Metadata standards and repositories for Applied Sciences/TNW

Relevant metadata standards

ISA-Tab

MIBBI (Minimum Information for Biological and Biomedical Investigations)

NeXus

OME-XML (Open Microscopy Environment XML)

PDBx/mmCIF (Protein Data Bank Exchange Dictionary and the Macromolecular Crystallographic Information Framework)

CIF (Crystallographic Information Framework)

QuDEx (Qualitative Data Exchange Format)

SDMX (Statistical Data and Metadata Exchange)

The Synthetic Biology Open Language (SBOL) & SBOL Visual

STRENDA

Croissant

MeSH (Medical Subject Headings), a controlled vocabulary used to index biomedical information (see also MeSH on demand, a tool to that automatically detects MeSH terms in a text).

Standard for Learning Object Metadata

Potentially relevant metadata standards

Genome Metadata

CF (Climate and Forecast) Metadata Conventions

CIM (Common Information Model)

CSMD (Core Scientific Metadata Model)

DIF (Directory Interchange Format)

ISO 19115

Observations and Measurements

CERIF (Common European Research Information Format)

Data Package

ABCD (Access to Biological Collection Data)

MODS (Metadata Object Description Schema)

EDAM-bioimaging

Repositories

DNA DataBank of Japan (DDBJ)

European Nucleotide Archive (ENA)

GenBank

dbSNP

European Variation Archive (EVA)

dbVar

Database of Genomic Variants Archive (DGVa)

EBI Metagenomics

NCBI Trace Archive

NCBI Sequence Read Archive (SRA)

International Nucleotide Sequence Database Collaboration

NCBI Assembly

Structural Biology Data Grid

Worldwide Protein Data Bank (wwPDB)

UniProtKB

Biological Magnetic Resonance Data Bank (BMRB)

Flowrepository

LIPID MAPS

PRIDE

SynBioHub

Open Energy Data Initiative (OEDI)

HuggingFace ML datasets (see blogpost for more info)

Reporting standards

• MIMARKS (and MINAS for ancient sequences)

• REFORMS: Reporting Standards for ML-based Science

RNA-seq/qpcr

• European Nucleotide Archive (ENA)

• Sequence Read Archive (SRA)

• Gene Expression Omnibus (GEO)

• ENCODE

• exRNA Atlas

• Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE)

Microscopy

• Repositories

  • IDR(see FAQ)

  • Electron Microscopy Data Bank (EMDB)

  • EMPIAR(Cryo-EM/ET, 3D EM)

  • Cell Image Library

  • BioImage Archive (2D EM, Light microscopy and other data)

    • Intro video on EMPIAR and BioImage Archive

• Image formats

  • OME (Swedlow et al. 2003)

  • Bio-Formats (Li et al. 2016)

• Metadata

  • REMBI: Recommended Metadata for Biological Images

  • light Microscopy Metadata Specifications (Hammer et al. 2021)

  • 3D Microscopy Metadata Standards (3D-MMS) (Ropelewski et al. 2021)

  • The Minimum Information for High Content Screening Microscopy Experiments (MIHCSME) is a metadata model and reusable tabular template for sharing and integrating high content imaging data. (Hosseini et al. 2023)

  • Tools such as Micro-Meta App & MethodsJ2

• Open blink project

• Confocal Microscopy Data: A Primer for Curators

• Community-developed checklists for publishing images and image analyses

• Recording analysis steps with ImageJ/Fiji or Galaxy Imaging

• RDM platforms like: OMERO, Cytomine, BISQUE and XNAT

• QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy

• the Digital Imaging and Communications in Medicine (DICOM) standard

Genomics

• GenBank, EMBL-Bank, DDBL (processed sequence data), Sequence Read Archive (raw sequencing data)

• Minimum Information about Highly Multiplexed Tissue Imaging (MITI) standard that applies best practices developed for genomics and for other microscopy data to highly multiplexed tissue images and traditional histology. (Schapiro et al. 2022)

