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globalbioticinteractions

Global Biotic Interactions provides access to existing species interaction datasets

https://github.com/globalbioticinteractions/globalbioticinteractions

Science Score: 59.0%

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 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    2 of 21 committers (9.5%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.5%) to scientific vocabulary

Keywords

biodiversity bioinformatics biology diet diseases ecoinformatics ecology eol etl-framework food-webs globi parasites pollinators species-interactions

Keywords from Contributors

ontologies genomics
Last synced: 6 months ago · JSON representation

Repository

Global Biotic Interactions provides access to existing species interaction datasets

Basic Info
Statistics
  • Stars: 135
  • Watchers: 21
  • Forks: 17
  • Open Issues: 372
  • Releases: 170
Topics
biodiversity bioinformatics biology diet diseases ecoinformatics ecology eol etl-framework food-webs globi parasites pollinators species-interactions
Created over 14 years ago · Last pushed 7 months ago
Metadata Files
Readme License

README.md

Welcome to Global Biotic Interactions (GloBI)

The mission of this project is to find efficient ways to normalize and integrate species interaction data to enable researchers and enthusiasts to answer questions like: Which species does an Angel Shark ( Squatina squatina ) eat in the Gulf of Mexico?

Please see https://globalbioticinteractions.org or https://github.com/globalbioticinteractions/globalbioticinteractions/wiki for more information.

Java CI DOI

Citing GloBI

Poelen, J. H., Simons, J. D., & Mungall, C. J. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics, 24, 148–159. doi:10.1016/j.ecoinf.2014.08.005

Licenses

gplv3cc-by-nc

Unless otherwise noted, source code is released under GLPv3 and data is available under Creative Commons Attribution 4.0 International License. We are trying to do the best we can to ensure that the references to the original data sources are preserved and attributed. If you feel that there are better ways to do this, please let us know.

Owner

  • Name: globalbioticinteractions
  • Login: globalbioticinteractions
  • Kind: organization

GitHub Events

Total
  • Create event: 18
  • Release event: 15
  • Issues event: 100
  • Watch event: 8
  • Issue comment event: 215
  • Push event: 137
  • Gollum event: 4
  • Pull request review event: 1
  • Pull request event: 5
  • Fork event: 2
Last Year
  • Create event: 18
  • Release event: 15
  • Issues event: 100
  • Watch event: 8
  • Issue comment event: 215
  • Push event: 137
  • Gollum event: 4
  • Pull request review event: 1
  • Pull request event: 5
  • Fork event: 2

