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VIVO

VIVO: a system for research discovery - Published in JOSS (2019)

https://github.com/vivo-project/vivo

Science Score: 95.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 9 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    17 of 83 committers (20.5%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords from Contributors

blackhole gravitational-lenses meshes pypi annotations simulations hydrology stellar exoplanets pde
Last synced: 4 months ago · JSON representation

Repository

VIVO is an extensible semantic web application for research discovery and showcasing scholarly work

Basic Info
  • Host: GitHub
  • Owner: vivo-project
  • License: bsd-3-clause
  • Language: Java
  • Default Branch: main
  • Homepage: http://vivoweb.org
  • Size: 117 MB
Statistics
  • Stars: 223
  • Watchers: 42
  • Forks: 134
  • Open Issues: 414
  • Releases: 17
Created about 13 years ago · Last pushed 5 months ago
Metadata Files
Readme License

README.md

VIVO: Connect, Share, Discover

Build Deploy DOI

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 ``` SOLRRESETCORE=false SOLR_VERBOSE=no

SOLRHOSTPORT=8983 SOLRCONTAINERPORT=8983

SOLR_CORES=./vivo-cores

VIVORESETHOME=false VIVO_VERBOSE=no

VIVOTDBFILE_MODE=direct

VIVOHOSTVIVOHOME=./vivo-home VIVOCONTAINERVIVOHOME=/usr/local/vivo/home

VIVOHOSTPORT=8080 VIVOCONTAINERPORT=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/docker-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://vivoweb.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

```tex @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} }

Owner

  • Name: VIVO Project
  • Login: vivo-project
  • Kind: organization
  • Email: vivo-tech@googlegroups.com

VIVO is a semantic web platform enabling research discovery.

JOSS Publication

VIVO: a system for research discovery
Published
July 26, 2019
DOI
Volume 4, Issue 39, Page 1182
Authors
Michael Conlon ORCID
University of Florida, Gainesville, Florida, US
Andrew Woods ORCID
Duraspace, Inc., Beaverton, OR, US
Graham Triggs ORCID
Duraspace, Inc., Beaverton, OR, US, Technische Informationsbibliothek (TIB) – German National Library of Science and Technology, Hannover, DE
Ralph O'Flinn ORCID
University of Alabama Birmingham, Birmingham, AL, US
Muhammad Javed ORCID
Cornell University, Ithaca, NY, US
Jim Blake ORCID
Cornell University, Ithaca, NY, US
Benjamin Gross ORCID
UNAVCO, Inc., Boulder, CO, US, Clarivate Analytics, Inc., Philadelphia, PA, US
Qazi Azim Ijaz Ahmad ORCID
Technische Informationsbibliothek (TIB) – German National Library of Science and Technology, Hannover, DE
Sabih Ali ORCID
Digital Science, London, UK
Martin Barber ORCID
Technische Informationsbibliothek (TIB) – German National Library of Science and Technology, Hannover, DE
Don Elsborg
University of Colorado, Boulder, CO, US
Kitio Fofack ORCID
Université du Québec à Montréal, Montréal, QC, CA
Christian Hauschke ORCID
Technische Informationsbibliothek (TIB) – German National Library of Science and Technology, Hannover, DE
Violeta Ilik ORCID
Columbia University, New York, NY, US
Huda Khan ORCID
Cornell University, Ithaca, NY, US
Ted Lawless ORCID
Clarivate Analytics, Inc., Philadelphia, PA, US, Brown University, Providence, RI, US
Jacob Levernier ORCID
University of Pennsylvania, Philadelphia, PA, US
Brian Lowe ORCID
Ontocale SRL, Bucharest, RO
Jose Luis Martin
Universidad Carlos III de Madrid, Madrid, ES
Steve McKay
Plum Analytics, Inc., Philadelphia, PA, US
Simon Porter ORCID
Digital Science, London, UK
Tatiana Walther ORCID
Technische Informationsbibliothek (TIB) – German National Library of Science and Technology, Hannover, DE
Marijane White
Oregon Health & Science University, Portland, OR, US
Stefan Wolff
Sächsische Landesbibliothek Staats und Universitätsbibliothek, Dresden, DE
Rebecca Younes
