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[STY] pacify style checkers and fix links (#581)
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| Original file line number | Diff line number | Diff line change |
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@@ -119,8 +119,7 @@ consecutive years as chair. BIDS Steering Group members may hold other | |
| BIDS roles at the same time, for example BEP Working Group chair. | ||
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| The BIDS Steering Group is the authority of last resort in addressing | ||
| conflicts among groups and alleged violations of the [Code of | ||
| Conduct](https://github.com/bids-standard/bids-specification/blob/master/CODE_OF_CONDUCT.md). | ||
| conflicts among groups and alleged violations of the [Code of Conduct](./bids_github/CODE_OF_CONDUCT.md). | ||
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| The Steering Group may delegate tasks as needed to fulfill its responsibilities. | ||
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@@ -141,8 +140,8 @@ aim of extending or modifying the BIDS standard into their domain of | |
| interest. This can be either an unspecified modality or derivative. | ||
| The BEP Lead and Working Group will determine how they organize their | ||
| work, following the BIDS governance standards laid out in section 4 of | ||
| this document and the BIDS [Code of | ||
| Conduct](https://github.com/bids-standard/bids-specification/blob/master/CODE_OF_CONDUCT.md). The BEP Working Group work is completed when their BEP has become a Merged BEP. | ||
| this document and the BIDS [Code of Conduct](./bids_github/CODE_OF_CONDUCT.md). | ||
| The BEP Working Group work is completed when their BEP has become a Merged BEP. | ||
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| ### BEP Leads Group | ||
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@@ -456,7 +455,7 @@ blog](http://reproducibility.stanford.edu/blog/) provides tutorials and | |
| community survey results. | ||
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| All BIDS community members are required to follow the | ||
| [BIDS code of conduct](https://github.com/bids-standard/bids-specification/blob/master/CODE_OF_CONDUCT.md). | ||
| [BIDS code of conduct](./bids_github/CODE_OF_CONDUCT.md). | ||
| Please contact the BIDS maintainers at [[email protected]](mailto:[email protected]) | ||
| if you have any concerns or would like to report a violation. | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,45 +1,52 @@ | ||
| # BIDS Impact | ||
|
|
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| The Brain Imaging Data Structure (BIDS) is an open global community driving the | ||
| standardization of neuroscience data across a broad and growing range of modalities | ||
| and health research disciplines. First released in June 2016, it is supported by a | ||
| worldwide research network and endorsed by organizations like the International | ||
| The Brain Imaging Data Structure (BIDS) is an open global community driving the | ||
| standardization of neuroscience data across a broad and growing range of modalities | ||
| and health research disciplines. First released in June 2016, it is supported by a | ||
| worldwide research network and endorsed by organizations like the International | ||
| Neuroinformatics Coordinating Facility ([INCF](https://www.incf.org/)). | ||
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| BIDS encompasses: | ||
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| - Over 40 domain-specific and modality-specific technical specifications across | ||
| scientific and technical domains. | ||
| - 100+ sample data models for BIDS specifications in | ||
| [bids-examples](https://github.com/bids-standard/bids-examples). Read more about | ||
| the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/). | ||
| - 2000 open datasets across repositories including | ||
| [OpenNeuro](https://www.openneuro.org). Read more about [BIDS Datasets](/docs/datasets/index.md). | ||
| - Open software conversion and analytics tools, and global infrastructure for | ||
| collaborating on emerging standards in neuroscience | ||
| [Poldrack, et al, 2024](https://direct.mit.edu/imag/article/doi/10.1162/imag_a_00103/119672/The-past-present-and-future-of-the-brain-imaging). | ||
| - ~30,000 annual website visits from a very large community of neuroscience researchers | ||
| actively consulting the BIDS specifications (April 2023-24). | ||
| - Over 300 BIDS contributors currently supporting and maintaining BIDS community | ||
| resources and tools. | ||
| - Open working processes through online collaborative tools including GitHub, | ||
| GitHub Pages, ReadTheDocs, Google Docs, and OSF. | ||
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| The BIDS core steering and maintainers groups work with the community to optimize open | ||
| adherence to FAIR principles (Findable, Accessible, Interoperable, and Reusable, | ||
| [Wilkinson, et al, 2016](https://www.nature.com/articles/sdata201618)) and to actively | ||
| - Over 40 domain-specific and modality-specific technical specifications | ||
| across scientific and technical domains. | ||
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| - 100+ sample data models for BIDS specifications | ||
| in the [bids-examples](../datasets/examples.md). | ||
| Read more about the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/). | ||
|
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| - 2000 open datasets across repositories | ||
| including [OpenNeuro](https://www.openneuro.org). | ||
| Read more about [BIDS Datasets](../datasets/index.md). | ||
|
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| - Open software conversion and analytics tools, | ||
| and global infrastructure for collaborating on emerging standards in neuroscience | ||
