Finding and Querying Networks

Last updated: July 29th, 2018

The public NDEx site includes a number of networks that are marked as "PUBLIC" and are therefore accessible without signing in to a user account. Public networks can be found, viewed, and queried but you cannot create new networks, upload, or download without signing in.

IMPORTANT NOTE: The screenshots in all our user manuals are for training purposes and might be different from the actual screen output you will obtain when working on the current NDEx version deployed to our public server.

Some Public Networks on NDEx

  • The collection of Nature-curated NCI Pathway Interaction Database networks
  • OpenBEL (BEL format)
    • BEL small corpus
    • BEL large corpus
  • A collection of lipid metabolic pathways from LIPID MAPS (BioPAX3 format)

Searching for Networks Based on Title and Description

  • Search text can be entered directly into the navigation bar.
  • The current search mode is displayed to the left of the search box and defaults to "Networks".
  • Try running an empty search: just click magnifying glass or press enter to search.
  • The system will return all the networks you have access to! The network search results page displays all the hits and provides basic info about the networks, such as format, owner, last modification date etc.
  • If you hover on a network name, a pop up window will display the network description.
  • Only public networks are returned in a search; a private network will only appear in a search if you have been granted access to that network by its administrator or if you are the owner of that network.

View a Network Found in a Search

  • To inspect a network, click its name.
  • The network page will open up: information about the network is displayed on the left (red line) and includes the counts of nodes and edges for the entire network, date of creation, UUID and links to the network administrators profiles. Network description and literature reference are also displayed if available. Toward the bottom, some network properties are also displayed
  • If a network is larger than 300 edges, no graphical display will be rendered and the main part of the page will only display a table containing a sample of 500 randomly selected edges.
  • The table has 3 tabs: one for Edges, one for Nodes and the last one for the Provenance history (red arrow).
  • On the right hand side, there is a link for the Advanced query interface (green arrow).

Advanced Search Capabilities

Starting from NDEx v1.3, a stand-alone Apache SOLR service is used to implement Lucene Indexing. Advanced search capabilities allow users to search (and query) networks using keywords or other network attributes. A complete list of the indexed attributes is available in the tables below.

SEARCH: Indexed network attributes

Note that some attributes below are highlighted in blue text. These are NDEx internal attributes and are not encoded in the CX networkAttributes aspect. In the case of attributes like ‘edgeCount', they are calculated values.

Attribute Description Type
labels Users can use this property to specify custom tags freetext
methods Description of methods used to generate the network freetext
networkType Specifies the type of interactions in the network (protein, genetic, chemical) freetext
organism Description of organisms associated with the network freetext
disease Description of diseases associated with the network freetext
tissue Description of organs, tissue types, cell types, and cell lines associated with the network freetext
rightsHolder Describes the holder of the rights to the network – same as dc:rightsHolder freetext
rights Description of the rights asserted by the rightsHolder – same as dc:rights. The indexing of this general field should aggregate not only the actual ‘rights’ attribute but the more specific rights attributes, such as copyright or license. In that way, network authors do not need to state information redundantly freetext
author Individuals responsible for creating the content of the network – see dc:contributors freetext
name Network title freetext
description A description of the network, its content and data sources freetext
version Network version string
creationTime Time at which the network was created date
modificationTime Time at which the network was last modified date
edgeCount Number of edges in the network integer
nodeCount Number of nodes in the network integer
visibility NDEx network visibility: Public, Private string
uuid This corresponds to the externalId ndexStatus element attribute string
owner This corresponds to the user account name that owns a network string

SEARCH: Indexed node attributes
Attribute Description Type
nodeName Name of node freetext
represents string
alias Alternative identifiers for node string

QUERY: Indexed node attributes
Attribute Description Type
nodeName Name of node freetext
represents string
alias Alternative identifiers for node string

Advanced Search Examples

  • You can search for networks using keywords: type "metabolism" in the search bar and hit enter.
  • The system returns all networks that have the term "metabolism" in their name, description or associated to its nodes and/or edges.

