dataset-phenotypes

Preparatory scripts for BIDS tabular phenotypic data in large neuroimaging datasets.

https://github.com/nimh-dsst/dataset-phenotypes

Science Score: 72.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
1 of 6 committers (16.7%) from academic institutions
✓
Institutional organization owner
Organization nimh-dsst has institutional domain (cmn.nimh.nih.gov)
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (12.0%) to scientific vocabulary

Keywords

abcd abcd-study abide abide-data bids data-dictionary dataset datasets hbn hcp nki phenotype phenotypic pnc tabular tabular-data ukb ukbb ukbiobank

Keywords from Contributors

neuroimaging degoogle data-standards

Last synced: 6 months ago · JSON representation ·

Repository

Preparatory scripts for BIDS tabular phenotypic data in large neuroimaging datasets.

Basic Info

Host: GitHub
Owner: nimh-dsst
License: cc0-1.0
Language: Python
Default Branch: main
Homepage: https://bids-phenotype.readthedocs.io
Size: 7.64 MB

Statistics

Stars: 9
Watchers: 5
Forks: 2
Open Issues: 13
Releases: 2

Topics

abcd abcd-study abide abide-data bids data-dictionary dataset datasets hbn hcp nki phenotype phenotypic pnc tabular tabular-data ukb ukbb ukbiobank

Created over 3 years ago · Last pushed over 2 years ago

Metadata Files

Readme License Citation

Big neuroimaging dataset BIDS tabular phenotype tools

Preparatory scripts to output BIDS phenotypic data dictionaries and transform phenotypic data to BIDS TSVs for common neuroimaging datasets.

These tools follow the guidelines of BIDS Extension Proposal 36 (BEP036). The hope is for researchers to embrace this BIDS Phenotypic Data standard by seeing examples in their favorite datasets.

Use GitHub Issues with this repository

The GitHub Issues page found here should be used to communicate all of the following:

Asking questions of any size or difficulty
Providing feedback on any file's inaccuracies or considering changes
Suggesting or requesting features
Making new dataset requests (describe how to download the phenotypic data dictionaries and phenotypic data and it will be added to the queue
Proposing ideas to improve the repository
Reporting bugs in scripts or any other repository files
Corrections to README.md files, dictionary entries, or whole assessments
Style suggestions or suggested common conventions for scripts, dictionaries, or README.md files
Anything else that isn't a code contribution or a pull request

How to Pull Request

Pull Requests (PRs) are also always welcome here to initiate a review of some fix or addition or change to the repository. Please fork, make your changes, and then initiate a PR from your fork back to this repository's main branch.

Contributors

Contributors are always welcome to add GitHub Issues (see section above). Thanks especially go to these wonderful people (emoji key):

_{Eric Earl}	_{Jessica Dafflon}	_{Josh Faskowitz}	_{RobertoFelipeSG}
_{Arshitha Basavaraj}	_{Dustin Moraczewski}	_{Adam Thomas}	_{Francisco Pereira}

This project follows the all-contributors specification. Contributions of any kind are welcome!

Owner

Name: National Institute of Mental Health Data Science & Sharing Team
Login: nimh-dsst
Kind: organization
Location: United States of America

Website: https://cmn.nimh.nih.gov/dsst
Repositories: 1
Profile: https://github.com/nimh-dsst

Supporting investigators within the NIMH intramural research program in creating, distributing, and leveraging large, open datasets to accelerate discovery.