| [Poldrack, et al, 2024](https://direct.mit.edu/imag/article/doi/10.1162/imag_a_00103/119672/The-past-present-and-future-of-the-brain-imaging). | ||
|
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| - ~ 30,000 annual website visits from a very large community of neuroscience researchers | ||
| actively consulting the BIDS specifications (April 2023-24). | ||
|
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| - Over 300 BIDS contributors currently supporting | ||
| and maintaining BIDS community resources and tools. | ||
|
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| - Open working processes through online collaborative tools | ||
| including GitHub, GitHub Pages, ReadTheDocs, Google Docs, and OSF. | ||
|
|
||
| The BIDS core steering and maintainers groups work with the community to optimize open | ||
| adherence to FAIR principles (Findable, Accessible, Interoperable, and Reusable, | ||
| [Wilkinson, et al, 2016](https://www.nature.com/articles/sdata201618)) and to actively | ||
| lower barriers to adoption. | ||
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| ## Measuring BIDS Impact | ||
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| ### Datasets | ||
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| Over the years, the number of shared datasets available to the public has | ||
| greatly increased. At its heart, adoption of the BIDS standard across datasets | ||
| aids in the sharing of data and collaboration of research through the standardization | ||
| of descriptive files names and the organization of data. BIDS organized datasets are | ||
| available through public repositories such as [Openneuro.org](https://openneuro.org/) | ||
| and the number of publicly available BIDS datasets continues to grow every year. | ||
| Over the years, the number of shared datasets available to the public has | ||
| greatly increased. At its heart, adoption of the BIDS standard across datasets | ||
| aids in the sharing of data and collaboration of research through the standardization | ||
| of descriptive files names and the organization of data. BIDS organized datasets are | ||
| available through public repositories such as [Openneuro.org](https://openneuro.org/) | ||
| and the number of publicly available BIDS datasets continues to grow every year. | ||
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| <!-- use snippet to include a file | ||
| https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets-notation | ||
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@@ -49,9 +56,9 @@ https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets- | |
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| ### Citation Count | ||
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| As the adoption of the BIDS standard across neuroimaging datasets has grown, so have | ||
| citations for work that uses BIDS data and BIDS apps. To aid in searching for publications | ||
| relevant to the BIDS standard, we have included some examples of BIDS references that are | ||
| As the adoption of the BIDS standard across neuroimaging datasets has grown, so have | ||
| citations for work that uses BIDS data and BIDS apps. To aid in searching for publications | ||
| relevant to the BIDS standard, we have included some examples of BIDS references that are | ||
| centralized in a [zotero group](https://www.zotero.org/groups/5111637/bids) | ||
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| <!-- use snippet to include a file | ||
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@@ -61,10 +68,10 @@ https://facelessuser.github.io/pymdown-extensions/extensions/snippets/#snippets- | |
| --8<-- "tmp/citation_per_year.html" | ||
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| ### GitHub stars | ||
| GitHub stars quantify the number of users that have marked a repository as a favorite and have | ||
| chosen to follow the changes made to that repository. Below is a table of GitHub repos that are | ||
| associated with the BIDS standard and their star count. By tracking repo interest via GitHub stars, | ||
| we can quantify which BIDS-associated tools are of the highest interest to the research community. | ||
| GitHub stars quantify the number of users that have marked a repository as a favorite and have | ||
| chosen to follow the changes made to that repository. Below is a table of GitHub repos that are | ||
| associated with the BIDS standard and their star count. By tracking repo interest via GitHub stars, | ||
| we can quantify which BIDS-associated tools are of the highest interest to the research community. | ||
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| | repository | stars | | ||
| | ----------------- | ------------------------------------------------------------------------------------------ | | ||
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@@ -97,7 +104,7 @@ Our list of contributors are captured in our | |
| We update the contributor appendix every specification release. As of July 2023, | ||
| we have over 300 credited contributors. | ||
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| The table below provides a brief account of the number of contributors per repository. Estimated demographics and affiliations | ||
| The table below provides a brief account of the number of contributors per repository. Estimated demographics and affiliations | ||
| of contributors is also provided below. | ||
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| | repository | all-contributors | github | | ||
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@@ -153,24 +160,24 @@ github-dependents-info --repo bids-standard/pybids --badgemarkdownfile ./dashboa | |
| ## BIDS History | ||
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| Since its origin, the BIDS standard has revolutionized the way in which neuroimaging | ||
