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Repositories in Profile – STRENDA DB

For chemists, it is crucial to know the advantages of different data repositories in order to find the best fit for their research data requirements. Here, we provide a brief overview of STRENDA DB as part of our series “repositories in profile”.

STRENDA DB – Standards for Reporting Enzymology Data

Figure 1: Screenshot STRENDA DB.

Basic information

❏      Creation date: 2016

❏      Country: DE

❏      Domain: Life Science, Chemistry, Biological and food chemistry, Molecular Chemistry

❏      Usage: Open Access (data view), registration required (data contribution)

❏      Target group: Biochemists, systems biologists, biocatalysts

❏      Number of datasets: 150

❏      Recommended by journals/societies: STRENDA Guidelines by over 55 international biochemistry journals recommended

❏      Listed in: re3data: r3d100012329, FAIRsharing: FAIRsharing.ekj9zx, Wikidata: Q58034053

Functionalities and technical information

❏      Content: Functional enzymology data (kinetic and experimental data)

❏      Content origin: From manuscripts, publications

❏      Searchable content: Enzyme kinetic data along with experimental conditions

❏      Accepted data types: Currently none, EnzymeML (in development)

❏      Used standards/ontologies: DataCite, InChI, EnzymeML (in development)

❏      Curation: Via automated data checking based on STRENDA Guidelines, fact sheet 

         (PDF) with submittable input data

❏      Access rights/license information/embargo: Creative Commons Attribution 4.0 International (CC BY 4.0), Term of Use, no embargo

❏      AAI solution: Internal user administration (user, administrator)

❏      Persistent Identifier system: DOI (Digital Object Identifier), PMID (PubMed Identifier)

❏      Authority identifier system: ORCID (Open Researcher and Contributor iD)

❏      Used Software: Oracle database, multilayer architecture

❏      Interfaces: HTML interface (GUI) 

❏      Further functionalities/tools: Automated plausibility and quality check/peer review

Repositories in Profile – SupraBank

For chemists, it is crucial to know the advantages of different data repositories in order to find the best fit for their research data requirements. Here, we provide a brief overview of SupraBank as part of our series “repositories in profile”.

SupraBank

Figure 1: Screenshot SupraBank.

Basic information

      Homepage: https://suprabank.org

❏      Creation date: 2019

❏      Country: DE

❏      Domain: Organic Chemistry

❏      Usage: Open Access (data view), registration required (data contribution)

❏      Target group: Chemists, biologists

❏      User documentation: – 

❏      Number of datasets: 4000, 3700 are curated

❏      Recommended by journals/societies: No

❏      Listed in: re3data: r3d100013265, FAIRsharing: bsg-d001818

Functionalities and technical information

❏      Content: Supramolecular interactions

❏      Content origin: From projects

❏      Searchable content: Experiments and related components according to the input 

         fields, molecule interactions, publications

❏      Accepted data types: JSON (DataCite), CDX (for 2D/3D molecule structure), PNG, 

         proprietary formats

❏      Used standards/ontologies: DataCite 4.0, Dublin Core for metadata tags

❏      Curation: Non-judgmental plausibility check

❏      Access rights/license information/embargo: CC licenses (CC0, BY, BY-SA), 

         embargo possible (unlimited)

❏      AAI solution: Internal user administration (anonymous and non-anonymous user, 

         data provider, administrator)

❏      Persistent Identifier system: DOI (Digital Object Identifier)

❏      Authority identifier system: ORCID (Open Researcher and Contributor iD) 

❏      Used Software: Relational database (PostgreSQL), Ruby on Rails

❏      Interfaces: Web interface (CSV, JSON, BibTex, RIS, Endnote)

❏      Further functionalities/tools: Molecules presented as picture, structure editor, 

         simulation modeler tool

Repositories in Profile – MassBank EU

For chemists, it is crucial to know the advantages of different data repositories in order to find the best fit for their research data requirements. Here, we provide a brief overview of MassBank EU as part of our series “repositories in profile”.

MassBank EU – High Quality Mass Spectral Database

Figure 1: Screenshot MassBank EU.

Basic information

❏      Homepage: https://massbank.eu/MassBank/

❏      Creation date: 2006

❏      Country: DE, JPN

❏      Domain: Chemistry, Life Science

❏      Usage: Open Access 

❏      Target group: Analytical chemists, metabolomics, biochemists, bioinformaticians

❏      User documentation: Is available on the website

❏      Number of datasets: https://massbank.eu/MassBank/RecordIndex

❏      Recommended by journals/societies: Official database of the Mass Spectrometry Society of Japan

❏      Listed in: re3data: r3d100011839, FAIRsharing: FAIRsharing.dk451a, bio.tools: massbank, Wikidata: Property:P6689 Q24088019, Identifiers.org: massbank, PubChem: Data Source ID: 23999

Functionalities and technical information

❏      Content: Mass spectral data of known, unknown and provisionally identified substances

❏      Content origin: From community users and projects

❏      Searchable content: Compound and mass spectrometry information, peaks

❏      Accepted data types: MassBank format

❏      Used standards/ontologies: Internal MassBank Record Format 

❏      Curation: Via MassBank record validator; GitHub issues 

❏      Access rights/license information/embargo: Copyright; individual licenses based on creative commons; no embargo

❏      AAI solution: GitHub (Read access uncontrolled, write access for allowed GitHub accounts)

❏      Persistent Identifier system: MassBank Record ID (Accession), USI (Universal Spectrum Identifier)

❏      Authority identifier system: No

❏      Interfaces: Interface for data import via Git (MassBank record format), interface for data export (JSON-LD), REST API

❏      Further functionalities/tools: RMassBank (separated data processing/analysis tool)