VIVO: Connect, Share, Discover

VIVO is an open source semantic web tool for research discovery -- finding people and the research they do.

VIVO supports editing, searching, browsing and visualizing research activity in order to discover people, programs, facilities, funding, scholarly works and events. VIVO's search returns results faceted by type for rapid retrieval of desired information across disciplines.

Resources

VIVO Project web site

https://vivo.lyrasis.org/

VIVO Project Wiki

https://wiki.lyrasis.org/display/VIVO/

Installation Instructions

Installation instructions for all releases can be found at this location on the wiki:
https://wiki.lyrasis.org/display/VIVODOC/All+Documentation

When you select the wiki pages for technical documentation for the release you would like to install at https://wiki.lyrasis.org/display/VIVODOC/All+Documentation, please open the Installing VIVO section and follow the instructions.

Docker

VIVO docker container is available at vivoweb/vivo with accompanying vivoweb/vivo-solr. These can be used independently or with docker-compose.

Docker Compose

Docker Compose variable substitution:

.env defaults

SOLR_RESET_CORE=false
SOLR_VERBOSE=no

SOLR_HOST_PORT=8983
SOLR_CONTAINER_PORT=8983

SOLR_CORES=./vivo-cores

VIVO_RESET_HOME=false
VIVO_VERBOSE=no

VIVO_TDB_FILE_MODE=direct

VIVO_HOST_VIVO_HOME=./vivo-home
VIVO_CONTAINER_VIVO_HOME=/usr/local/vivo/home

VIVO_HOST_PORT=8080
VIVO_CONTAINER_PORT=8080

• SOLR_RESET_CORE: Convenience to reset VIVO Solr core when starting container. Caution, will require complete reindex.

• SOLR_VERBOSE: Increase log verbosity.

• SOLR_HOST_PORT: Host port binding for solr service port mapping.

• SOLR_CONTAINER_PORT: Container port binding for solr service port mapping.

• SOLR_CORES: Solr cores data directories on your host machine which will mount to volume in docker container. Set this environment variable to persist your Solr data on your host machine.

• VIVO_RESET_HOME: Convenience to reset VIVO home when starting container. Caution, will delete local configuration, content, and configuration model.

• VIVO_VERBOSE: Increase log verbosity.

• VIVO_TDB_FILE_MODE: TDB file mode. See https://jena.apache.org/documentation/tdb/configuration.html#file-access-mode.

• VIVO_HOST_VIVO_HOME: VIVO home directory on your host machine which will mount to volume in docker container. Set this environment variable to persist your VIVO data on your host machine.

• VIVO_CONTAINER_VIVO_HOME: VIVO home directory within the container.

• VIVO_HOST_PORT: Host port binding for VIVO Tomcat service port mapping.

• VIVO_CONTAINER_PORT: Container port binding for VIVO Tomcat service port mapping.

Before building VIVO, you will also need to clone (and switch to the same branch, if other than main) of Vitro. The Vitro project must be cloned to a sibling directory next to VIVO so that it can be found during the build.

Build and start VIVO.

1. In VIVO (with Vitro cloned alongside it), run:

mvn clean package -s installer/example-settings.xml
docker-compose up

Docker Image

To build and run local Docker image.

docker build -t vivoweb/vivo:development .
docker run -p 8080:8080 vivoweb/vivo:development

Community

There are several ways to contact and join the VIVO community. All of them are listed at https://vivo.lyrasis.org/contact/

Contributing Code

If you would like to contribute code to the VIVO project, please read instructions at this page. Contributors welcome!

Citing VIVO

If you are using VIVO in your publications or projects, please cite the software paper in the Journal of Open Source Software:

• Conlon et al., (2019). VIVO: a system for research discovery. Journal of Open Source Software, 4(39), 1182, https://doi.org/10.21105/joss.01182

BibTeX

@article{Conlon2019,
  doi = {10.21105/joss.01182},
  url = {https://doi.org/10.21105/joss.01182},
  year = {2019},
  publisher = {The Open Journal},
  volume = {4},
  number = {39},
  pages = {1182},
  author = {Michael Conlon and Andrew Woods and Graham Triggs and Ralph O'Flinn and Muhammad Javed and Jim Blake and Benjamin Gross and Qazi Asim Ijaz Ahmad and Sabih Ali and Martin Barber and Don Elsborg and Kitio Fofack and Christian Hauschke and Violeta Ilik and Huda Khan and Ted Lawless and Jacob Levernier and Brian Lowe and Jose Martin and Steve McKay and Simon Porter and Tatiana Walther and Marijane White and Stefan Wolff and Rebecca Younes},
  title = {{VIVO}: a system for research discovery},
  journal = {Journal of Open Source Software}
}