Repository · FAIRsharing

Global Natural Products Social Molecular Networking (GNPS)

Spectra

Global Natural Products Social Molecular Networking (GNPS) is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. GNPS aids in identification and discovery throughout the entire life cycle of data; from initial data acquisition and analysis, to post publication exploration. GNPS provides the ability to analyze a data set and to compare it to all publicly available datasets by building on the computational infrastructure of the University of California San Diego (UCSD) Center for Computational Mass Spectrometry (CCMS), and providing public dataset deposition and/or retrieval through the Mass Spectrometry Interactive Virtual Environment (MassIVE) data repository. To provide open and transparent solutions for mass spectrometry (MS) data reuse, data sharing, and analysis reproducibility, the GNPS Dashboard collaborative interactive web application, provides tools to facilitate the exploration of liquid and gas chromatography(LC/GC)–mass spectrometry (MS) data for collaborative examination. The GNPS Dashboard is a hands-on platform for use of private and publicly available MS data, including files stored at long-term MS data repositories such as GNPS/MassIVE, MetaboLights, ProteomeXchange, and the Metabolomics Workbench.

Website
Record in FAIRsharing (doi:10.25504/FAIRsharing.8b203d)
Subjects: Bioinformatics, Metabolomics, Proteomics

Documentation, events and training

bio.tools API and tool documentation

GNPS API documentation (same homepage)

What is known per question

The questions of the decision tree, with what FAIRsharing says about this repository. ✓ supported, ✗ excluded, ? not known.

What kind of data do you want to archive?

✓ Spectra
? Crystal structures
? Computational chemistry
? Catalysis
? Compounds and reactions
? Bioassays and chemical biology
? Materials and polymers
? Images and microscopy
? Something else

Subjects: Bioinformatics; Metabolomics; Proteomics

Domains: Mass spectrum

Does the journal or publisher you publish with require or recommend a repository?

? Yes
? No
? I do not know

FAIRsharing has no information on this.

Which discipline does your data belong to?

FAIRsharing has no information on this.

Which publisher?

FAIRsharing has no information on this.

Does your funder have requirements for where data is archived?

? Yes
? No
? I do not know

FAIRsharing has no information on this.

Which funder?

FAIRsharing has no information on this.

Does your institution offer a data repository?

? Yes
? No
? I do not know

FAIRsharing has no information on this.

Which institution?

FAIRsharing has no information on this.

Can your data be shared openly?

✓ Yes, openly available
? Yes, after an embargo
✗ Only with restrictions

Data access: open: CC0 by default for batch upload

Data deposition: open: free login required

How large is your dataset?

? Less than 1 GB
? 1 GB to 50 GB
? 50 GB to 1 TB
? More than 1 TB

FAIRsharing has no information on this.

Why can the data not be open?

? It contains personal data
? Commercial or intellectual property reasons
? Safety or security concerns
? A data sharing agreement limits it

FAIRsharing has no information on this.

Under which license do you want to share the data?

✓ CC0 / public domain
? CC BY
? Another open license
? Not decided yet

Licences: Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication

Do you need a persistent identifier, such as a DOI, for citing the data?

? Yes, a DOI
? Any persistent identifier will do
? No

FAIRsharing has no information on this.

Must the data be stored in a specific region?

✗ In the European Union
? In a specific country
✓ No preference

Country: United States

Must archiving be free of charge?

? Yes, free only
? A fee is fine

FAIRsharing has no information on this.

Which country?

✓ 1 of 15 in the list ✗ excludes 14

Country: United States