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.
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.
- ruby 3.2.1+
- Elasticsearch 7.6.1+
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"