1. The NDEx Project
A Network Commons for Biology

2. The Need for a Network Commons
• We need a commons for the rapidly expanding corpus of
biological network models.
• Network models are not communicated effectively by figures,
tables, or supplementary information in journal articles.
• While excellent repositories of pathways and molecular
interactions exist, there is currently no public forum where
biologists can easily exchange and publish computable
network models of all types and formats
– This is especially true for network models produced via systematic
mining and integration of large-scale molecular data.
• Lacking this infrastructure, network models can be effectively
inaccessible to those who have the most knowledge to
interpret them and the most to gain from their successful
interpretation.

3. The Need for a Network Commons
• We need a central resource where network models
of diverse types can be found by their relevance to
particular genes, functions, or diseases.
• Once found, scientists must be able to acquire
those networks in easily computable forms.
• We need facile pre-publication sharing of network
models among collaborators.
– To enable biological interpretation and review.
– To accelerate the development of biological network-
related algorithms.

4. The Need
A Place to Share
Networks

5. The Need
A Place to Publish
Networks
E2F4 and RBL2 Version 1.0

6. The Need
A Place to Find
and Use Networks
Application

7. NDEx
The Network Data Exchange
• The NDEx project will create a durable,
collaborative, web resource to
capture knowledge of the structure
and function of biological networks.
• Researchers will use NDEx to access,
share, and publish biological
knowledge in multiple network
formats.

8. A Unified Network Resource
NDEx
Networks from
systematic
data analysis
Large-scale data
Networks designed
by experts
Interaction Data

9. A Unified Network Resource
• Scientists using NDEx will have a unified
interface to search models of all types:
simple and sophisticated, large and
small, data-derived, text-mined, or
manually curated.
• This juxtaposition of diverse networks
expressed in a common environment will
provide an unmatched opportunity to
compare and contrast models, aiding
researchers in hypothesis generation and
model refinement.

10. NDEx
The Network Data Exchange
A Project of the
Cytoscape
Consortium
Cytoscape Core
Development
Team
NDEx Public
Website
NDEx Open-Source
Server Software

11. NDEx Users
• As an NDEx user, your account will
have a home page, analogous to
LinkedIn or Facebook.
• Other users can see the information
and networks that your have made
public or have shared with them.

12. NDEx Users
test network on MDM2 interaction with cell-cycle, primarily via
p53. Includes E2F downstream and interactions with RBL2
My Networks
Dexter Pratt
My collection of
networks center around
some specific genes
involved in cancer
proliferation and
survival, including
FOX03, RBL2, and
MUC1.inferred process ontology XGMML 2686 nodes / 3976 edgesv 1.0.1
cell cycle inhibitors OpenBEL 288 nodes / 433 edgesv 2.3
cell cycle and MDM2 BioPAX 55 nodes / 109 edges
p53 upstream OpenBEL 77 nodes / 143 edges
PFE2536 vs. LN229 Diff 12076 nodes / 0 edges
cell cycle and MDM2 XGMML 2686 nodes / 3976 edgesv 1.0.1
welcome, Dexter sign out helpNDEx Networks GroupsMy Account Users

13. Sharing
• As with popular file-sharing systems
such as Google Docs, NDEx users can
manage access to the networks that
they upload.

14. Sharing
Jane owns the network that she has uploaded.
Jane
Cindy
permission
accessupload
She grants access permission to Cindy.

15. NDEx Organizations
• Groups in NDEx may correspond to
organizations such as companies,
academic institutions, or laboratories.
• Groups may also be informal
associations created for purposes of
collaboration.

16. NDEx Organizations
test network on MDM2 interaction with cell-cycle, primarily via
p53. Includes E2F downstream and interactions with RBL2
Ideker Lab
Our research focuses
on using genome-scale
measurements to
construct computer-
aided models of
cellular processes and
disease. These models
have the potential to
revolutionize biology
and medicine by
providing a blueprint of
normal and diseased
cell functions and by
allowing researchers to
simulate the effects of
drugs on cells long
before they are tested
in humans. The Ideker
Lab is a member of
both the San Diego
Center for Systems
Biology (SDCSB) and
the National Resource
for Network Biology
(NRNB).
inferred process ontology XGMML 2686 nodes / 3976 edgesv 1.0.1
cell cycle inhibitors OpenBEL 288 nodes / 433 edgesv 2.3
cell cycle and MDM2 BioPAX 55 nodes / 109 edges
p53 upstream OpenBEL 77 nodes / 143 edges
PFE2536 vs. LN229 Diff 12076 nodes / 0 edges
cell cycle and MDM2 XGMML 2686 nodes / 3976 edgesv 1.0.1
Networks
welcome, Dexter sign out helpNDEx Networks GroupsMy Account Users

