Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/bionomia/bionomia-api

API for Bionomia

https://github.com/bionomia/bionomia-api

Science Score: 26.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.6%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

API for Bionomia

Basic Info
  • Host: GitHub
  • Owner: bionomia
  • License: mit
  • Language: Ruby
  • Default Branch: master
  • Homepage:
  • Size: 247 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 0
Created about 6 years ago · Last pushed 10 months ago
Metadata Files
Readme License

README.md

Bionomia-API

Sinatra app for API behind Bionomia, which is used 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.

Build Status

End User Documentation

See https://bionomia.net/developers on Search, Parsing and access to structured data. See https://bionomia.net/parse to try the parser and see https://bionomia.net/reconcile on making use of the reconciliation endpoint in OpenRefine and as an add-on in Google Sheets.

Development Requirements

  1. ruby 3.3.6+
  2. Elasticsearch 7.6.1+

Synonyms File

The synonyms file for indexing of common nicknames is included in /synonyms/synonyms.txt and is referenced in https://github.com/bionomia/bionomia/blob/master/lib/elastic/elastic_user.rb as a relative path to the elasticsearch.yml configuration file, usually in /etc/elasticsearch on a Linux-based install. The easiest way to make use of this is to make a symlink from /etc/elasticsearch/synonyms.txt to this synonyms.txt file.

Whenever this synonyms.txt file is updated, the elasticsearch service must be closed and reopened as follows:

  $ curl -X POST "localhost:9200/bionomia_users/_close?pretty"
  $ curl -X POST "localhost:9200/bionomia_users/_open?pretty"

Owner

  • Name: Bionomia
  • Login: bionomia
  • Kind: organization

Linking natural history specimens to the world's collectors

GitHub Events

Total
  • Push event: 8
Last Year
  • Push event: 8

Dependencies

Gemfile rubygems
  • byebug >= 0
  • config >= 0
  • dwc_agent >= 0
  • elasticsearch ~> 7.17
  • haml ~> 5.2.2
  • pagy >= 0
  • rack-contrib >= 0
  • rack-test >= 0
  • rake >= 0
  • require_all >= 0
  • rest-client >= 0
  • rspec >= 0
  • sinatra >= 0
  • thin >= 0
  • typhoeus >= 0
Gemfile.lock rubygems
  • activesupport 7.0.4
  • byebug 11.1.3
  • concurrent-ruby 1.1.10
  • config 4.0.0
  • daemons 1.4.1
  • deep_merge 1.2.2
  • diff-lcs 1.5.0
  • domain_name 0.5.20190701
  • dry-configurable 0.16.1
  • dry-container 0.11.0
  • dry-core 0.9.0
  • dry-inflector 0.3.0
  • dry-initializer 3.1.1
  • dry-logic 1.3.0
  • dry-schema 1.11.2
  • dry-types 1.6.1
  • dry-validation 1.9.0
  • dwc_agent 3.0.1.4
  • elasticsearch 7.17.1
  • elasticsearch-api 7.17.1
  • elasticsearch-transport 7.17.1
  • ethon 0.15.0
  • eventmachine 1.2.7
  • faraday 1.10.2
  • faraday-em_http 1.0.0
  • faraday-em_synchrony 1.0.0
  • faraday-excon 1.1.0
  • faraday-httpclient 1.0.1
  • faraday-multipart 1.0.4
  • faraday-net_http 1.0.1
  • faraday-net_http_persistent 1.2.0
  • faraday-patron 1.0.0
  • faraday-rack 1.0.0
  • faraday-retry 1.0.3
  • ffi 1.15.5
  • haml 5.2.2
  • http-accept 1.7.0
  • http-cookie 1.0.5
  • i18n 1.12.0
  • mime-types 3.4.1
  • mime-types-data 3.2022.0105
  • minitest 5.16.3
  • multi_json 1.15.0
  • multipart-post 2.2.3
  • mustermann 3.0.0
  • namae 1.1.1
  • namecase 2.0.0
  • netrc 0.11.0
  • pagy 5.10.1
  • rack 2.2.4
  • rack-contrib 2.3.0
  • rack-protection 3.0.2
  • rack-test 2.0.2
  • rake 13.0.6
  • require_all 3.0.0
  • rest-client 2.1.0
  • rspec 3.11.0
  • rspec-core 3.11.0
  • rspec-expectations 3.11.1
  • rspec-mocks 3.11.1
  • rspec-support 3.11.1
  • ruby2_keywords 0.0.5
  • sinatra 3.0.2
  • temple 0.8.2
  • thin 1.8.1
  • tilt 2.0.11
  • typhoeus 1.4.0
  • tzinfo 2.0.5
  • unf 0.1.4
  • unf_ext 0.0.8.2
  • zeitwerk 2.6.1
.github/workflows/ruby.yml actions
  • actions/checkout v2 composite
  • ruby/setup-ruby 473e4d8fe5dd94ee328fdfca9f8c9c7afc9dae5e composite