Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

https://github.com/Materials-Data-Science-and-Informatics/awesome-fair

A curated list of awesome stuff around the FAIR principles for (scientific) data, i.e that data is findable, accessable, interoperable and re-usable.
https://github.com/Materials-Data-Science-and-Informatics/awesome-fair

List: awesome-fair

ai-ready awesome awesome-list data-provenance data-science digital-objects fair fair-digital-objects fair-principles fdo interoperability metadata metadata-information metadata-management metadata-standard provenance research-data research-data-management

Last synced: 3 months ago
JSON representation

A curated list of awesome stuff around the FAIR principles for (scientific) data, i.e that data is findable, accessable, interoperable and re-usable.

Lists

README 

        


	pyds

	


	


	





# Awesome FAIR





Awesome






> A by the [Helmholtz metadata collaboration (HMC)](https://helmholtz-metadaten.de/en) curated list of awesome stuff around the FAIR principles for (scientific) data, i.e that data is findable, accessable, interoperable and re-usable. The list is organized in use cases of data producers, data users, data curators and data provides. 'FAIR' is not the same as 'open', but there is overlap.



## Contents

* [Resources about the FAIR principles](#resources-about-the-fair-principles)

    * [FAIR Digital Object and related projects](#fair-digital-object-and-related-projects)

* [FAIR assessment](#fair-assessment)

* [Organizations and Communities](#organizations-and-communities)

* [Metadata formats and standards](#metadata-formats-and-standards)

* [Ontology services](#ontology-services)

	* [Related semantics lists](#related-semantics-lists)

* [Finding datasets and software](#finding-datasets-and-software)

* [Software and software publications](#software-and-software-publications)

* [Provenance tracking](#provenance-tracking)

	* [Related workflow tools lists](#related-workflow-tools-lists)

* [Metadata management](#metadata-management)

* [Your own repository setup](#your-own-repository-setup)

* [Awesome meta data sources](#awesome-meta-data-sources)

* [Related lists](#related-lists)



## Resources about the FAIR principles



* [Barend Mons article in Nature 578, 491 (2020)](https://doi.org/10.1038/d41586-020-00505-7) - Proposition to invest 5% of research funds in ensuring data are reusable.



* [Cost of not having FAIR research data](https://op.europa.eu/s/sV6Z) - A 2018 European Commission Cost-benefit analysis for FAIR research data (Written by PwC EU Services).



* [The FAIR Guiding Principles for scientific data management and stewardship](https://doi.org/10.1038/sdata.2016.18) - This Comment in [Sci Data](https://www.nature.com/sdata/) is the first formal publication of the FAIR Principles (2016).



* [GO FAIR Zotero Library](https://www.zotero.org/groups/2345721/fair_data_resources/) - Nice collection of publications around the FAIR principles.



### FAIR Digital Object and related projects



* [DataPLANT ARC Tool Talk](https://www.youtube.com/watch?v=dOMNzY5rUlE&t=2137s) - NFDI4plants interpretation of the FDO based on GitHub repository and RO Crate.



* [DONA Suggested Reading](https://www.dona.net/suggested-reading-documents) - The history of the Digital Object Architecture (DOA) back into the 80s.



* [FAIR Digital Objects Forum](https://fairdo.org/) - General platform for discussions on the advancement and development of FAIR Digital Objects.



* [FAIR Digital Object Framework](https://fairdigitalobjectframework.org/) - A WIP specification for an FDO infrastructure based on linked data / RDF.



* [FAIR DO publications](https://www.rd-alliance.org/group/data-fabric-ig/wiki/fair-do-publications) - Relevant publications (concept papers and specs) by RDA working groups on FDOs.



* [RO Crate](https://www.researchobject.org/ro-crate/) - Pragmatic approach combining existing technologies and ontologies into a metadata standard for annotating scientific. datasets.



* [PID services registry](https://pidservices.org/) - A searchable registry for PID services.



## FAIR assessment



* [FAIR Evaluation Services](https://fairsharing.github.io/FAIR-Evaluator-FrontEnd/#!/) - A FAIR assessment tool from FAIRsharing, [code](https://github.com/FAIRMetrics/Metrics).



