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Open Sustainable Technology

A curated list of open technology projects to sustain a stable climate, energy supply, biodiversity and natural resources.

SMBD

Facilitate a community of practice for aligning marine biological data to Darwin Core for sharing to Ocean Biodiversity Information System (OBIS).
https://github.com/ioos/bio_data_guide

Category: Biosphere
Sub Category: Biodiversity Data Cleaning and Standardization

Keywords

darwin-core data data-management marine-biology marine-data obis tutorials

Keywords from Contributors

transforms measur archiving observation optimize conversion animals compose projection generic

Last synced: about 1 hour ago
JSON representation

Repository metadata

Standardizing Marine Biological Data Working Group - An open community to facilitate the mobilization of biological data to OBIS.

README.md

BioDataGuide

Hello and welcome to the Darwin Core Marine Example Compendium! (We're calling it the BioDataGuide for short.) Here, we document relevant resources and standards
which apply to various marine biological data types. This is a growing guide that is put together by scientists and
data managers responsible for transforming their data to meet international standards.

This guide is meant for data managers, scientists, or technicians new to transforming/publishing/mobilizing data.
There is a general introduction to the world of international data integration, followed by some specific examples of
data transformations.

To contribute to this guide see CONTRIBUTING.md

Standardizing Marine Biological Data Working Group (SMBD)

Purpose

The purpose of the SMBD is to facilitate a community of practice for aligning marine biological data to Darwin Core
for sharing to OBIS. We do this by empowering our community members - which consist of federal, state,
local, tribal, and private data managers, scientists, computer programmers, and everything in between - with the tools
and knowledge to mobilize marine biological data.

How do we do it?

We host quarterly meetings, a Slack space, and this GitHub repository to provide various mechanisms for community members
to participate.

The primary focus of the working group is to help you get past any blockers you might be experiencing during the
mobilization process. Below is a list of example blockers we've seen already:

  • What does the Darwin Core data model look like?
  • What about metadata?
  • How do I automatically collect scientific names for my species observations?
  • How can I best represent my data in Darwin Core?
  • I need help munging my data using R (or Python)!
  • How do I deal with dates when I only know the year?

Those and many more questions can be answered through this working group!

Who can join?

Anyone!

  • Do you have Taxonomic Occurrence data and want to share it?
  • Have you ever wanted to chat about biological data standards, programming, or biodiversity?

👋 If so: This is the place for you.

📆 How to participate?

We have open monthly meetings every 2nd Wednesday of the month at 16:00 ET to discuss marine biological data issues.
Please feel free to join us!

Checkout our current contributors:

Made with contrib.rocks.

About this repository

There are multiple resources in this GitHub repository, including:

  • 📓 Living documentation for anyone working with, learning about, or contributing to IOOS's best practices for biological data.
  • 🗄️ Datasets being actively worked on by community members.
  • ♻️ Code and documentation used on other datasets that can be re-used.
  • 🧰 Tools to help you navigate the organizational, technical, and social challenges of publishing data.

❓ Have Questions? ❓

  • See the "issues" tab above to ask questions or discuss with the IOOS biodata community.
  • Also try searching for related issues which are open or have been closed (ie answered).

Got Data to Share?

  • 💬 open an issue in the issues tab above and tell us about it.
  • 💾 small datasets can be uploaded into ./datasets/ so we can directly help you align with best practices.
  • 🔗 dataset repositories or other hosted data can be included in the links in the Datasets section below.

Also, check out CONTRIBUTING.md

Our training & workshops

Datasets

The ./datasets/ directory in this repository contains small datasets which meet one of the following criteria:

  • 👷 the community is currently aligning this data
  • 📓 the dataset is retained as an instructive example
  • 🙊 the lazy maintainers of this repo haven't cleaned it out yet

Ideally each dataset should contain a README.md file with details about the data and the ingestion process for this dataset.
See more on this in the contribute example applications guidance. A few datasets are highlighted below as especially instructive examples:

The Standardizing Marine Bio Data Guide

See the guide here.