• MIAME standard for micro array data (Brazma et al. 2001)

• Minimum information about a genome sequence (MIGS) specification (Field et al. 2008)

• Minimum reporting guidelines for biological and biomedical investigations: the MIBBI project (Taylor et al. 2008)

• Minimum Information Standards (MIxS) established a community-based mechanism for sharing genomic data through a common framework

• FAIR genomes for the medical setting

• MINSEQE describes the Minimum Information about a high-throughput nucleotide SEQuencing Experiment that is needed to enable the unambiguous interpretation and facilitate reproduction of the results of the experiment.

• MinSCe is a minimum set of single-cell metadata categories and a checklist of information that can be used to describe a single-cell assay in sufficient detail to enable the analysis of transcriptomic data

• Running projects such as: https://www.ga4gh.org/product/experiments-metadata-standard/

• https://genomicsstandardsconsortium.github.io/mixs/

• From FASTQ to BAM

Tools

• ioChem-BD

• Procedures for systematic capture and management of analytical data in academia

Simulation outputs

• SED-ML

• Minimum Information About a Simulation Experiment (MIASE)

Open Research

Open Research: Examples of good practice, and resources across disciplines

Other

• Dr. Christoph Steinbeck on “Informatics, Datasets and the Curation of the Future”

MRI data

• Brain MRI data sharing guide

• The Open Brain Consent

Image Data

• XNAT Central (neuroimaging, but also from oncology, orthopaedics and cardiology)

• The Cancer Imaging Archive

Publications & articles

• Theisen et al. 2023
• How to get microscopes to speak the same language
• Reproducible and replicable CFD: it’s harder than you think

Battery

[..E]arly independent battery-data activities include those of Battery Archive, BIG-MAP [(BattINFO ontology)], Batteries Europe, and the Faraday Institution. Their diversity of locations and formats underscores the critical need for a singular approach to improve uniformity.38,41 - Ward et al. 2022

• BEEP: A Python library for Battery Evaluation and Early Prediction

• Galvanalyser is a system for automatically storing data generated by battery cycling machines in a database

• Battery Microstructures Library

• MATBOX: Microstructure Analysis Toolbox (Li-ion batteries)

• BruggemanEstimator: Open Source Code for Estimating the Tortuosity Estimation of Lithium Ion Battery Porous Electrodes from SEM images

• TauFactor is an application for calculating tortuosity factors from tomographic data.

• Battery Data Toolkit, converts battery testing data from native formats to a standardized HDF5 file.

• Ontologies for battery data (BattINFO & BVCO)

  • “There are currently two major ongoing initiatives dedicated to ontologizing the battery domain: The Battery Interface Ontology (BattINFO) and the Battery Value Chain Ontology (BVCO). BattINFO describes batteries on the cell level and below, including not only components, materials, and their interfaces, but also electrochemical processes, models, and characterization data. The objective of BattINFO is to support AI workflows and interoperability of battery data in the research and development community. On the other hand, BVCO describes aspects of the battery value chain with a strong focus on battery manufacturing and recycling. Both BattINFO and BVCO stem from the top-level ontology EMMO and are publicly available under open-source licenses.”

• BIG-MAP Data Management Plan article + deliverable

• Repositories:

  • Inorganic Crystal Structure Database (ICSD)

  • Materials Cloud

  • Materials Project

  • Computational Materials Repository

Bio–nano

Minimum information reporting in bio–nano experimental literature (MIRIBEL)

CFD

• Machine Learning for Computational Fluid Dynamics

• Courses:

  • ME 702 Computational Fluid Dynamics

  • Computational Fluid Dynamics

• Books for Computational Fluid Dynamics

• Fluid Mechanics 101

• Computational Fluid Dynamics (CFD) - A Beginner’s Guide

More information

• Metadata Standards Catalog

• FAIRsharing.org