Using ElasticSearch as a fast, flexible, and scalable solution to search occurrence records and checklists

Christian Gendreau, Canadensys Marie-Elise Lecoq, GBIF France

Introduction

ElasticSearch is an open source, document oriented, distributed search engine, built on top of Apache Lucene.

From ElasticSearch GitHub page

Setup

•  Java 6 or higher •  Download : # wget …elasticsearch-0.90.5.zip •  Unzip

Configuration

•  Name your cluster •  Replication and multi-shard are enabled by default •  Start : # bin/elasticsearch

Add data

Using the REST API

$ curl -XPUT 'http://localhost:9200/twitter/tweet/1' -d '{ "user" : "kimchy", "post_date" : "2009-11-15T14:12:12", "message" : "trying out Elastic Search" }'

Import data

Rivers •  Document-based database (mongoDB) •  JDBC (relational database) •  Data source (wikipedia, Twitter)

Mapping

•  Schema-less •  Customize indexing •  Customize querying

ElasticSearch at Canadensys

Database of Vascular Plants of Canada (VASCAN)

data.canadensys.net/vascan

Our ElasticSearch index Index structure for scientific names •  autocompletion : edge_ngram filter

o  “carex” -> “ca”,”car”,”care”,”carex” •  genus first letter : pattern_replace filter

o  “carex feta” -> “c. feta” •  epithet : path_hierarchy tokenizer

o  “carex feta” -> “feta”

ElasticSearch at GBIF France

Data stored in ElasticSearch are updated upon MongoDB changes.

The search engine requests elasticsearch using filters like taxon, date, place, dataset and geolocalisation. Statistic calculation using facets

ElasticSearch at GBIF France

ElasticSearch - Solr

•  Solr and elasticsearch both tries to solve the same problem with no much differences

•  Development setup and production deployment (replication / sharding) easier with elasticsearch

•  By default, the elasticsearch is well configured for Lucene and customization remains easy.

Facets

•  “Group by” in SQL •  Mostly used for calculate statistics

•  Example :

curl -XGET [...] "facets" : {

”dataset" : { "terms" : { "field" : ”dataset",

"order" : "term” …

API and libraries

REST API o  interoperability between different programming languages o  HTTP request

Java API

o  more efficient than REST API due to the binary API use. o  built in marshaling(data formatting on the network)

Query - RESTfull API

Example: $ curl localhost:9200/vascan/_search?pretty=1 -d

'{"query":{ "match":{ "name" :{ "query":"carex" } } } }’

Query - Java API

Code example: ... SearchRequestBuilder srb = client.prepareSearch(INDEX_NAME)

.setQuery(QueryBuilders .boolQuery() .should(QueryBuilders.matchQuery("vernacular_name",text))

.setTypes(VERNACULAR_TYPE); ...

Pitfalls

•  Error reporting (index creation, river creation) •  Results may be hard to predict using complex queries •  Documentation

•  With each mapping modification comes a free reindex from data

Future

•  Scientific Name analyzer •  Geospatial component

Thank you!