NDEx, the Network Data Exchange

Abstract

Networks are a powerful and flexible methodology for expressing biological knowledge for computation and communication. Network-encoded information can include systematic screens for molecular interactions, biological relationships curated from literature, and outputs from analysis of Big Data. NDEx, the Network Data Exchange (www.ndexbio.org), is an online commons where scientists can upload, share, and publicly distribute networks. Networks in NDEx receive globally unique accession IDs and can be stored for private use, shared in pre-publication collaboration, or released for public access. Standard and novel data formats are accommodated in a flexible storage model. Organizations can use NDEx as a distribution channel for networks they generate or curate. Developers of bioinformatic applications can store and query NDEx networks via a common programmatic interface. NDEx helps expand the role of networks in scientific discourse and facilitates the integration of networks as data in publications. It is a step towards an ecosystem in which networks bearing data, hypotheses, and findings flow easily between scientists.

Figure 1. Access Control, Network Data Structures, and Provenance History in NDEx

(A) Examples of access control relationships for networks in NDEx. User 1 owns the red, green, and blue networks. She shares the red network directly with user 2, the green network with the members of community group 3, and makes the blue network a public network available to any user or by anonymous query. (B) Example of one edge represented in the NDEx network data model (Supplemental Materials 10). Each box in the diagram is a network element, labeled with its type and id. Edge 25 connects nodes 4 and 12 by the subject and object relationships. The meaning of edge 25 is set by the predicate relationship to baseTerm 33, “phosphorylates”. BaseTerm objects define the vocabulary used by the network, and the primary meaning of node 4 is set by the represents relationship to baseTerm 26, “AKT1”. Node 12 represents baseTerm 97, “GSK3B”. Both baseTerm 97 and baseTerm 26 are associated with namespace 2, indicating that they are standard human gene symbols. Both nodes have user-defined properties “fc” and “pv” associated with them, used to record differential expression data that was mapped onto the network. Edge 25 has a user-defined property “tissue” = “brain” used by the authors to indicate the tissue context. The edge is also annotated with evidence text by support 44 associated with citation 51, the article from which the text was derived. (C) Abstract representation of the provenance history for network 5 in Figure 2. The provenance history records the workflow that led to the network as a tree structure of events, NDEx networks, and other resources.

Figure 2. NDEx Workflow

Example workflow in which network 1 is created by systematic analysis of genome scale data and stored in NDEx, network 2 is produced by a Cytoscape analysis that takes network 1 as an input, network 3 represents a canonical pathway uploaded from literature, and network 4 is the output of a bioinformatic script that operates on networks 2 and 3. Network 4 is made public and read-only and becomes part of a publication. Network 4 is viewed by readers of the publication using an NDEx-capable web application that enables them to directly act on the network data, such as saving a private copy to an NDEx account as network 5.