bioMine

bioMine is a full‐text natural language search engine for biomedical literature. bioMine provides search capabilities based on the full‐text content of documents belonging to a database composed of scientific articles and allows users to submit their search queries using natural language. Beyond the text content of articles, the system engine also uses article metadata, empowering the search by considering extra information from picture and table captions. bioMine is publicly released as an open‐source system under the MIT license.

Compiling from source

bioMine source code requires Maven (https://maven.apache.org) for compilation. To compile from source, follow the next steps after cloning the repository:

1 - From the main bioMine project directory, compile the code and generate executable .jar files:

mvn clean install

Preparing Solr + environment

1 - Install the bioLinker dependency

mvn install:install-file -Dfile=/path/to/bioLinker-1.0-SNAPSHOT.jar -DgroupId=csfg \
 -DartifactId=bioLinker -Dversion=1.0-SNAPSHOT -Dpackaging=jar       

Note: /path/to/bioLinker-1.0-SNAPSHOT.jar should be replaced by the path to the jar located in biomine-index/src/lib.

2 - Download and install/unzip Solr (https://lucene.apache.org/solr/guide/6_6/getting-started.html)

3 - Run SolrCloud, following the instructions (https://lucene.apache.org/solr/guide/7_1/getting-started-with-solrcloud.html)

4 - To use bioMine index schemas and configuration for Solr, check the instructions at the README file in the bioMine solr folder.

5 - Prepare a config.properties file with proper paths and configurations. For this, use the config.properties.DEFAULT provided in the repository. Make sure that the variable server.url is pointing to the active Solr-zookeper port.

 server.url=localhost:9983

Note: default should be 9983 (8983 + 1000)

Running bioMine

1 - To run bioMine, use:

java -DbioMine.config=config.properties -jar biomine-service/target/biomine-service-1.0-SNAPSHOT.jar

Using bioMine

After following the previous steps, bioMine will likely be running on localhost:8080. Requests can be sent and received through CURL, such as

curl -X GET --header 'Accept: application/json' 'http://localhost:8080/biomine/indexer/index/status'

To access querying and indexing funcionalities through REST, we suggest using Swagger. If running on localhost:8080, follow the next steps: 1 - Go to http://localhost:8080/swagger-ui.html 2 - Click on "biomine-controller" to expand section 3 - To use a funcionality, fill out the required fields, and click on "try it out" to submit it

Citing bioMine

Hayda Almeida, Ludovic Jean-Louis, Marie-Jean Meurs

An open source and modular search engine for biomedical literature retrieval,

Computational Intelligence. July 2017 doi: 10.1111/coin.12125

@article{almeida2018open,
  title={An open source and modular search engine for biomedical literature retrieval},
  author={Almeida, Hayda and Jean-Louis, Ludovic and Meurs, Marie-Jean},
  journal={Computational Intelligence},
  volume={34},
  number={1},
  pages={200--218},
  year={2018},
  publisher={Wiley Online Library}
}