Cornell University, Ithaca, NY, US
Editor
Jason Clark ORCID
Tags
ontology semantic-web linked-data research-discovery open-scholarship linked-open-data open-science
View PDF Review Thread Software Archive

GitHub Events

Total
  • Issues event: 79
  • Watch event: 18
  • Delete event: 1
  • Issue comment event: 87
  • Push event: 21
  • Pull request review comment event: 90
  • Pull request review event: 138
  • Pull request event: 59
  • Fork event: 6
  • Create event: 2
Last Year
  • Issues event: 79
  • Watch event: 18
  • Delete event: 1
  • Issue comment event: 87
  • Push event: 21
  • Pull request review comment event: 90
  • Pull request review event: 138
  • Pull request event: 59
  • Fork event: 6
  • Create event: 2

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 4,934
  • Total Committers: 83
  • Avg Commits per committer: 59.446
  • Development Distribution Score (DDS): 0.901
Past Year
  • Commits: 70
  • Committers: 7
  • Avg Commits per committer: 10.0
  • Development Distribution Score (DDS): 0.229
Top Committers
Name Email Commits
rjy7 r****7@4****3 489
hlm7 h****7@4****3 486
tworrall t****2@c****u 323
Graham Triggs g****s@d****g 299
ejc12 e****2@4****3 247
jeb228 j****8@4****3 222
mb863 m****3@4****3 222
j2blake j****8@c****u 222
tworrall t****l@4****3 187
stellamit s****t@4****3 182
j2blake j****e@4****3 170
cdtank c****k@4****3 160
brianjlowe b****3@c****u 151
nac26 n****6@4****3 135
sjm222 s****2@4****3 130
hjkhjk54 h****4@4****3 113
Georgy Litvinov g****v@t****u 111
ryounes r****s@4****3 101
bdc34 b****4@4****3 99
manolobevia m****a@4****3 76
bkoniden b****n@4****3 56
bjl23 b****3@4****3 50
mbarbier m****r@4****3 47
hudajkhan h****4@c****u 46
briancaruso b****o@4****3 42
cdtank c****"@4****3 42
Holly Mistlebauer h****7@c****u 42
Dragan Ivanovic c****c@u****s 40
kongchinhua k****a@4****3 33
cappadona c****a@4****3 33
and 53 more...
Committer Domains (Top 20 + Academic)
cornell.edu: 7 tib.eu: 3 duraspace.org: 2 uqam.ca: 2 uns.ac.rs: 1 ufl.edu: 1 wustl.edu: 1 lib-hlm7.library.cornell.edu: 1 colorado.edu: 1 library.tamu.edu: 1 viggio.com: 1 b.abbies.us: 1 tamu.edu: 1 duke.edu: 1 gwu.edu: 1 lyrasis.org: 1 symplectic.co.uk: 1 indiana.edu: 1 uab.edu: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 195
  • Total pull requests: 90
  • Average time to close issues: almost 2 years
  • Average time to close pull requests: 6 months
  • Total issue authors: 19
  • Total pull request authors: 14
  • Average comments per issue: 1.3
  • Average comments per pull request: 1.32
  • Merged pull requests: 46
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 52
  • Pull requests: 64
  • Average time to close issues: about 2 months
  • Average time to close pull requests: about 1 month
  • Issue authors: 13
  • Pull request authors: 9
  • Average comments per issue: 0.42
  • Average comments per pull request: 0.81
  • Merged pull requests: 37
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • chenejac (133)
  • litvinovg (30)
  • hauschke (25)
  • brianjlowe (7)
  • gneissone (4)
  • milospp (3)
  • markuskotte (2)
  • matthiasluehr (2)
  • abidfakhrealam (2)
  • balmas (2)
  • GarrettArm (2)
  • MHector1 (1)
  • jesielviana (1)
  • chartgerink (1)
  • isl3 (1)
Pull Request Authors
  • litvinovg (51)
  • milospp (16)
  • chenejac (11)
  • hauschke (10)
  • ivanmrsulja (7)
  • gneissone (6)
  • wwelling (6)
  • michel-heon (4)
  • kaladay (2)
  • zparvez2z (2)
  • brianjlowe (2)
  • ghost (2)
  • mconlon17 (1)
  • EDemerzel (1)
Top Labels
Issue Labels
Jira (59) Open (47) Improvement (29) Major (28) Bug (26) minor (22) dynamic API (17) Medium (15) High (10) Blocker (9) Installation and Configuration (7) User Experience (7) Documentation (6) New Feature (5) Low (5) Epic (5) Multiple Language Support (4) Complex (4) Ontology support (4) Ontology (4) In Review (3) Ready for Test (3) Simple (3) Reopened (3) Received (3) Critical (3) Custom forms (3) External services (3) Solr / Search (2) Data Management (2)
