The data management collection is curated and endorsed by Australian BioCommons and is designed to support life sciences researchers understand the best practices and procedures involved in the stages of the data lifecycle. The collection consists of training materials and documentation from reputable sources such as EMBL-EBI Training and NCBI Training, and covers topics like data sharing and data reuse.
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Skip tool table| Resource | Description | Topic(s) | Format | Provider |
|---|---|---|---|---|
| A guide to organising data associated to a publication using BioStudies | A webinar covering processes of data retrieval and submission to BioStudies.
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Data sharing | Webinar | EMBL-EBI |
| An Introduction to Accessing NCBI Resources on the Command Line using EDirect for Biologists |
A workshop teaching biological researchers how to use the command line to search and fetch NCBI data, focusing on creating bash commands to download and organize files and constructing search queries with the EDirect toolkit
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Data collection, data reuse | Workshop | NCBI |
| An Introduction to NCBI Cloud Computing for Biologists |
A workshop covering how to use AWS services like Athena to mine metadata from the NCBI SRA database for dataset selection, perform sequence alignment analysis with MagicBlast, and visualize aligned data in the NCBI Genome Data Viewer browser application.
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Data collection, Data reuse, Data analysis, Genomics | Workshop | NCBI |
| An NCBI Guide to Finding and Analyzing Metagenomic Data | A workshop covering how to search and retrieve and perform analysis on metagenomic sequencing data from NCBI
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Data analysis, Data reuse, Metagenomics | Workshop | NCBI |
| ArrayExpress in BioStudies | A tutorial introducing ArrayExpress and describing Annotare tool and MAGE-TAB spreadsheet method for data submission.
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Data sharing | Online tutorial | EMBL-EBI |
| BioSamples Quick tour | A tutorial introducing the BioSamples database and the concept of a biosample. It also provides website navigation tips, and directs users to more information on accessing and downloading data from BioSamples.
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Data sharing | Online tutorial | EMBL-EBI |
| Bringing data to life, Data management for the biomolecular sciences | A tutorial encompassing concepts of data management e.g. the data management cycle, data management tools (DMPonline and Data stewardship wizard), FAIRness vs Openness, benefits/challenges of data sharing, and ontologies/standards (e.g. The Ontology Lookup Service (OLS) and The Experimental Factor Ontology (EFO)) to be used to describe/annotate data.
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Online tutorial | EMBL-EBI | |
| Data publishing and archival | These slides focus on topics such as discipline-specific repositories, generalist repositories, the FAIRDOM platform, and reproducible models in FAIRDOM.
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Data planning, Genomics | Slides | ELIXIR Luxembourg |
| Describing data consistently | What metadata is and why it is important to keep track of this information in biological experiments.
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Data planning, Data sharing | Short Video | EMBL-EBI |
| Functional Genomics - Submitting data | A tutorial covering the importance of data submission, metadata templates like MIAME and MINSEQE, submission timelines, and submission locations for functional genomics data (e.g. ArrayExpress and GEO). It also discusses secondary databases like Expression Atlas.
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Data sharing, Genomics | Online tutorial | EMBL-EBI |
| Getting Started with NCBI Data in Python | A workshop demonstrating effective use of python programming, BioPython package and Jupyter notebooks to facilitate download, analysis and visualisation of data in a reproducible fashion.
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Data collection, Data reuse, Data analysis | Workshop | NCBI |
| Introduction to exploring genome-phenome data with EGA | A webinar offering an overview of EGA, discussing its controlled access data, the process for gaining access through the Data Access Committee, the use of DUO ontology for tagging data, and a live demo of pyEGA3 for downloading permitted data.
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Data planning, Genomics | Webinar | EMBL-EBI |
| Metabolights - Quick Tour | A tutorial offering an introduction to Metabolights, a summary of data submission and retrieval processes, along with additional support resources.
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Data sharing, Metabolomics | Online tutorial | EMBL-EBI |
| MetaboLights: the home for metabolomics experiments and derived information | A webinar introducing MetaboLights, metabolomics, and the Metabolomics Standards Initiative (MSI), demonstrating how to navigate the MetaboLights site to explore study information and providing a brief overview of study submission.
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Data sharing, Metabolomics | Webinar | EMBL-EBI |
| MGnify portal - Submitting metagenomics data to the European Nucleotide Archive | A tutorial with a detailed walkthrough for submitting metagenomics data to ENA for analysis by MGnify, highlighting metadata standardization, the use of templates like GSC MIxS for contextual information, and submission methods through ENA or the MGnify browser
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Data sharing, Metagenomics | Online tutorial | EMBL-EBI |
| Nucleotide sequencing data submission and retrieval at the ENA | A webinar introducing the background of the European Nucleotide Archive (ENA), data and metadata models, submission and retrieval processes, submission methods, and tools for data download.
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Data collection, Data reuse, Data sharing | Webinar | EMBL-EBI |
| Open access: Data sharing and submission | A webinar with discussion regarding importance of sharing research data and infrastructure available at EMBL-EBI to support sharing. It also describes data submission process to IntAct and ComplexPortal.
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Data sharing | Webinar | EMBL-EBI |
| Open with purpose: How and why to make your data open | A webinar about open access data, examples of making BioSamples submissions FAIR, open data at IntAct database and how PMC Europe is promoting open access publicationg
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Data planning | Webinar | EMBL-EBI |
| PRIDE - Quick tour | A tutorial with an overview of PRoteomics IDEntification (PRIDE) database, how to search and download datasets from PRIDE and an introduction of PRIDE tools: Proteome Xchange Submission Tool and PRIDE Inspector (to assess the quality of a dataset).
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Proteomics, Data sharing | Online tutorial | EMBL-EBI |
| PRIDE database: Proteomics data submission, access and visualisation | A webinar covering proteomics data submission process including a demo for Proteome Xchange Submission Tool.
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Data sharing, Proteomics | Webinar | EMBL-EBI |
| Submitting metagenomic data to ENA | A webinar with an introduction of ENA, INSDC agreement, the ENA data and metadata model, how to structure a metagenomic study and submit metagenomics data to ENA.
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Data sharing, Metagenomics | Webinar | EMBL-EBI |
| Submitting your genome wide association study data to the GWAS Catalog | A webinar offering a detailed guide on submitting data to the GWAS Catalog, including user account setup, data format conversion, metadata provision, and validation using a command-line tool, with an emphasis on explaining metadata columns.
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Data sharing | Webinar | EMBL-EBI |
| Tips on managing and sharing data | Basic tips on managing and sharing data to maximise its re-use in the future.
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Data planning | Guide | EMBL-EBI |
| Understanding Proteomes | A webinar with an introduction to the proteomes and how to find and download relevant protein datasets. It also includes a UniProt demonstration to find proteomic data with user queries.
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Data collection, Data reuse, Proteomics | Webinar | EMBL-EBI |
| Using Publicly available data | A tutorial about publicly available data and importance of licenses to make the data open. Topics covered include data formats, controlled vocabularies, ontologies, reporting guidelines, minimum reporting checklists and importance of unique identifiers for data artefacts.
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Data collection, data reuse | Online tutorial | EMBL-EBI |
| Variant submission and data access at the European Variation Archive | A webinar providing an overview of the European Variation Archive (EVA) and its integration with other EBI resources, a live demo of the EVA interface for accessing data via web, FTP, or API, and clarification on using SS and RS IDs for variant access/reference.
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Data sharing, Data reuse | Webinar | EMBL-EBI |