* [F-uji](https://www.f-uji.net/) - An (online) tool which can provide a FAIR score for a given PID based on a metric created by FAIRsFAIR, [code](https://github.com/pangaea-data-publisher/fuji).



## Organizations and Communities



* [EuDat](https://www.eudat.eu/) - Collaborative European data infrastructure.



* [FAIRsharing](https://fairsharing.org/) - A curated resource on data and metadata standards, inter-related to databases and data policies. 



* [Research Data Alliance](https://www.rd-alliance.org/) - International organization and communication platform for establishing standards and recommendations concerning research data publication.



* [The Turing Way](https://the-turing-way.netlify.app/welcome.html) - Handbook and community for reproducible, ethical and collaborative data science.



## Metadata formats and standards



* [DataCite](https://schema.datacite.org/) - Metadata schema developed by international community with increasing adoption by repositories



* [Data Catalog (DCAT)](https://www.w3.org/TR/vocab-dcat-2/) - RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web.



* [Dublin Core Metadata Initiative Terms](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/) - Dublin Core Metadata Element Set, is a set of fifteen "core" elements for describing resources.



* [JSON LD Playground](https://json-ld.org/playground/) - Convert JSON-LD data between various representations.



* [JSON Schema](https://json-schema.org/) - Standard for the description of structural constraints in order to do validation of JSON objects.



* [Provenance Primer (PROV)](https://www.w3.org/TR/2013/NOTE-prov-primer-20130430/) - This primer document provides an accessible introduction to the PROV data model for provenance interchange on the Web.



* [Resource Description Framework (RDF)](https://www.w3.org/RDF/) - RDF is a standard model for data interchange on the Web. 



* [Schema.org](https://schema.org/) - Well-established and industry-accepted vocabulary providing semantics for common entities like Person, Organization, Dataset, etc.



* [SKOS](https://www.w3.org/2009/08/skos-reference/skos.html) - The Simple Knowledge Organization System (SKOS) is a common data model for sharing and linking knowledge organization systems via the Semantic Web.



## Ontology services



* [Ontobee](http://www.ontobee.org/) - A linked ontology data server to support ontology term dereferencing, linkage, query and integration. 

See also this [publication](https://academic.oup.com/nar/article/45/D1/D347/2770665).



* [Ontology Lookup Service](https://www.ebi.ac.uk/ols/index) - OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions.



### Related semantics lists

Also see 

* [awesome-ontology](https://github.com/ozekik/awesome-ontology) - A curated list of ontology things.

* [awesome-semantic-tools](https://github.com/costezki/awesome-semantic-tools) - List of projects related to Ontology engineering and Semantic Web technologies.



## Finding datasets and software



* [Datacite commons](https://commons.datacite.org/) - Search through the metadata indexed by Datacite.



* [EuDat B2find](http://b2find.eudat.eu/) - Search through metadata of datasets accumulated by EuDat.



* [Microsoft academy](https://academic.microsoft.com/home) - Mircosoft academy search through a pid graph created by microsoft (shutdown end of 2021).



* [OpenAIRE explorer](https://explore.openaire.eu/) - Search through the metadata indexed by openaire.



* [Schole explorer](https://scholexplorer.openaire.eu/) - A data literature interlinking service (former scholix), indexes links between data and journal publications. It also provides interfaces and APIs to query the graph.



* [Research Software Repository](https://research-software.nl/) - Aggregates research software from various sources with information about the problem it solves and its scientific domain.



## Software and software publications



* [CITATION.CFF](https://citation-file-format.github.io/) - Plain text files with human- and machine-readable citation information for software (and datasets). Supported by GitHub, Zenodo, Zotero.



* [Citable code with Zenodo & GitHub](https://guides.github.com/activities/citable-code/) - Make GitHub repositories citable with Zenodo DOI.



* [CodeMeta](https://codemeta.github.io/) - CodeMeta works on providing a minimal metadata schema for science software and code, in JSON and XML to create a concept vocabulary that can be used to standardize the exchange of software metadata across repositories and organizations. 



* [fossology](https://github.com/fossology/fossology) - FOSSology is an open source license compliance software system and toolkit. You can run license, copyright and export control scans from the command line.



* [HERMES](https://github.com/hermes-hmc/workflow) - A CI based workflow to create and publish software publications to well known repositories. 