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: Big neuroimaging dataset BIDS tabular phenotype tools
message: 'If you use this software, please cite it.'
type: software
authors:
  - given-names: Eric
    family-names: Earl
    email: eric.earl@nih.gov
    affiliation: Data Science & Sharing Team, National Institute of Mental Health, Bethesda, MD, USA.
    orcid: https://orcid.org/0000-0001-5512-0083
  - given-names: Jessica
    family-names: Dafflon
    affiliation: Data Science & Sharing Team and Machine Learning Team, National Institute of Mental Health, Bethesda, MD, USA.
    orcid: https://orcid.org/0000-0003-2540-0927
  - given-names: Roberto
    family-names: Salamanca-Giron
    affiliation: Human Cortical Physiology and Neurorehabilitation Section, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
  - given-names: Josh
    family-names: Faskowitz
    affiliation: Section on Functional Imaging Methods, National Institute of Mental Health, Bethesda, MD, USA.
    orcid: https://orcid.org/0000-0003-1814-7206
  - given-names: Arshitha
    family-names: Basavaraj
    affiliation: Data Science & Sharing Team, National Institute of Mental Health, Bethesda, MD, USA.
    orcid: https://orcid.org/0000-0002-6984-7969
  - given-names: Dustin
    family-names: Moraczewski
    affiliation: Data Science & Sharing Team, National Institute of Mental Health, Bethesda, MD, USA.
    orcid: https://orcid.org/0000-0002-0422-3135
  - given-names: Francisco
    family-names: Pereira
    affiliation: Machine Learning Team, National Institute of Mental Health, Bethesda, MD, USA.
  - given-names: Adam
    family-names: Thomas
    affiliation: Data Science & Sharing Team, National Institute of Mental Health, Bethesda, MD, USA.
    orcid: https://orcid.org/0000-0002-2850-1419
identifiers:
  - type: doi
    value: 10.5281/zenodo.7517469
    description: The Zenodo record of the GitHub repository.
repository-code: https://github.com/ericearl/dataset-phenotypes
abstract: Preparatory scripts to output BIDS phenotypic data dictionaries and transform phenotypic data to BIDS TSVs for common neuroimaging datasets.
keywords:
  - phenotype
  - tabular
  - bids
  - data sharing
  - neuroimaging
license: CC0-1.0
version: v1.0.0
date-released: 2023-01-09

GitHub Events

Total

Watch event: 2

Last Year

Watch event: 2

Committers

Last synced: over 1 year ago

All Time

Total Commits: 125
Total Committers: 6
Avg Commits per committer: 20.833
Development Distribution Score (DDS): 0.44

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Eric Earl	e**l@n**v	70
Arshitha Basavaraj	a**4@g**m	22
allcontributors[bot]	4****]	16
Jessica Dafflon	j**n@g**m	12
josh faskowitz	j**z@g**m	3
Josh Faskowitz	f****t	2

Committer Domains (Top 20 + Academic)

nih.gov: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time

Total issues: 28
Total pull requests: 19
Average time to close issues: about 2 months
Average time to close pull requests: 9 days
Total issue authors: 3
Total pull request authors: 5
Average comments per issue: 1.61
Average comments per pull request: 1.26
Merged pull requests: 19
Bot issues: 0
Bot pull requests: 8

Past Year

Issues: 5
Pull requests: 0
Average time to close issues: 14 days
Average time to close pull requests: N/A
Issue authors: 1
Pull request authors: 0
Average comments per issue: 0.6
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

ericearl (21)
JessyD (3)
Arshitha (2)

Pull Request Authors

allcontributors[bot] (8)
Arshitha (5)
ericearl (2)
JessyD (2)
faskowit (1)

Top Labels

Issue Labels

enhancement (19) documentation (9) medium priority (8) good first issue (7) bug (6) low priority (4) high priority (4) help wanted (1)

Pull Request Labels

enhancement (3) documentation (1) high priority (1) medium priority (1)

Dependencies

.github/workflows/release.yml actions

JRubics/poetry-publish v1.17 composite
actions/checkout v3 composite

poetry.lock pypi

et-xmlfile 1.1.0
numpy 1.24.3
numpy 1.25.0
openpyxl 3.1.2
pandas 2.0.2
python-dateutil 2.8.2
pytz 2023.3
six 1.16.0
toml 0.10.2
tzdata 2023.3
xmltodict 0.13.0

pyproject.toml pypi

openpyxl ^3.1.2
pandas ^2.0.2
python ^3.8,<4.0
xmltodict ^0.13.0

requirements.txt pypi

mkdocs-material *

dataset-phenotypes

Science Score: 72.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Big neuroimaging dataset BIDS tabular phenotype tools

Use GitHub Issues with this repository

How to Pull Request

Contributors

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies