Overview and tutorial on how to dkNET, the NIDDK Information Network

1. Introduction to dkNET:
Overview and use cases

2. Outline of presentation
1. Introduction to dkNET
2. Introduction to SciCrunch platform
3. Overview of structure and content of dkNET portal
4. Tutorial
Searching through dkNET
Signing up for an account
Saving searches
Signing up for search alerts
Creating collections
Citation/usage analytics
5. Free session

3. Informatics and the Data Deluge
• It is quite difficult to access, collate, and filter the incredible array of
information and data in the public domain.
• dkNET was established in recognition of the need to interconnect
research communities, both basic and clinical, by providing seamless
access to large pools of resources and data relevant to the mission of
NIDDK.
• dkNET provides a single point-of-entry for discovering this information
to allow researchers to make good decisions in the research process,
thereby increasing both the speed and efficiency of the process.
3

4. Database
Software Application
Data Analysis Service
Topical Portal
Core Facility
Ontology
Software Resource
Years:
dkNET Offers…
• A search portal to find community-
vetted research resources: materials,
data and tools for your research
• Access to hundreds of databases
across biomedicine with one easy
search
• Personalized search and display of
results
• Information hub for community news
and social networking
• Support for resource providers
http://dknet.org @dknet_Info

5. dkNET Investigator's RetreatJune16, 2014
Shared
Resources
dkNET is built on the SciCrunch platform
Resource Identification Portal
Neuroscience
dkNET
Drug Design
• Pull from and
push to a
common pool
of data
• Customize
according to
communities
• Common
interface
elements
across
platforms

6. How to use dkNET

7. dkNET ESP mtg 06/15/16
Register for dkNET for customized functions
Help and Tutorials
available under About

8. Type 1 diabetes: One path

9. Simultaneous search across 3 indices
Results are returned in order of specificity, i.e., Community resources are
presented first if they are available. But all searches are executed across indices
Community
More
resources
Literature
Specialized
NIDDK-relevant
resources
200+
databases
across
biomedicine
Literature

10. Community resources
NURSA
BCBC
DiaComp
GUDMAP
T1DB
MMPC
NIDDK Central Repository
dkNET Community Funding
AddGene: Plasmids
Clinical trials.gov: Clinical trials and data
Antibody Registry: 2M+ antibodies
Integrated animals: Model organism databases
SciCrunch Resource Registry: 13K+ tools
Grants.gov
NIDDK-funded resources and centers Additional relevant databases vis SciCrunch

11. Community resource
navigation
● Organized according to main
categories of research
resources
● Subcategories are specific to
each category
● Faceted search to drill down
into a single source
Search tip: Start with a
general term, and use the
facets and filters to refine
your search

12. Demo: Search and Display in Community
Resources
Search: Rodent models for Type 1 Diabetes

13. Type 1 diabetes: One path
2. Select
“organism”
1. Enter: Type 1 diabetes into
the search bar
3. Click
search icon

14. Results from
Community
resources
Navigation:
Click on “Any”
to remove
“Organism”
filter
Individual
records in
snippet view
Feedback
Category: Organism

15. Narrowing down search results
• Using categories and subcategories
• Category graph for overview and faceting
• Snippet view vs table view
• Using facets and filters within a source
• Exporting results

16. Community view: Subcategory vs source
• Use the facets in the
side panel to narrow
down results
• Select by subcategory
or source
• Subcategory: results
presented across all
sources as snippets
• Source: Results are
returned from a single
source as a table

17. 3 sources
Click to view
record details
Click to view
details about
the source
Alert: This
resource is
archival
Add to a
personal
collection
Snippet view: Each record is displayed
separately

18. Selecting a source reveals specialized facets and filters
Expand
number of
columns
visible
Source
specific facet;
click to view
unique filters
Executes
filtered search
Export results
as CSV (1000
result limit)
Table view: Displays records within a
single source

19. Make sure to click
“Perform search” after
selecting filters. May
have to scroll down a bit.
Select filter
Remove filter

20. Search tip: Navigation
Use the breadcrumbs in the
upper right corner of the
search window to return to
an earlier state
Click organisms to
go back to original
search results

21. Explore another source: DiaComp

22. Structure of dkNET
Rodent models of Type 1
diabetes
1. Type 1 diabetes
2. Organism
3. Mouse
4. Integrated animals
5. Phenotype
6. Mouse
7. DiaComp
Data View
Category
SubcategoryMore
Literature
Materials
Data
Resource
Protocols
Organism
Rat
Community
Fly Worm
Source
Facet
MMPC BCBC
Species Background Gene
DiaComp
Phenotype
Integrated
Mouse

23. Short cut
Use the category graph
to get an overview of
categories and sources
and use it to select
search results
Available at
the top of the
left side panel
Selects:
Integrated
animals +
mouse

24. Creating a collection
When browsing in snippet
view, you can create a
custom collection of search
results within or across
sections. Collections are
saved in your account and
can be added to at a future
date.
You must have an
account and be logged
in to use this feature
Select existing
collection or create a
new one. Then click
on + to add item
Add to or remove
item from collections
by clicking the + or -
Click icon next to
record to add to a
collection
Icon turns green
when item is in a
collection. Click to
view collection

25. Viewing and Managing Collections

26. Using vocabulary services and other search tips
• Putting quotes around a phrase, e.g., “Type 1 diabetes” will search for the entire
phrase. With no quotes, dkNET interprets query as Type + 1 + diabetes,
accounting for some false positives
• dkNET will attempt to match search terms to community ontologies to provide
synonyms, acronyms and related terms. Click “Query expansion” to view additional
terms. Synonyms and acronyms may be removed if they cause false positives.
• Terms may also be selected from the pull down menu
• dkNET supports boolean operators, “AND”, “OR” and - (=NOT)
• Searches may be saved (account required for saving beyond current session)

27. Select: Type 1 diabetes mellitus from pull down menu
Note that “” are placed around
the term to search for the entire
phrase; synonyms etc are
joined by an “OR”
Autocomplete adds two
useful synonyms
“Type 1 diabetes mellitus” OR “IDDM” OR “insulin-
dependent diabetes mellitus”

28. Creating a boolean query
• Search terms may be
joined manually by
adding “AND” and
“OR” ; the default is
AND
• Adding a - before a
term executes a NOT
query, e.g., excludes
search results with
that term
Manually added “Type 1
diabetes” and “juvenile
diabetes” joined by OR
“Type 1 diabetes mellitus” OR “IDDM” OR “insulin-dependent
diabetes mellitus” OR “Type 1 diabetes” OR “juvenile diabetes”
Manually added terms are
joined with vocabulary
expansions

29. Saving searches
Search strings can be
saved for future use
• You must have an
account and be logged
in to save searches for
future sessions
• You can sign up for
alerts to be notified
when new or updated
records are added to
dkNET
Click here to save a
new search
Click here to set up
notification
preferences
Run a previously
saved search
Click to save search
or run a previously
saved search
Note that saved search will save not only the the search
terms but also selected categories, filters and facets

30. Demo: Using More Resources and Literature
Find: Cell lines for Type 1 Diabetes

31. Navigate back to
“Any”

32. Search in “More
resources”

33. Navigation in More Resources
• Snippets are
individual
sources
• Categories are
different
system levels
or data types
More resources index
Over 200 sources are
available from across
biomedicine
Click to view
categories

34. Each index is organized slightly differently
Community More resources Literature
Navigation differs across indices
Resource
categories
Sources
Data
and/or
resource
type
System
level
Individual
records
Source
Functions
and filters
Results
display
Functions
and filters
Results
display
Collections
and
Analytics
Analytics
Facets
Articles
Functions
and filters
Results
display