Pull Request Labels
bugfix (4) small PR (2) dynamic API (2) middle PR (1) Blocker (1)

Packages

  • Total packages: 4
  • Total downloads: unknown
  • Total dependent packages: 1
    (may contain duplicates)
  • Total dependent repositories: 54
    (may contain duplicates)
  • Total versions: 92
repo1.maven.org: org.vivoweb:vivo-api

VIVO project

  • Versions: 23
  • Dependent Packages: 1
  • Dependent Repositories: 18
Rankings
Dependent repos count: 5.7%
Forks count: 17.4%
Average: 19.8%
Stargazers count: 23.2%
Dependent packages count: 33.0%
Last synced: 4 months ago
repo1.maven.org: org.vivoweb:vivo-home

VIVO project

  • Versions: 23
  • Dependent Packages: 0
  • Dependent Repositories: 18
Rankings
Dependent repos count: 5.7%
Forks count: 17.4%
Stargazers count: 23.2%
Average: 24.1%
Dependent packages count: 50.1%
Last synced: 4 months ago
repo1.maven.org: org.vivoweb:vivo-webapp

VIVO project

  • Versions: 23
  • Dependent Packages: 0
  • Dependent Repositories: 18
Rankings
Dependent repos count: 5.7%
Forks count: 17.4%
Stargazers count: 23.2%
Average: 24.1%
Dependent packages count: 50.1%
Last synced: 4 months ago
repo1.maven.org: org.vivoweb:vivo-project

VIVO project

  • Versions: 23
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Forks count: 12.2%
Stargazers count: 16.8%
Average: 27.4%
Dependent repos count: 32.0%
Dependent packages count: 48.9%
Last synced: 4 months ago

Dependencies

api/pom.xml maven
  • javax.servlet:javax.servlet-api 3.1.0 provided
  • javax.servlet:jsp-api 2.0 provided
  • com.itextpdf:itextpdf 5.5.12
  • javax.xml:jaxrpc-api 1.1
  • org.apache.httpcomponents:fluent-hc 4.5.3
  • org.vivoweb.dependencies:oim.vivo.scimapcore 1.0
  • org.vivoweb:orcid-api-client 0.6.4
  • org.vivoweb:vitro-api
  • org.vivoweb:vitro-dependencies
  • junit:junit 4.13.1 test
  • org.vivoweb:vitro-api test
home/pom.xml maven
  • org.vivoweb:vitro-home
installer/home/pom.xml maven
  • org.vivoweb:vitro-languages-home-core 1.12.3-SNAPSHOT
  • org.vivoweb:vivo-home
  • org.vivoweb:vivo-languages-home-core 1.12.3-SNAPSHOT
installer/pom.xml maven
  • org.vivoweb:vivo-api 1.12.3-SNAPSHOT
  • org.vivoweb:vivo-home 1.12.3-SNAPSHOT
  • org.vivoweb:vivo-webapp 1.12.3-SNAPSHOT
installer/webapp/pom.xml maven
  • javax.servlet:jsp-api 2.0 provided
  • javax.servlet:servlet-api 2.5 provided
  • org.vivoweb:vitro-languages-webapp-core 1.12.3-SNAPSHOT
  • org.vivoweb:vivo-api
  • org.vivoweb:vivo-languages-webapp-core 1.12.3-SNAPSHOT
  • org.vivoweb:vivo-webapp
pom.xml maven
  • org.vivoweb:vitro-api 1.12.3-SNAPSHOT
  • org.vivoweb:vitro-dependencies 1.12.3-SNAPSHOT
  • org.vivoweb:vitro-home 1.12.3-SNAPSHOT
  • org.vivoweb:vitro-webapp 1.12.3-SNAPSHOT
  • org.vivoweb:vitro-api 1.12.3-SNAPSHOT test
selenium/pom.xml maven
  • junit:junit 4.13.1 test
  • org.seleniumhq.selenium:selenium-java 2.48.2 test
webapp/pom.xml maven
  • org.vivoweb:vitro-webapp
  • org.vivoweb:vivo-api 1.12.3-SNAPSHOT
.github/workflows/build.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/setup-java v1 composite
.github/workflows/codeql-analysis.yml actions
  • actions/checkout v2 composite
  • github/codeql-action/analyze v1 composite
  • github/codeql-action/autobuild v1 composite
  • github/codeql-action/init v1 composite
.github/workflows/deploy.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/setup-java v1 composite
.github/workflows/docker.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/setup-java v1 composite
  • docker/build-push-action v2 composite
  • docker/login-action v1 composite
  • docker/setup-buildx-action v1 composite
  • docker/setup-qemu-action v1 composite
Dockerfile docker
  • tomcat 9-jdk11-openjdk build
docker-compose.yml docker
  • vivoweb/vivo-solr latest