A guided tutorial showing how to use the Neuroscience Information Framework to find data and tools related to the genetics of addiction. Presented at the Genetics of Addiction Workshop, Jackson Labs, Aug 28-Sept 1, 2014.

1. A guided tutorial of the
Neuroscience Information
Framework
NIF Registry and Data Federation
Genetics of Addiction Workshop
Jackson Laboratories
Aug 28-Sept 1 2014

2. 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

3. Part 1
EXPLORING THE NIF RESOURCE
REGISTRY

4. 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

5. Explore the Registry
• Use facets
on the side
– Select:
Organism
– Select:
Mouse
• To return to
browsing,
remove
filter
Optogenetics
data set
reinforcement
learning

6. Many ways to explore the Registry
• Select:
Table
view
• Select:
Facet
graph

7. Use facets to explore resources
available

8. NIF connects you to resources

9. Part 2
EXPLORING THE NIF DATA
FEDERATION

10. Exploring the data space
• Select:
Data
• Click: Type
of data
Looking for a specific
database?:
-Select:
Sort by:
alphabetically

11. Facet graph works here too!
• Only it’s called:
– Category graph at
this level
• But it works the
same way
• Select:
– Gene
– Select: Gemma

12. Exploration of NIF Data Space:
Progressive refinement of search
Query Addiction
Index
Category
Source
Facet/Filter
Registry Data
Gene
Gemma
Gene Organism
Geo
Expression
level
Literature
Integrated
Expression
More effective to start with a general query and use
the navigation to refine search

13. 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

14. Additional filters
• Sometimes
facets aren’t
very useful
– Description
fields
– Free text
– Poorly
controlled
vocabulary
• NIF provides
additional
filters

15. Filter 1: Add an additional search term
• If you are
in a source
already,
the filter
will be
applied to
the source

16. Filter 2: In column filter
• NIF lets
you search
within
columns

17. 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

18. 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.

19. 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

20. 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”

21. 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