35. Several sources have information
• Selecting “Cell” from
system level or “Cell
lines” from Type of
data will return a list
of sources with
results
• Selecting a source
will pull up custom
filters
• Note: Collections are
not available from the
More Resource menu

36. Featured resource: Cellosaurus-integrated cell line directory
New resources
are constantly
being added
via other
SciCrunch
communities

37. dkNET Literature
Synonyms
Easy to browse
abstracts
Easy sorting
functions
Altmetrics

38. Review: Simultaneous search across 3 indices
Results are returned in order of specificity, i.e., Community resources are
presented first if they are available. But all searches are executed across indices
Community
More
resources
Literature
Specialized
NIDDK-relevant
resources
200+
databases
across
biomedicine
Literature

39. dkNET connects resources
Social media
Research resource analytics
Other SciCrunch communities
More
resources
LiteratureCommunity
RRID’s

40. RRIDs
An easy, practical method for improving reproducibility
and transparency

41. dkNET ESP mtg 06/15/16
Unique ID’s for all! Resource Identification Initiative
• It is currently impossible to
query the biomedical literature
to find out what research
resources have been used to
produce the results of a study
• authors don’t provide enough
information to unambiguously
identify key research resources
• Impossible to find all studies
that used a resource
• Critical for reproducibility and
data mining
• Critical for trouble-shooting
Faulty Antibodies Continue to Enter US
and European Markets, Warns Top Clinical
Chemistry Researcher-Genome Web Daily,
October 11, 2013

42. dkNET ESP mtg 06/15/16
Authors supply database accession numbers for key
research resources used in research

43. Resource IDs from NIF aggregated databases
•A single portal for
authors
•>25 authoritative
databases
•One search
interface
•Simple directions
•Prominent “Cite
This” button
•Help desk
RII Portal
http://scicrunch.org/resources

44. Which Journals now ask for RRIDs?
• ~25 Elsevier Journals –
• BMC –
• Frontiers
• Cell Press
• Wiley (JCN, J. Neuro. Research,
Brain and Behavior)
• Endocrine Soc journals?
http://scicrunch.com/resolver/RRID:nlx_144509
Nagging authors is most
effective, typesetting allows
apps to run smoothly

45. Who is using…tracking resource usage
• dkNET provides tools and services for identifying and
tracking research resources
• Resource providers: who is using my resource?
• Individual researchers: Who is using this resource and what
other resources are related to it?

46. What is a good antibody
against CART?
Query: CART
Materials > Antibodies > Antibody Registry (81 results)

47. Click on category to
sort

49. Who is using my resource?
For resource providers…
Query: My resource
Category: Resources

50. dkNET ESP mtg 06/15/16
Type in Your Resource and Search

51. dkNET ESP mtg 06/15/16
Select your resource
Click on resource
name

52. dkNET ESP mtg 06/15/16
Subscribe to New References and/or Claim Ownership
Lists mentions in the
open access
literature

53. dkNET ESP mtg 06/16/16
Resource Analytics

54. dkNET ESP mtg 06/15/16
Manage Resource References Subscription

55. dkNET ESP mtg 06/15/16
Manage Resource Reference Subscription: Choose to subscribe or unsubscribe
to user notifications via the dkNET website and/or e-mail

56. Some use cases to try
Q1. Funding Opportunities
Find funding opportunity announcements related to obesity that expire in 2016.
Q2. Research Materials
Can you find validated monoclonal antibodies against Thyroid Stimulating
Hormone Receptor (TSHR) or thyrotropin receptor?
Q3. Clinical Trials
How many clinical trial datasets related to type 1 diabetes are available?
Q4. Model Organisms
Can you find animal models of polycystic kidney disease?
Q5. I’m looking for animal models for Type 1 diabetes
DiaComp has 3 mice listed and Rat Genome Database has 1 rat strain listed that are asserted to be models of Type 1
diabetes (and 2 more that might be relevant). Can you find them?