[Source]: Mass Spectrometry Interactive Virtual Environment (MassIVE)

[gtsueng]

Source Name

Mass Spectrometry Interactive Virtual Environment (MassIVE)

Source URL

https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp

API Documentation: https://ccms-ucsd.github.io/MassIVEDocumentation/#api/#massive-dataset-information

Source Description

MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. MassIVE datasets can be assigned ProteomeXchange accessions to satisfy publication requirements.

Short Description

MassIVE is an NIH supported repository that includes mass spectrometry data.

Source Access

No access issue, account not needed Sample record: https://massive.ucsd.edu/ProteoSAFe/proxi/v0.1/datasets/MSV000094651

Source Funding

NIH

Source Relevance

NIAID high priority resource

Related WBS task

• [ ] Check here if this repository is funded by NIAID (https://github.com/NIAID-Data-Ecosystem/nde-roadmap/issues/11)
• [ ] Check here if this repository only has IID data (https://github.com/NIAID-Data-Ecosystem/nde-roadmap/issues/12)
• [X] 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

• [X] License check- Can this source be included?
• [X] Class check- Does this source have the right class of research output for inclusions?
• [X] NIAID Review- Does NIAID approve of the inclusion of this source?
• [x] Data access check- Have data access issues been resolved?
• [x] Structured data check- Does this source have structured data?
• [x] Mapping check- Has the properties from this source been mapped to the schema?
• [x] 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]

MassIVE has a list of their public datasets here: https://massive.ucsd.edu/ProteoSAFe/datasets.jsp#%7B%22query%22%3A%7B%7D%2C%22table_sort_history%22%3A%22createdMillis_dsc%22%7D

[gtsueng]

This repository was discussed during the biweekly meeting dated 2024.04.30. Per the discussion, we will create a parser for this resource.

[gtsueng]

The mapping for this resource can be found here: https://docs.google.com/spreadsheets/d/115bj6yY7jOt3w_23SIcmRer1OijoD8wQDADcVpgC_wk/edit#gid=779139043

Note that the each MassIVE Dataset record appears to have and assigned doi for the record as well as license information that's viewable from the record, but does not seem to appear in the API json response

Example record on website: https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000094651

Vs metadata retrievable from the API: https://massive.ucsd.edu/ProteoSAFe/proxi/v0.1/datasets/MSV000094651

[gtsueng]

This source is now available on Staging: https://data-staging.niaid.nih.gov/search?q=&filters=%28includedInDataCatalog.name%3A%28%22MassIVE%22%29%29

The following issues have been identified and are in the process of being addressed

• [ ] strange display of special characters
• [ ] Missing DOI's (MassIVE's API doesn't include these values, even though they're available on the site)
• [ ] Missing license information (also not included in records retrieved via MassIVE API, but available on the site)

[gtsueng]

Per the discussion at the bi-weekly meeting dated 2024.06.25, moving forward, the NIAID team should be looped in on all communications with any repository including technical discussions.

For the record, @DylanWelzel please forward any email chains you received regarding your inquiries to MassIVE to NIAIDDataEcosystem@mail.nih.gov