* [SOMEF](https://github.com/KnowledgeCaptureAndDiscovery/somef) - Extract software publication metadata from README and other docs automatically using ML and other techniques to reduce the amount of boilerplate work for the developer.



### Related research software lists

* [awesome-research-software-registies](https://github.com/NLeSC/awesome-research-software-registries) - Awesome list for where one can register or upload research software.

* [awesome-rse](https://github.com/hifis-net/awesome-rse) - An awesome collection of resources around research software engineering.



## Provenance tracking



* [AiiDA](https://www.aiida.net/) - Automated Interactive Infrastructure and Database for Computational Science (AiiDA) to automatically track provenance of simulation workflows and all associated data, [code](https://github.com/aiidateam/aiida-core).



* [DataLad](https://www.datalad.org/) - A free and open-source distributed data management system for everyone. It is based on git-annex with manual to automatic provenance tracking, [code](https://github.com/datalad/datalad).



* [MLflow](https://mlflow.org/) - Tool to track the provenance of machine learning applications, [code](https://github.com/mlflow/mlflow/).



* [CWL](https://www.commonwl.org) - Domain-agnostic and community-driven open standard for description and execution of research workflows that supports provenance tracking ([CWLProv](https://github.com/common-workflow-language/cwltool/blob/main/CWLProv.rst)) in a standard-compliant way using the existing RO Crate, PROV and BagIt standards.



* [PROV-O Primer](https://www.w3.org/TR/2013/NOTE-prov-primer-20130430/) - An introduction to the data model of [Provenance Ontlogy (PROV-O)](https://www.w3.org/TR/2013/REC-prov-o-20130430/)



### Related workflow tools lists

There is overlap with these more general lists of workflow tools, but not every pipeline or workflow manager includes good provenance tracking.

* [awesome-pipeline](https://github.com/pditommaso/awesome-pipeline) - A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin.

* [Awesome workflow engines](https://github.com/meirwah/awesome-workflow-engines) - Curated list of awesome open source workflow engines.

* [Computational Data Analysis Workflow Systems](https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems) - A list of existing workflow systems.



## Metadata management



## Your own repository setup



* [Dataverse](https://dataverse.org/) - Open source research data repository software [code](https://github.com/IQSS/dataverse).



* [EuDat B2share](https://b2share.eudat.eu/) - A repository by EuDat, but the software is open sourc, bases in invenio and one can setup own instances of it, [code](https://github.com/EUDAT-B2SHARE/b2share).



* [Invenio](https://invenio-software.org/) - Open source customizable software to setup large scale digital repositories, library systems and data repositories, [code](https://github.com/inveniosoftware/invenio).



* [InvenioRDM](https://inveniosoftware.org/products/rdm/) - The turn-key research data management repository based on Invenio framework and Zenodo.



## Awesome meta data sources



* [Microsoft academy graph](https://doi.org/10.5281/zenodo.2628216) - All the data and links from Mircosoft academy (shutdown end of 2021).



* [Openaire graph](https://doi.org/10.5281/zenodo.4707307) - All metadata contained in the openaire graph.



* [Scholix](http://www.scholix.org/schema) - A schema for scholarly links. Implemented and deployed by several scholarly link providers.



* [CrossRef](https://www.crossref.org/) - Organization building connections between related entities, building a queryable graph.



## Related lists

Awesome lists related to several points.



* [awesome-rse](https://github.com/hifis-net/awesome-rse) - An awesome list by HIFIS collecting information about research software engineering, touching FAIRness and sustainability

* [awesome-rse-policies](https://github.com/hifis-net/awesome-rse-policies) - An awesome list by HIFIS collecting information about research software engineering policies, touching FAIRness and sustainability



* [Awesome-open-climate-science](https://github.com/pangeo-data/awesome-open-climate-science) - An open science related list specific to the domain of Atmospheric, Ocean, and Climate science.

* [Awesome-open-science-software](https://github.com/INRIA/awesome-open-science-software) - A list of open science resources and software.

* [Awesome Curated Tools](https://github.com/chow-petit/awesome-curated-tools) - A curated list of digital tools we use, ranging from accounting and data science to scientific research and liquid democracy.



## Contributing

Contributions are welcome! :sunglasses: 

If you want to contribute please read the contribution guideline.