17. NDEx Collaboration Groups
They collaboratively develop a pre-publication
network private to the E2F working group.
Jane Jones creates an NDEx group,
then invites her collaborators to join.
The E2F Working Group
Jane
Phil Cindy

18. Cooperation with Existing Repositories
NDEx does not compete with
existing repositories
NDEx is a
publishing channel
for repositories
Repositories appear as NDEx organizations and they retain
attribution and control over any content they choose to
publish via NDEx.

19. Multiple Formats
XGMMLGPML
NDEx will handle all common network data formats, including
BioPAX, SBML, SBGN, GPML, OpenBEL, PSI-MI, SIF, and XGMML.

20. Format Translation
Full translationPartial translation
Task-specific translators
Full semantic interoperability between existing network
formats is an open issue, therefore the NDEx project will
focus on task-oriented format translation services
developed to support specific use cases.

21. NDEx as a Publication Medium
• Beyond sharing, NDEx will enable the
publication of stable versions of networks.
• Networks can be explicitly created as
dated versions including publication
meta- data.
• Published versions will be immutable and
will be assigned stable URIs and DOIs,
making the networks and their contents
suitable for reference by publications, by
other networks, and by analytic
applications.

22. Publish
The Jones Lab
E2F4 and RBL2 Version 1.0
The Jones Lab model of RBL2 and E2F4 interaction:
an immutable version made publically accessible
at a stable URI and DOI.

23. NDEx as a Review Medium
• By creating a infrastructure for
communities to share networks, NDEx will
support the development of new
methods to review and verify biological
knowledge expressed in networks.
• As network models become central to
the interpretation of large-scale data, it is
critical to ensure that their content is up-
to-date and verified.

24. Review
NDEx provides a substrate on which review,
discussion, and crowdsourcing tools can be created.

25. Combine Public and Private
Information
NDEx can be deployed as a private, secure site.
Proprietary networks integrated with mirrored public networks.
Public Site
User has access to
public networks
Selected networks are
mirrored to a
private NDEx server
Private Site
User has access to
both proprietary
networks and mirrored
public networks

26. A Hub for Applications
• NDEx is based on a REST web API which will
not only power the public website, but also
enable access by other applications,
including Cytoscape.
• In the spirit of the successful history of
Cytoscape plug-ins, the community will be
supported in the creation of new utilities and
analytic tools using NDEx via the API.
• Custom applications and scripts will also be
able to access and manipulate networks via
the API, making it easy for scientists to
develop novel network based analyses.

27. A Hub for Applications
Web
API
Cytoscape
Other Web Applications
Programming Languages
Apps
Client Libraries
NDEx Website
NDEx

28. Access via Cytoscape
As a first step in integration, a
new Cytoscape App will enable
users to access the NDEx website
directly from Cytoscape
Users will be able to sign in
to NDEx via the NDEx App,
download networks to
Cytoscape for processing
and then store results in
their account.

29. NDEx Network Utilities
• The NDEx website will include simple
utilities:
– Browse networks.
– Visualize networks.
– Compare networks.
– Map data to networks.
– Merge, intersect, and edit networks.
– Transform identifiers.
– Convert networks between formats.

30. Prototype: Example Visualization
These early examples demonstrate the easy
access and use of networks retrieved from
NDEx via its REST API.

31. Synergy with the Community
• The NDEx project is poised to play a role
synergistic with existing programs and resources in
systems biology and bioinformatics.
• The Ideker lab is a member of the Sage
Bionetworks Federation and, together with Sage,
will fully integrate NDEx with the Synapse system.
• The NDEx project will work with groups creating
systems that provide access to clinical
measurement data, pharmacological data, and
other data relevant to research and drug
discovery, such as eTRIKS/tranSMART and Open
PHACTS, offering a storage and communication
mechanism for networks derived by analyses of
these data.

32. Coming Soon
NDEx Beta Release
Q4 2013
dexter@ndexbio.org
www.ndexbio.org