Committers

Last synced: 6 months ago

All Time
  • Total Commits: 4,735
  • Total Committers: 21
  • Avg Commits per committer: 225.476
  • Development Distribution Score (DDS): 0.511
Past Year
  • Commits: 187
  • Committers: 3
  • Avg Commits per committer: 62.333
  • Development Distribution Score (DDS): 0.016
Top Committers
Name Email Commits
Jorrit Poelen j****n@g****m 2,317
jhpoelen j****n@x****l 1,770
Jorrit Poelen j****t@j****l 543
James Simons j****s@t****u 42
reiz r****z@g****m 18
Chris Mungall c****m@b****g 17
dependabot[bot] 4****]@u****m 9
jrfep j****s@g****m 3
Jonathan Leitschuh J****h@g****m 2
José Augusto Salim z****l@u****m 2
omahs 7****s@u****m 2
Brian Hayden b****n@u****a 1
BrianHayden b****n@h****i 1
Jorrit Poelen 1****n@u****m 1
Katja Seltmann e****s@g****m 1
Mariya Dimitrova m****v@g****m 1
Shannon VanWagner v****r@g****m 1
mdrishti 4****i@u****m 1
proopnarine p****e@c****g 1
reiz r****1@g****m 1
tmitchell1 T****l@t****u 1
Committer Domains (Top 20 + Academic)
tamucc.edu: 2 calacademy.org: 1 google.com: 1 helsinki.fi: 1 unb.ca: 1 berkeleybop.org: 1 gmx.com: 1 jhpoelen.nl: 1 xs4all.nl: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 1,060
  • Total pull requests: 28
  • Average time to close issues: 6 months
  • Average time to close pull requests: 12 days
  • Total issue authors: 89
  • Total pull request authors: 9
  • Average comments per issue: 3.4
  • Average comments per pull request: 0.64
  • Merged pull requests: 19
  • Bot issues: 0
  • Bot pull requests: 17
Past Year
  • Issues: 76
  • Pull requests: 7
  • Average time to close issues: 13 days
  • Average time to close pull requests: about 5 hours
  • Issue authors: 8
  • Pull request authors: 2
  • Average comments per issue: 1.63
  • Average comments per pull request: 0.86
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 5
View more stats
Top Authors
Issue Authors
  • jhpoelen (811)
  • seltmann (42)
  • jhammock (30)
  • qgroom (13)
  • zedomel (7)
  • arw36 (7)
  • mdrishti (6)
  • BarbaraMeulenbelt (6)
  • coding46 (6)
  • neilcobb (5)
  • kbseah (5)
  • millerse (4)
  • KatjaSchulz (4)
  • Daniel-Mietchen (4)
  • jemmybutton (3)
Pull Request Authors
  • dependabot[bot] (17)
  • JLLeitschuh (2)
  • zedomel (2)
  • mdrishti (2)
  • simatei (1)
  • omahs (1)
  • tmitchell1 (1)
  • jhpoelen (1)
  • shannon-vanwagner (1)
Top Labels
Issue Labels
suggest to index (302) new feature (124) needs review (68) bug (41) globi3 (33) external issue (24) experimental (18) needs manual transcription (14) non-open data (13) optimization (9) discussion (5) documentation (5) needs vocabulary / ontology (5) data management (2) workaround exists (1) needs parser (1)
Pull Request Labels
dependencies (17) java (1)

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 164
proxy.golang.org: github.com/globalbioticinteractions/globalbioticinteractions
  • Versions: 164
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago

