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| - description: '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). ' | ||
| name: PRIDE - Quick tour | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Proteomics | ||
| - Data Sharing | ||
| type: Online tutorial | ||
| url: https://www.ebi.ac.uk/training/online/courses/pride-quick-tour/submitting-data-to-pride/ | ||
| - description: A webinar covering proteomics data submission process including a demo | ||
| for Proteome Xchange Submission Tool. | ||
| name: 'PRIDE database: Proteomics data submission, access and visualisation' | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Proteomics | ||
| - Data Sharing | ||
| type: Webinar | ||
| url: https://www.ebi.ac.uk/training/events/pride-database-proteomics-data-submission-access-and-visualisation/ | ||
| - description: '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. ' | ||
| name: Understanding Proteomes | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Proteomics | ||
| - Data Collection | ||
| - Data Reuse | ||
| type: Webinar | ||
| url: https://www.ebi.ac.uk/training/events/understanding-proteomes/ | ||
| - description: '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. ' | ||
| name: Submitting metagenomic data to ENA | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Metagenomics | ||
| - 'Data Sharing ' | ||
| type: Webinar | ||
| url: https://www.ebi.ac.uk/training/events/submitting-metagenomic-data-ena/ | ||
| - description: 'A workshop covering how to search and retrieve and perform analysis | ||
| on metagenomic sequencing data from NCBI ' | ||
| name: An NCBI Guide to Finding and Analyzing Metagenomic Data | ||
| provider: NCBI | ||
| topics: | ||
| - Metagenomics | ||
| - Data Analysis | ||
| - Data Reuse | ||
| type: Workshop | ||
| url: https://www.nlm.nih.gov/ncbi/workshops/2022-10_Guide-to-Metagenomics/workshop-details.html | ||
| - description: 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 | ||
| name: MGnify portal - Submitting metagenomics data to the European Nucleotide Archive | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Metagenomics | ||
| - 'Data Sharing ' | ||
| type: Online tutorial | ||
| url: https://www.ebi.ac.uk/training/online/courses/mgnify-portal/ | ||
| - description: A tutorial offering an introduction to Metabolights, a summary of data | ||
| submission and retrieval processes, along with additional support resources. | ||
| name: Metabolights - Quick Tour | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Metabolomics | ||
| - Data Sharing | ||
| type: Online tutorial | ||
| url: https://www.ebi.ac.uk/training/online/courses/metabolights-quick-tour/ | ||
| - description: 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. | ||
| name: 'MetaboLights: the home for metabolomics experiments and derived information' | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Metabolomics | ||
| - Data Sharing | ||
| type: Webinar | ||
| url: https://www.ebi.ac.uk/training/events/metabolights-home-metabolomics-experiments-and-derived-information/ | ||
| - description: 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 | ||
| name: 'Open with purpose: How and why to make your data open' | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Data Planning | ||
| type: Webinar | ||
| url: https://www.ebi.ac.uk/training/events/open-purpose-how-and-why-make-your-data-open/ | ||
| - description: 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. | ||
| name: Using Publicly available data | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Data Collection | ||
| - Data Reuse | ||
| type: Online tutorial | ||
| url: https://www.ebi.ac.uk/training/online/courses/using-publicly-available-data/ | ||
| - description: '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. ' | ||
| name: Bringing data to life, Data management for the biomolecular sciences | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Data Planning | ||
| - Data Sharing | ||
| - Data Reuse | ||
| type: Online tutorial | ||
| url: https://www.ebi.ac.uk/training/online/courses/bringing-data-to-life-data-management/ | ||
| - description: '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. ' | ||
| name: 'Open access: Data sharing and submission' | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Data Sharing | ||
| type: Webinar | ||
| url: https://www.ebi.ac.uk/training/events/open-access-data-sharing-and-submission/ | ||
| - description: A webinar covering processes of data retrieval and submission to BioStudies. | ||
| name: A guide to organising data associated to a publication using BioStudies | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Data Sharing | ||
| type: Webinar | ||
| url: https://www.ebi.ac.uk/training/events/guide-organising-data-associated-publication-using-biostudies/ | ||
