Bionomia
Parse people names from biodiversity occurrence data, apply basic regular expressions and heuristics to disambiguate them, and to make these occurrence records as entities that can be claimed by people via ORCID.
https://github.com/bionomia/bionomia
Category: Biosphere
Sub Category: Biodiversity Data Cleaning and Standardization
Keywords from Contributors
transforms measur optimized archiving conversion generic annotation observation animals install
Last synced: about 20 hours ago
JSON representation
Repository metadata
Sinatra app to parse people names from biodiversity occurrence data, apply basic regular expressions and heuristics to disambiguate them, and to make these occurrence records as entities that can be claimed by people via ORCID.
- Host: GitHub
- URL: https://github.com/bionomia/bionomia
- Owner: bionomia
- License: mit
- Created: 2020-06-11T21:47:57.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2025-04-23T22:19:26.000Z (4 days ago)
- Last Synced: 2025-04-25T12:07:08.256Z (3 days ago)
- Language: Haml
- Homepage: https://bionomia.net
- Size: 49.8 MB
- Stars: 16
- Watchers: 1
- Forks: 8
- Open Issues: 54
- Releases: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
README.md
Bionomia
Sinatra app to parse people names from structured biodiversity occurrence data, apply basic regular expressions and heuristics to disambiguate them, and then allow them to be claimed by authenticated users via ORCID. Authenticated users may also help other users that have either ORCID or Wikidata identifiers. The web application lives at https://bionomia.net.
Translations
Strings of text in the user interface are translatable via config/locales. Large pages of text are fully translatable in the views/static_i18n/ directory.
Requirements
- ruby 3.3.6s+
- Elasticsearch 8.10.2+
- MySQL 8.0.34+
- Redis 7.0.12+
- Apache Spark 3+
- Unix-based operating system to use GNU parallel to process GBIF downloads
Installation
$ git clone https://github.com/bionomia/bionomia.git
$ cd bionomia
$ gem install bundler
$ bundle install
$ mysql -u root bionomia < db/bionomia.sql
$ cp config/settings/development.yml.sample config/settings/development.yml
# Adjust content of development.yml
# Copy and edit production.yml and test.yml as above
$ RUBY_YJIT_ENABLE=true rackup -p 4567 config.ru
License
The MIT License (MIT)
Copyright (c) David P. Shorthouse
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Citation (CITATION.cff)
cff-version: 1.2.0
message: If you use this software, please cite it using these metadata.
title: Bionomia application code
abstract: Link natural history specimens to the world's collectors. The application lives at https://bionomia.net.
authors:
- family-names: Shorthouse
given-names: David
orcid: "https://orcid.org/0000-0001-7618-5230"
date-released: "2024-12-06"
license: MIT
repository-code: "https://github.com/bionomia/bionomia"
Owner metadata
- Name: Bionomia
- Login: bionomia
- Email:
- Kind: organization
- Description: Linking natural history specimens to the world's collectors
- Website: https://bionomia.net
- Location:
- Twitter: BionomiaTrack
- Company:
- Icon url: https://avatars.githubusercontent.com/u/66799173?v=4
- Repositories: 3
- Last ynced at: 2023-03-09T08:55:14.919Z
- Profile URL: https://github.com/bionomia
GitHub Events
Total
- Issues event: 10
- Watch event: 2
- Delete event: 8
- Issue comment event: 12
- Push event: 192
- Pull request event: 20
