotype (Phenotype:"increased expression")• Protocol (Protocol:immunohistochemistry)
• To use these categories, just place the category first, followed by a ":" then what you want to look for in that category.
What should I do when I get a lot of extraneous results?
• If you are getting a lot of results that aren’t relevant, there are things you can do
1. Use filters and facets
2. Remove synonyms
Sometimes synonyms have terms that cause a false positive result
I’ve found a result set; then what?
• Go to source and explore further
• Download result set– Limited to 1000
results– API keys available
for more• Coming soon:
“shopping cart”
Adding a resource to NIF• Anyone can add a
resource to the NIF Registry– Takes only a few
minutes– We curate all added
resources• Or just let us know if
we’re missing something
• For deeper registration, contact us
Warning! Current resource registration pipeline requires that you have an account in Neurolex (http://neurolex.org) before starting. It is actually easier to go through the Resource Identification
Portal: http://scicrunch.com/resource