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org.opencb.cellbase:cellbase

High-Performance NoSQL database and RESTful web services to access to most relevant biological data. Found a bug or have an idea for a new feature? Let us know at https://zettagenomics.com/academic/

https://github.com/opencb/cellbase

Science Score: 36.0%

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
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    3 of 39 committers (7.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.1%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

High-Performance NoSQL database and RESTful web services to access to most relevant biological data. Found a bug or have an idea for a new feature? Let us know at https://zettagenomics.com/academic/

Basic Info
  • Host: GitHub
  • Owner: opencb
  • License: apache-2.0
  • Language: Java
  • Default Branch: develop
  • Homepage:
  • Size: 153 MB
Statistics
  • Stars: 92
  • Watchers: 27
  • Forks: 53
  • Open Issues: 168
  • Releases: 86
Created almost 13 years ago · Last pushed 11 months ago
Metadata Files
Readme License

docs/README.md

description: Welcome to CellBase!

Overview

During the last years the advances of high-throughput technologies in biology have produced an unprecedented growth of repositories and databases storing relevant biological data. Today there is more biological information than ever but unfortunately the current status of many of these repositories is far from being optimal many times. Some of the most common problems are: a) information is spread out in many small repositories and databases, b) lack of standards between different repositories, c) unsupported databases, d) specific and unconnected information, etc.

All these problems make very difficult: a) to integrate or join many different sources into only one database to work or analyze experiments; b) to access and query this information in programmatically way.

To cope with all these problems we have designed and developed a NoSQL database that integrates the most relevant biological information about genomic features and proteins, gene expression regulation, functional annotation, genomic variation and systems biology information. We use the most relevant repositories such as Ensembl, Uniprot, ClinVar, COSMIC or IntAct among many others (you can browse them Data sources and species). The information integrated covers:

  • Core features: genes, transcripts, exons, proteins, genome sequence, etc.
  • Regulatory: Ensembl regulatory, TFBS, miRNA targets, CTCF, Open chromatin, etc.
  • Functional annotation: OBO ontologies (Gene Ontology, Human Disease Ontology), etc.
  • Genomic variation: Ensembl Variation, ClinVar, COSMIC, etc.
  • Systems biology: IntAct , Reactome, gene co-expression, etc.

To make this entire database accessible to researchers, an exhaustive RESTful Web service API has been implemented. This API contains many methods that will facilitate researchers to query and obtain different biological information from a single database saving a lot of time. Another benefit is that researchers can make easily queries about different biologTical topics and link all this information together as all information is integrated.

Currently Homo sapiens, Mus musculus and other 20 species are available and many others will be included soon. Results are offered in JSON format, making all this information accessible to both software or web applications.

Availability

Cellbase is a centralised database that integrates lots of information from several main genomic and biological databases used for genomic annotation and clinical variant prioritisation. See Overview for details.

CellBase is open-source and freely available at https://github.com/opencb/cellbase

You can search CellBase using your favourite programming language:

| | installation | API | docs | tutorials | | :--- | :--- | :--- | :--- | :--- | | REST API | | | RESTful Web Services | | | Python | pypi | | | | | R | Bioconductor | | | Vignette | | Java | Installation | Javadoc | | |

CellBase is open-source and freely available at https://github.com/opencb/cellbase

Publications

CellBase was published at Nucleic Acids Research (2012):

http://nar.oxfordjournals.org/content/40/W1/W609.short

Owner

  • Name: Open source for Computational Biology
  • Login: opencb
  • Kind: organization
  • Email: ignacio.medina@zettagenomics.com
  • Location: Cambridge, UK

GitHub Events

Total
  • Release event: 5
  • Watch event: 3
  • Delete event: 15
  • Issue comment event: 13
  • Member event: 3
  • Push event: 83
  • Pull request review event: 26
  • Pull request event: 31
  • Create event: 25
Last Year
  • Release event: 5
  • Watch event: 3
  • Delete event: 15
  • Issue comment event: 13
  • Member event: 3
  • Push event: 83
  • Pull request review event: 26
  • Pull request event: 31
  • Create event: 25