Dependencies

elton4n/pom.xml maven
  • org.eol:eol-globi-neo4j-index 0.24.1-SNAPSHOT
eol-globi-cache/pom.xml maven
  • ${project.groupId}:eol-globi-lib ${project.version}
  • ${project.groupId}:eol-globi-resource-remote ${project.version} test
eol-globi-data-sources/pom.xml maven
  • ${project.groupId}:eol-globi-cache ${project.version}
  • ${project.groupId}:eol-globi-jcoord ${project.version}
  • com.healthmarketscience.jackcess:jackcess 2.1.6
  • com.univocity:univocity-parsers 2.3.0
  • org.apache.jena:jena-tdb ${jena.version}
  • org.codehaus.swizzle:swizzle-stream 1.6.2
  • org.gbif:dwca-io 2.11
  • org.jsoup:jsoup 1.14.2
  • rome:rome 1.0
  • ${project.groupId}:eol-globi-resource-remote ${project.version} test
eol-globi-datasets/pom.xml maven
  • org.eol:eol-globi-datasets 1.1-SNAPSHOT
  • org.globalbioticinteractions:elton4n 0.24.1-SNAPSHOT
eol-globi-geo/pom.xml maven
  • org.eol:eol-globi-lib 0.6-SNAPSHOT
  • org.geotools:gt-shapefile 10.3
eol-globi-jcoord/pom.xml maven
  • uk.org.mygrid.resources.jcoord:jcoord 1.0
eol-globi-lib/pom.xml maven
  • com.fasterxml.jackson.core:jackson-core ${jackson.version}
  • com.fasterxml.jackson.core:jackson-databind ${jackson.version}
  • com.vividsolutions:jts 1.13
  • joda-time:joda-time 2.10.1
  • org.apache.commons:commons-collections4 4.4
  • org.apache.commons:commons-text 1.3
  • org.eol:eol-globi-resource-local ${project.version}
  • org.globalbioticinteractions:doi4j 0.1.0
  • org.mapdb:mapdb ${mapdb.version}
eol-globi-neo4j/pom.xml maven
  • ${project.groupId}:eol-globi-lib ${project.version}
  • org.neo4j:neo4j ${neo4j.version}
  • org.neo4j:neo4j-slf4j ${neo4j.version}
eol-globi-neo4j-index/pom.xml maven
  • ${project.groupId}:eol-globi-data-sources ${project.version}
  • ${project.groupId}:eol-globi-neo4j-index-export ${project.version}
  • ${project.groupId}:eol-globi-taxon-resolver ${project.version}
  • cglib:cglib-nodep 2.2
  • commons-cli:commons-cli 1.2
  • org.slf4j:slf4j-simple ${slf4j.version}
  • org.neo4j.community:it-test-support ${neo4j.version} test
eol-globi-neo4j-index-export/pom.xml maven
  • ${project.groupId}:eol-globi-neo4j ${project.version}
  • com.github.dfabulich:sitemapgen4j 1.0.4
  • commons-codec:commons-codec ${commons-codec.version}
eol-globi-parent/pom.xml maven
  • junit:junit 4.13.1 test
  • org.hamcrest:hamcrest-all 1.3 test
  • org.mockito:mockito-core 1.9.0 test
eol-globi-registry/pom.xml maven
  • ${project.groupId}:eol-globi-data-sources ${project.version}
  • ${project.groupId}:eol-globi-resource-remote ${project.version}
eol-globi-resource-local/pom.xml maven
  • ${project.groupId}:eol-globi-resource ${project.version}
  • commons-io:commons-io ${commons-io.version}
  • org.apache.commons:commons-lang3 ${commons-lang3.version}
  • org.ostermiller:utils 1.07.00
  • org.slf4j:jcl-over-slf4j ${slf4j.version}
  • org.slf4j:slf4j-api ${slf4j.version}
eol-globi-resource-remote/pom.xml maven
  • ${project.groupId}:eol-globi-resource-local ${project.version}
  • commons-net:commons-net 3.6
  • org.apache.httpcomponents:httpclient ${httpcomponents.version}
  • org.apache.httpcomponents:httpmime ${httpcomponents.version}
eol-globi-rest/pom.xml maven
  • javax.mail:mail 1.4 provided
  • javax.servlet:servlet-api 2.5 provided
  • com.fasterxml.jackson.dataformat:jackson-dataformat-xml ${jackson.version}
  • commons-validator:commons-validator 1.4.0
  • javax.transaction:jta 1.1
  • org.aspectj:aspectjweaver 1.6.12
  • org.eclipse.jetty:jetty-servlets 9.4.41.v20210516
  • org.eol:eol-globi-lib 0.24.1-SNAPSHOT
  • org.eol:eol-globi-resource-remote 0.24.1-SNAPSHOT
  • org.hibernate.validator:hibernate-validator 6.2.0.Final
  • org.neo4j.driver:neo4j-java-driver 1.7.5
  • org.slf4j:slf4j-simple ${slf4j.version}
  • org.springframework:spring-aop 3.2.18.RELEASE
  • org.springframework:spring-aspects 3.2.18.RELEASE
  • org.springframework:spring-context-support 3.2.18.RELEASE
  • org.springframework:spring-tx 3.2.18.RELEASE
  • org.springframework:spring-webmvc 3.2.18.RELEASE
  • org.eol:eol-globi-neo4j-index 0.24.1-SNAPSHOT test
  • org.glassfish:jakarta.el 3.0.3 test
  • org.neo4j.test:neo4j-harness ${neo4j.version} test
  • org.springframework:spring-test 3.2.18.RELEASE test
eol-globi-taxon-resolver/pom.xml maven
  • ${project.groupId}:eol-globi-lib ${project.version}
  • ${project.groupId}:eol-globi-resource-remote ${project.version}
  • org.apache.lucene:lucene-analyzers-common ${lucene.version}