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

info@neuinfo.org

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