generate2vivo

generate2vivo is an extensible Data Ingest Tool for the open source software VIVO. It currently queries metadata from Datacite Commons, ROR and ORCID and maps them to the VIVO ontology using sparql-generate. The resulting RDF data can be exported to a VIVO instance directly or returned in a HTTP response.

• Available queries
  • Datacite Commons
  • ROR
  • ORCID
• Installation
• Run in Command Line
• Extensible

Available queries

The data sources and queries that are currently available are listed below.

Datacite Commons

For Datacite Commons the following queries are available:

• organization : This method gets data about an organization by passing a ROR id.
• organizationPlusPeople: This method gets data about an organization and its affiliated people by passing a ROR id.
• organizationPlusPeoplePlusPublications:This method gets data about an organization and its affiliated people and their respective publications by passing a ROR id.
• person: This method gets data about a person by passing an ORCID id.
• personPlusPublications: This method gets data about a person and their publications by passing an ORCID id.
• work: This method gets data about a work by passing an DOI.

ROR

For ROR there are 2 queries available:

• organization: This method gets data about an organization by passing a ROR id.
• organizationPlusChildren: This method gets data about an organization and all their sub-organizations by passing a ROR id.

ORCID

For ORCID the following queries are available:

• personPlusWorks: This method gets data about a person and their works by passing an ORCID id.
• currentEmployeesPlusWorks: This method gets data about an organization's current employees and their works by passing a ROR id.

Installation

1. Clone the repository to a local folder using git clone https://github.com/vivo-community/generate2vivo.git
2. Change into the folder where the repository has been cloned.
3. Open src/main/resources/application.properties and change your VIVO details accordingly. If you don't provide a vivo.url, vivo.email or vivo.password, the application will not import the mapped data to VIVO but return the triples in format JSON-LD.
4. Run the application:

• If you have maven and a JDK for Java 11 installed, you can run the application directly via mvn spring-boot:run.

• Alternatively you can compile & run the application in Docker (with or without Java setup):

  # with Java setup:
  mvn package
  docker build -t g2v .
  docker run -p 9000:9000 -t g2v
  
  # without Java setup
  docker build -f DockerfileBuild -t g2v .
  docker run -p 9000:9000 -t g2v
  

5. A minimal swagger-ui will be available at http://localhost:9000/swagger-ui/.

Run in Command Line

Alternatively you can run the queries from the command line using the sparql-generate executable JAR-file. All queries are placed in folder src/main/resources/sparqlg and come with a sparql-generate-conf.json. Its structure and use are explained in detail on the sparql-generate website.

Extensible

The software is easily extensible, meaning you can add and remove data sources.

For example, if you are not interested in using Datacite Commons, just remove the folder from src/main/resources/sparqlg and the respective controller in the package eu.tib.controller.

On the other hand, if you would like to add a data source:

• add a folder with your queries under src/main/resources/sparqlg and include a sparql-generate-conf.json (its structure is described on the sparql-generate website).
• add a controller in eu.tib.controller that retrieves your input and calls your query like responseService.buildResponse(queryid, input)
  • the connection between controller and the according query is made by the queryid. You need to supply the path within the resources folder to your sparql-generate-conf.json.
  • put your input into a Map and every key-value-pair will be available in your query as a binding, where ?key will be replaced with value.