  • You can also use wildcards: if you type "met*" the system will return all networks that have metabolism, metabolic, methionine, metformin and the met gene referenced in their title, description, nodes or edges. In the screenshot below, the last network has the keyword "metabolic" in its description (red circle).

  • However, if you tipe "name:met*", the system will only return networks that have those terms in their name: in the screenshot below, you can see that the network called Biosynthesis of Sterols is missing as the term "metabolic" is contained in its description.

  • If you know the unique identifier (UUID) of a network, you can search NDEx using this information.
  • type "uuid": in the search bar followed by the UUID of the network you are looking for.

  • You can search networks specifying a range of values: type "nodeCount:[11 TO 79]" in the search bar and press enter.
  • The system will return all the available networks that have between 11 and 79 nodes.

  • You can search networks based on when they were created or last modified.
  • type "creationTime:[2016-02-26T00:00:01Z TO 2016-02-27T23:59:59Z]" and press enter.
  • The system will return all available networks that were created between 12:01 am on Feb 26, 2016 and 11:59 pm on Feb 27, 2016. Do not confuse creation time with last modification time (red circle below).

  • You can search networks owned by a certain account. To do this, typea range of values: type owner: followed by the user account name. For example, try to search for owner:ndextutorials
  • The system will return all the available networks that are owned by the account "ndextutorials".
  • You can perform complexes searches combining several keywords and properties. For example, let's search all networks that:
    • have the keyword ‘metabolism" in their name
    • have no more than 5000 edges
  • Type "name:metabolism AND edgeCount:[1 TO 5000]" and press enter to get the results

  • Starting from NDEx 2.1, you can decide to perform Search Term Expansion on genes and proteins. This feature expands your search term(s) to all its possible synonims and runs a search using all of them. This makes sure that you will find all networks that have your genes/proteins of interest even if the genes/proteins of interest are listed using an uncommon synonim or an alternative identifier.
  • Search Expansion is limited to human terms only. So, if you search for a yeast gene/protein, the search will be performed accordingly but no Term Expansion will occur.
  • Performing a search for human genes/proteins with Term Expansion will return more results compared to the same search performed without Term Expansion.
  • To use the Search Term Expansion feature, just type your genes/proteins of interest in the search box and mark the "Search Term Expansion" checkbox below:

  • Please not that Search Term Expansion is not compatible with Lucene Syntax.
  • For more information and details about Lucene Syntax, please refer to the Lucene Documentation.

Query for a Neighborhood in a Network

NDEx allows users to run 2 types of queries: Simple or Advanced.

Simple Query
The simple Query can be used to find nodes in a network based on user-defined query terms. Users can type their query terms (for example a gene name) in the query control text box (red arrow), and then select the desired depth:
- 1-Step finds only the immediate neighbors of the node(s) specified by the query term(s).
- 2-step finds finds also nodes connected to the immediate neighbors, thus generating a much larger result.
- Interconnect only finds short paths between the nodes specified in the query string. The resulting subnetwork attempts to answer the question: “How are these genes related to each other?”. Therefore it is only appropriate for queries selecting 2 or more nodes. Query nodes for which no short paths are found to any other query node will appear as “orphans”, nodes that have no connections at all.

  • For example, type "brca2", select a depth of "1-step" and click the "Run Query" button.

  • The retrieved neighborhood pictured below is a small network specified by the "brca2" term, consisting of "106 nodes" and "236 edges".
  • All the retrieved nodes and edges can be interactively inspected using the graph and info panel on the right
  • Users can also inspect the query result in tabular format or download the result as a tab-separated text file thanks to the buttons available in the bottom right corner of the screen
  • Logged in users also have the option to save the result to their NDEx account page
  • Click "Back to Original Network" to clear your query result and go back to the previous screen
  • For large networks, users can decide to set the query result as display sample of their network and override the default, system-generated sample view. To do this, simply click the "Set Sample" button available in the query result page.
  • Finally, users can decide to open their query result in Cytoscape to further annotate the network or run an analysis. If all requirements are satisfied, the "Open in Cytoscape" button will be colored and available to click.