| - description: ' | ||
| 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' | ||
| name: An Introduction to Accessing NCBI Resources on the Command Line using EDirect | ||
| for Biologists | ||
| provider: NCBI | ||
| topics: | ||
| - Data Collection | ||
| - Data Reuse | ||
| type: Workshop | ||
| url: https://ncbiinsights.ncbi.nlm.nih.gov/event/command-line-03-2023/ | ||
| - description: '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. ' | ||
| name: Getting Started with NCBI Data in Python | ||
| provider: NCBI | ||
| topics: | ||
| - Data Collection | ||
| - Data Analysis | ||
| - Data Reuse | ||
| type: Workshop | ||
| url: https://ncbiinsights.ncbi.nlm.nih.gov/event/getting-started-with-ncbi-data-in-python-04-22/ | ||
| - description: 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. | ||
| name: BioSamples Quick tour | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Data Sharing | ||
| type: Online tutorial | ||
| url: https://www.ebi.ac.uk/training/online/courses/biosamples-quick-tour/ | ||
| - description: What metadata is and why it is important to keep track of this information | ||
| in biological experiments. | ||
| name: Describing data consistently | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Data Planning | ||
| - 'Data Sharing ' | ||
| type: Short Video | ||
| url: https://www.ebi.ac.uk/training/online/courses/bioinformatics-terrified/what-makes-a-good-bioinformatics-database/describing-data-consistently/ | ||
| - description: Basic tips on managing and sharing data to maximise its re-use in the | ||
| future. | ||
| name: Tips on managing and sharing data | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Data Planning | ||
| type: Guide | ||
| url: https://www.ebi.ac.uk/training/online/courses/bioinformatics-terrified/tips-on-managing-and-sharing-data/ | ||
| - description: These slides focus on topics such as discipline-specific repositories, | ||
| generalist repositories, the FAIRDOM platform, and reproducible models in FAIRDOM. | ||
| name: Data publishing and archival | ||
| provider: ELIXIR Luxembourg | ||
| topics: | ||
| - Genomics | ||
| - Data Planning | ||
| type: Slides | ||
| url: https://zenodo.org/record/5524794 | ||
| - description: ' | ||
| 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.' | ||
| name: An Introduction to NCBI Cloud Computing for Biologists | ||
| provider: NCBI | ||
| topics: | ||
| - Genomics | ||
| - Data Collection | ||
| - Data Analysis | ||
| - Data Reuse | ||
| type: Workshop | ||
| url: https://www.nlm.nih.gov/oet/ed/ncbi/2022_07_cloud.html | ||
| - description: 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. | ||
| name: Functional Genomics - Submitting data | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Genomics | ||
| - Data Sharing | ||
| type: Online tutorial | ||
| url: https://www.ebi.ac.uk/training/online/courses/functional-genomics-iii-submitting-data/ | ||
| - description: 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. | ||
| name: Introduction to exploring genome-phenome data with EGA | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Genomics | ||
| - Data Reuse | ||
| type: Webinar | ||
| url: https://www.ebi.ac.uk/training/events/introduction-exploring-genome-phenome-data-ega/ | ||
| - description: 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. | ||
| name: Submitting your genome wide association study data to the GWAS Catalog | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Genomics | ||
| - Data Sharing | ||
| type: Webinar | ||
| url: https://www.ebi.ac.uk/training/events/submitting-your-genome-wide-association-study-data-gwas-catalog/ | ||
| - description: 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. | ||
| name: Nucleotide sequencing data submission and retrieval at the ENA | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Genomics | ||
| - Data Collection | ||
| - Data Sharing | ||
| - Data Reuse | ||
| type: Webinar | ||
| url: https://www.ebi.ac.uk/training/events/nucleotide-sequencing-data-submission-and-retrieval-ena/ | ||
| - description: 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. | ||
| name: Variant submission and data access at the European Variation Archive | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Data Sharing | ||
| - Data Reuse | ||
| type: Webinar | ||
| url: https://www.ebi.ac.uk/training/events/variant-submission-and-data-access-european-variation-archive/ | ||
| - description: 'A tutorial introducing ArrayExpress and describing Annotare tool and | ||
| MAGE-TAB spreadsheet method for data submission. ' | ||
| name: ArrayExpress in BioStudies | ||
| provider: EMBL-EBI | ||
| topics: | ||
| - Data Sharing | ||
| type: Online tutorial | ||
| url: https://www.ebi.ac.uk/training/online/courses/arrayexpress-in-biostudies/#vf-tabs__section--overview |