- Fork event: 1
- Create event: 8
Last Year
- Issues event: 10
- Watch event: 2
- Delete event: 8
- Issue comment event: 12
- Push event: 192
- Pull request event: 20
- Fork event: 1
- Create event: 8
Committers metadata
Last synced: 6 days ago
Total Commits: 2,931
Total Committers: 6
Avg Commits per committer: 488.5
Development Distribution Score (DDS): 0.016
Commits in past year: 465
Committers in past year: 2
Avg Commits per committer in past year: 232.5
Development Distribution Score (DDS) in past year: 0.002
| Name | Commits | |
|---|---|---|
| David Shorthouse | d****e@g****m | 2883 |
| JCGiron | e****e@g****m | 26 |
| dependabot[bot] | 4****] | 17 |
| Marianna Simoes | m****s@g****m | 2 |
| Matthew Blissett | m****t@g****g | 2 |
| Jiří Podhorecký | t****r | 1 |
Committer domains:
- gbif.org: 1
Issue and Pull Request metadata
Last synced: 2 days ago
Total issues: 115
Total pull requests: 155
Average time to close issues: 4 months
Average time to close pull requests: about 18 hours
Total issue authors: 14
Total pull request authors: 4
Average comments per issue: 1.91
Average comments per pull request: 0.1
Merged pull request: 142
Bot issues: 0
Bot pull requests: 24
Past year issues: 17
Past year pull requests: 34
Past year average time to close issues: 12 days
Past year average time to close pull requests: 1 day
Past year issue authors: 4
Past year pull request authors: 2
Past year average comments per issue: 0.76
Past year average comments per pull request: 0.06
Past year merged pull request: 29
Past year bot issues: 0
Past year bot pull requests: 0
Top Issue Authors
- dshorthouse (79)
- abubelinha (13)
- debpaul (3)
- DavidFichtmueller (2)
- mjy (2)
- dimus (2)
- Archilegt (2)
- tmcelrath (2)
- rdmpage (2)
- kcopas (2)
- jhpoelen (2)
- mnhn-paul (2)
- nickynicolson (1)
- michaelbravothomas (1)
Top Pull Request Authors
- dshorthouse (128)
- dependabot[bot] (24)
- MichalTorma (2)
- trendspotter (1)
Top Issue Labels
- enhancement (48)
- new feature (8)
- bug (6)
- documentation (3)
- high priority (3)
- help wanted (2)
- dependencies (1)
Top Pull Request Labels
- dependencies (24)
- ruby (24)
Dependencies
- byebug >= 0 development
- rake >= 0 development
- rspec >= 0 development
- actionview >= 0
- active_record_union >= 0
- activerecord >= 0
- activerecord-import >= 0
- activesupport >= 0
- addressable >= 0
- biodiversity >= 0
- capitalize-names >= 0
- charlock_holmes >= 0
- chronic >= 0
- colorize >= 0
- composite_primary_keys >= 0
- config >= 0
- counter_culture >= 0
- dwc-archive >= 0
- dwc_agent >= 0
- elasticsearch ~> 7.17
- haml >= 0
- htmlentities >= 0
- i18n >= 0
- i18n_data >= 0
- iso_country_codes >= 0
- mysql2 >= 0
- namae >= 0
- nokogiri >= 0
- oauth2 >= 0
- oj >= 0
- omniauth-orcid >= 0
- pagy >= 0
- parallel >= 0
- passenger >= 0
- pluck_to_hash >= 0
- pony >= 0
- rack-contrib >= 0
- rack-test >= 0
- rack-tracker >= 0
- redis >= 0
- require_all >= 0
- rest-client >= 0
- rgl >= 0
- rss >= 0
- ruby-filemagic >= 0
- ruby-progressbar >= 0
- rubysl-securerandom >= 0
- rubyzip >= 0
- sanitize >= 0
- sidekiq >= 0
- sinatra >= 0
- sinatra-cacher >= 0
- sinatra-contrib >= 0
- sinatra-flash >= 0
- sinatra-outputbuffer >= 0
- sinatra-support >= 0
- sitemap_generator >= 0
- sparql-client >= 0
- sucker_punch >= 0
- thin >= 0
- twitter >= 0
- typhoeus >= 0
- wikidata-client >= 0
- 157 dependencies
- actions/checkout v3 composite
- ruby/setup-ruby v1 composite
Score: 6.040254711277415