We are documenting, in the form of a 📓 Guide, relevant resources and standards which apply to various marine biological data sets.
This is a work in progress, a growing guide that is being put together by scientists and data managers responsible for transforming their data to meet international standards.
The Guide is exported into multiple formats, including a pdf and an epub document.
Chapters are written in R Markdown files; contributions are welcome!

Technical details of how to work with the book can be found in /refs/building-the-data-guide.md.

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Biddle"
  given-names: "Mathew"
  orcid: "https://orcid.org/0000-0003-4897-1669"
- family-names: "Johnson"
  given-names: "Brett"
  orcid: "https://orcid.org/0000-0001-9317-0364"
title: "Biological Data Guide"
version: 1.0.0
url: "https://github.com/ioos/bio_data_guide"

Owner metadata

GitHub Events

Total
Last Year

Committers metadata

Last synced: 5 days ago

Total Commits: 479
Total Committers: 20
Avg Commits per committer: 23.95
Development Distribution Score (DDS): 0.599

Commits in past year: 63
Committers in past year: 7
Avg Commits per committer in past year: 9.0
Development Distribution Score (DDS) in past year: 0.492

Name Email Commits
Mathew Biddle 8****e 192
Tylar m****r@g****m 73
Brett Johnson b****n@g****m 57
Ben Best b****n@e****m 36
Dylan Pugh 3****h 32
zach z****h@h****g 26
Abby Benson a****n@u****v 25
Tim van der Stap t****p@h****g 7
timvdstap 6****p 6
dependabot[bot] 4****] 6
gbaillie-onc 6****c 4
Laura Brenskelle 1****e 3
Emilio Mayorga e****a@g****m 3
7yl4r g****t@t****o 2
Stephen Formel s****l@u****v 2
Dolapo Salim Olatoye 9****m 1
Michael Lonneman m****n@g****m 1
SCCOOS 3****s 1
daltonkell d****3@g****m 1
mstoessel m****l@o****u 1

Committer domains:

Issue and Pull Request metadata

Last synced: 1 day ago

Total issues: 161
Total pull requests: 46
Average time to close issues: 8 months
Average time to close pull requests: 9 days
Total issue authors: 101
Total pull request authors: 10
Average comments per issue: 3.25
Average comments per pull request: 1.13
Merged pull request: 44
Bot issues: 0
Bot pull requests: 6

Past year issues: 9
Past year pull requests: 12
Past year average time to close issues: 1 day
Past year average time to close pull requests: 1 day
Past year issue authors: 5
Past year pull request authors: 6
Past year average comments per issue: 1.22
Past year average comments per pull request: 0.67
Past year merged pull request: 11
Past year bot issues: 0
Past year bot pull requests: 6

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/ioos/bio_data_guide

Top Issue Authors

  • MathewBiddle (30)
  • 7yl4r (10)
  • albenson-usgs (4)
  • sformel-usgs (3)
  • francisjm (3)
  • emiliom (3)
  • laurabrenskelle (3)
  • mckenziekatee (3)
  • aureliemoulins (2)
  • LLTeed (2)
  • timvdstap (2)
  • MarineLebrec (2)
  • lardinois21 (2)
  • Ovalenciamedez (2)
  • nimrodishmael (2)

Top Pull Request Authors

  • MathewBiddle (26)
  • dependabot[bot] (6)
  • Dylan-Pugh (5)
  • 7yl4r (2)
  • laurabrenskelle (2)
  • DolapoSalim (1)
  • gitter-badger (1)
  • bbest (1)
  • sformel-usgs (1)
  • emiliom (1)

Top Issue Labels

  • data help (112)
  • workshop (98)
  • Stale (77)
  • book (12)
  • documentation (7)
  • bug (5)
  • question (4)
  • published (2)
  • iooscodesprint (1)
  • duplicate (1)

Top Pull Request Labels

  • dependencies (1)

Dependencies

.github/workflows/deploy_bookdown.yml actions
  • Cecilapp/GitHub-Pages-deploy v3 composite
  • actions/checkout v3 composite
  • actions/checkout master composite
  • actions/download-artifact v1.0.0 composite
  • actions/upload-artifact v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
.github/workflows/dataset-reminder.yml actions
  • actions/stale v8 composite

Score: 7.972466015974565