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BioASQ GoPubMed Service Client

Java client and Gson objects for GoPubMed services used for BioASQ task, which can be configured to directly access the official gopubmed.org server, or access a remote proxy server which can cache and reroute the request to reduce request frequency through properties file.

An example can be found here.

Use in a Maven project

Configure your pom.xml by adding this repository

<repository>
  <id>ziy-mvnrepo-releases</id>
  <name>ziy GitHub Personal Repo</name>
  <url>https://raw.github.com/ziy/mvn-releases/master/</url>
</repository>

and adding this dependency

<dependency>
  <groupId>edu.cmu.lti.oaqa.bio</groupId>
  <artifactId>bioasq-gopubmed-client</artifactId>
  <version>0.0.6</version>
</dependency>

Properties syntax

DEIIS students: Please see the course project instruction to configure your hwX-ID.properties file.

Others:

pubmed.search.service = PUBMED_SEARCH_SERVICE_URL
linked.life.data.service = LINKED_LIFE_DATA_SERVICE_URL
disease.ontology.service = DISEASE_ONTOLOY_SERVICE_URL
gene.ontology.service = GENE_ONTOLOGY_SERVICE_URL
jochem.service = JOCHEM_SERVICE_URL
mesh.service = MESH_SERVICE_URL
uniprot.service = UNIPROT_SERVICE_URL
require.session.url = true
  1. The values of the properties should be configured according to the instruction, e.g. http://gopubmed.org/web/gopubmedbeta/bioasq/pubmed.
  2. "require.session.url = true" is required for the official service, but for accessing proxy server, which may be set to false.
  3. According to Apache Commons Configuration, the configuration file should be placed in the current directory, in the user home directory, or in the classpath.