| research is done. The origin of the BIDS standard is commonly traced back to 2014, | ||
| when a social media post ignited a deeper discussion about a new way of sharing | ||
| data, that would ultimately lead to a set of standards that would improve scientific | ||
| collaboration efforts. | ||
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| Following this initial discussion (and on the shoulders of many many volunteer hours | ||
| by maintainers and the community at large) the BIDS standard saw significant adoption | ||
| in the neuroimaging research landscape and continues to expand every day. A more complete | ||
| history and discussion about the future of the BIDS landscape can be found in this | ||
| research is done. The origin of the BIDS standard is commonly traced back to 2014, | ||
| when a social media post ignited a deeper discussion about a new way of sharing | ||
| data, that would ultimately lead to a set of standards that would improve scientific | ||
| collaboration efforts. | ||
|
|
||
| Following this initial discussion (and on the shoulders of many many volunteer hours | ||
| by maintainers and the community at large) the BIDS standard saw significant adoption | ||
| in the neuroimaging research landscape and continues to expand every day. A more complete | ||
| history and discussion about the future of the BIDS landscape can be found in this | ||
| [recent publication](https://pmc.ncbi.nlm.nih.gov/articles/PMC10516110/). | ||
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| The BIDS standard continues to be adopted by a larger share of the community each year. | ||
| The BIDS standard continues to be adopted by a larger share of the community each year. | ||
| We have seen a large and growing number of visitors to the BIDS website. A large number of | ||
| BIDS users also continue to explore the BIDS Specification and contribute to the community every month. | ||
| BIDS users also continue to explore the BIDS Specification and contribute to the community every month. | ||
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| We also document centers, institutes, and databases around the world that have implemented BIDS as | ||
| their organizational structure. While the list continues to grow, an initial list of centers and the associated | ||
| BIDS initiatives or database can be found | ||
| BIDS initiatives or database can be found | ||
| [here](https://docs.google.com/spreadsheets/d/1aySjPpEGGQwFcOavkQdcvk2t2UMXt_zoTzWLWUmq20M/edit#gid=0). | ||
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| ### Website and Specification traffic dashboards | ||
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@@ -204,8 +211,8 @@ that have implemented BIDS as their organizational structure. | |
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| ### Neurostars | ||
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| We also track the interest and usage of the BIDS standard via discussions on Neurostars | ||
| to help us estimate trends in usage. Below is a snapshot as of ??? (date). | ||
| We also track the interest and usage of the BIDS standard via discussions on Neurostars | ||
| to help us estimate trends in usage. Below is a snapshot as of ??? (date). | ||
| <!-- | ||
| TODO add automation to update every 6 months | ||
| --> | ||
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@@ -231,12 +238,11 @@ As of July 1, 2020, we have 183 people signed up for our | |
| [BIDS email list](https://forms.gle/JFo2aEkYbKY4EbmE6) and 412 members on our | ||
| [google group](https://groups.google.com/forum/#!forum/bids-discussion). | ||
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| ## How the BIDS team can help you | ||
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| If you are in the process of putting together a grant, **please email/message | ||
| the pillar lead** that is most closely associated with your proposed grant or the | ||
| BIDS maintainers email ([[email protected]](mailto:[email protected])) | ||
| the pillar lead** that is most closely associated with your proposed grant or the | ||
| BIDS maintainers email ([[email protected]](mailto:[email protected])) | ||
| so we may help support this. Our organization is structured into 3 pillars: standard, | ||
| tools, and collaboration. | ||
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@@ -246,7 +252,7 @@ writers or related initiatives to receiving a letter of support from the | |
| Steering Group. | ||
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| Regarding **requesting a letter of support** - please submit a drafted letter of | ||
| support to the collaboration lead or the BIDS maintainers email | ||
| support to the collaboration lead or the BIDS maintainers email | ||
| ([[email protected]](mailto:[email protected])) so we may review internally. | ||
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| Please include how you plan on giving back to the BIDS community. The primary | ||
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@@ -264,9 +270,9 @@ For example, please find our [NIH-R24 Brain Initiative BIDS-Derivatives grant](h | |
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| A listing of the previous grants can be found [here](../collaboration/acknowledgments.md) | ||
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| ## Citing BIDS in your project | ||
| You can find information on citing BIDS standards for specific modalities and | ||
| citing BIDS in general | ||
| ## Citing BIDS in your project | ||
| You can find information on citing BIDS standards for specific modalities and | ||
| citing BIDS in general | ||
| [in the specification](https://bids-specification.readthedocs.io/en/latest/introduction.html#citing-bids) | ||
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| <!-- | ||
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