[Source]: The Network Data Exchange (NDEx)

[gtsueng]

Source Name

The Network Data Exchange (NDEx)

Source URL

https://www.ndexbio.org/index.html#/

Source Description

The NDEx Project provides an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge.
One of the goals of the project is to create a home for models that are currently available only as figures, tables, or supplementary information, such as networks produced via systematic mining and integration of large-scale molecular data.
The NDEx project does not compete with existing pathway and interaction databases, such as Pathway Commons, KEGG, or Reactome; instead, NDEx provides a novel, common distribution channel for these efforts, preserving their identity and attribution rather than subsuming them.

Source Abstract

The Network Data Exchange (NDEx) is a NIH supported generalist repository that includes generalist data.

Source Genre

generalist

Source Access

No access issue, account not needed for publicly-accessible records. Many (but not all) Network records have enough overlapping metadata fields for inclusion as "Dataset" records; however, this will not include properties exclusive to a Pathway/Network type class.

Example Network records

• https://www.ndexbio.org/viewer/networks/ac27ffe4-45d0-11ed-b7d0-0ac135e8bacf
• https://www.ndexbio.org/viewer/networks/b036e442-be28-11ed-a79c-005056ae23aa
• https://www.ndexbio.org/viewer/networks/82b7194f-07b0-11ee-aa50-005056ae23aa
  -- As seen in these examples, the available metadata properties vary greatly, so it may be necessary to map many records to ensure exhaustive capture of the metadata available

Source Funding

National Institutes of Health [U24CA184427]

Source Relevance

This source was prioritized for inclusion by the NIAID/ODSET team. Additionally, the source maintainers have expressed interest in integrating with the Discovery Portal

Related WBS task

• Check here if this repository is funded by NIAID
• Check here if this repository only has IID data
• Check here if this is a generalist repository with IID data (https://github.com/NIAID-Data-Ecosystem/nde-roadmap/issues/12)

For internal use only. Assignee, please select the status of this issue

• Not yet started
• In process
• Blocked
• Will not include

Status Description

No response

Source to-do list

• License check- Can this source be included?
• Class check- Does this source have the right class of research output for inclusions?
• NIAID Review- Does NIAID approve of the inclusion of this source?
• Data access check- Have data access issues been resolved?
• Structured data check- Does this source have structured data?
• Mapping check- Has the properties from this source been mapped to the schema?
• Parser check- Has the parser been written?
• Parsed data check- Has a sanity check on the data obtained from this source been performed?
• Merge data- Has the crawler/plugin been successfully integrated with the system?
• Issues could not be resolved - Add as a single record via the DDE

[gtsueng]

@DylanWelzel ndex is the next repo to generate a parser for. It may be using property value pairs similar to how MassIVE was doing it.

[DylanWelzel]

Great I’ll look into it

[gtsueng]

@hartwickma, @lisa-mml, @rshabman, @sudvenk,

Based on our productive discussions at the in-person/hybrid meeting dated 2024.09.24, we have abstracted the VDJ server informative slide deck into a "report" template slide deck to be used with any integrated resource that will hopefully help with the decision-making. We then applied this template to NDEx, a repository awaiting approval in Staging.

The integration report for NDEx is here: https://docs.google.com/presentation/d/1Y-fiYltovhQ4WrINu8bJjus2exDsdP38/edit#slide=id.p1 and a templated email draft to contact NDEx can be found linked in the report slide deck

[hartwickma]

Hi @gtsueng, thanks for providing this draft report of the NDex integration. Since we discussed the idea of a QA/QC report being a standard procedure, please create a new GitHub issue with a an easily identifiable title that we can use to have an ongoing discussion about the design of a standard report and email template that can be modified for each repository.
Additionally, this GH issue is not appearing in the 'For NIAID Review' tab. Can you check that items that need NIAID attention are being accurately titled and labeled? Thanks so much, please let me know if we can provide additional information or details.

[gtsueng]

Hi @hartwickma, @sudvenk,

Per your request, a separate issue has been created for the templates themselves that we can use to further the discussion on the templates: https://github.com/NIAID-Data-Ecosystem/niaid-feedback/issues/159

I am changing the status of this issue back to 'review requested--staging' as this repository is still awaiting approval for production.

Regarding your other request to investigate why it's not appearing in the For NIAID review board, the reason is that this particular issue/ticket is tagged as a repository issue/ticket. We were previously asked to put such tickets in a separate board for repositories only and NOT the For NIAID review board. As such it (as well as other repositories) appear in the Repository board.

Please let me know if you would like this behavior changed, and we will be happy to accommodate.

[gtsueng]

@DylanWelzel The default topicCategory value for all records in this repository should be set to: "Molecular interactions, pathways and networks" (http://edamontology.org/topic_0602) (formatted as a DefinedTerm object)

@ZubairQazi can run the topic classification for these records to add additional topicCategories; however, please be mindful that many of these records have poor descriptions so please spot check records where the combined name+description <100 characters