ndex overview - 080713
TRANSCRIPT
The NDEx ProjectA Network Commons for Biology
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.
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.
The Need
A Place to Share Networks
The Need
A Place to Publish Networks
E2F4 and RBL2 Version 1.0
The Need
A Place to Findand Use Networks
Application
NDExThe 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.
A Unified Network Resource
NDEx
Networks from systematic
data analysis
Large-scale data
Networks designedby experts
Interaction Data
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.
NDExThe Network Data Exchange
A Project of the Cytoscape Consortium
Cytoscape Core Development
Team
NDEx Public Website
NDEx Open-SourceServer Software
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.
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
Sharing
• As with popular file-sharing systems such as Google Docs, NDEx users can manage access to the networks that they upload.
Sharing
Jane owns the network that she has uploaded.
Jane
Cindy
permission
accessupload
She grants access permission to Cindy.
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.
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
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
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.
Multiple Formats
XGMMLGPML
NDEx will handle all common network data formats, including BioPAX, SBML, SBGN, GPML, OpenBEL, PSI-MI, SIF,
and XGMML.
Format Translation
Full translation Partial 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.
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.
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.
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.
Review
NDEx provides a substrate on which review, discussion, and crowdsourcing tools can be
created.
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
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.
A Hub for Applications
Web API
Cytoscape
Other Web Applications
Programming Languages
Apps
Client Libraries
NDEx Website
NDEx
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.
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.
Prototype: Example Visualization
These early examples demonstrate the easy access and use of networks retrieved from
NDEx via its REST API.
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.