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 4,014
  • Total Committers: 39
  • Avg Commits per committer: 102.923
  • Development Distribution Score (DDS): 0.768
Past Year
  • Commits: 245
  • Committers: 5
  • Avg Commits per committer: 49.0
  • Development Distribution Score (DDS): 0.584
Top Committers
Name Email Commits
imedina i****s@g****m 931
Javier Lopez j****d@g****m 844
Julie Sullivan j****n@g****m 814
Joaquín Tárraga Giménez j****a@g****m 195
Pablo Arce p****e@b****g 188
Swaathik s****k@g****m 159
imedina i****a@c****s 125
Javi Lopez f****z@e****k 109
JuanfeSanahuja j****a@z****m 100
dapregi d****9@g****m 100
melsiddieg m****g@g****m 59
Pablo Arce p****a@g****m 57
Jacobo Coll Moragón j****7@g****m 49
marnau m****1@g****m 47
Julie Sullivan j****n@g****k 35
wbari w****i@g****m 29
Francisco Salavert Torres f****t@c****s 22
juanrizetta j****z@z****m 21
lcruz l****z@j****s 18
frasator f****r@g****m 18
javi j****i@j****) 16
dapregi d****l@g****k 12
mbleda m****a@g****m 10
Alejandro Alemán a****n@c****s 8
Kevin Savage k****e 6
Cristina Yenyxe Gonzalez Garcia c****e@e****k 6
Marcus Robinson m****i@m****m 6
Antonio a****r@b****g 5
antonior a****r@a****) 4
Philip Hamid p****o@i****m 4
and 9 more...
Committer Domains (Top 20 + Academic)
cipf.es: 4 genomicsengland.co.uk: 3 ebi.ac.uk: 3 bioinfomgp.org: 3 zettagenomics.com: 2 antonior-precision-t1600.(none): 1 microsoft.com: 1 javi-portege-r830.(none): 1 juntadeandalucia.es: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 15
  • Total pull requests: 179
  • Average time to close issues: 12 months
  • Average time to close pull requests: 26 days
  • Total issue authors: 9
  • Total pull request authors: 13
  • Average comments per issue: 0.67
  • Average comments per pull request: 0.81
  • Merged pull requests: 119
  • Bot issues: 0
  • Bot pull requests: 9
Past Year
  • Issues: 0
  • Pull requests: 46
  • Average time to close issues: N/A
  • Average time to close pull requests: 10 days
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.65
  • Merged pull requests: 30
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • imedina (5)
  • julie-sullivan (3)
  • bbitarello (1)
  • jmrodriguezc (1)
  • praveenraj2018 (1)
  • juanfeSanahuja (1)
  • ameintjes (1)
  • lauralopezreal (1)
  • mbsimonovic (1)
  • jtarraga (1)
Pull Request Authors
  • jtarraga (74)
  • juanfeSanahuja (72)
  • julie-sullivan (23)
  • dependabot[bot] (9)
  • imedina (7)
  • juanrizetta (5)
  • j-coll (4)
  • awab-ahmed (4)
  • phamidko (4)
  • dapregi (3)
  • squinker (1)
  • Lucioric2000 (1)
  • casep (1)
Top Labels
Issue Labels
bug (4) task (4) enhancement (2) new feature (2) client (1) test (1) database (1)
Pull Request Labels
dependencies (9) bug (4) client (2) database (1)

Packages

  • Total packages: 19
  • Total downloads:
    • pypi 132 last-month
  • Total docker downloads: 30,382
  • Total dependent packages: 43
    (may contain duplicates)
  • Total dependent repositories: 18
    (may contain duplicates)
  • Total versions: 542
  • Total maintainers: 2
pypi.org: pycellbase

Python client for CellBase

  • Versions: 40
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 132 Last month
Rankings
Forks count: 5.7%
Dependent packages count: 7.3%
Stargazers count: 7.7%
Average: 11.0%
Downloads: 12.1%
Dependent repos count: 22.1%
Maintainers (2)
imedina dapregi
Last synced: 11 months ago
repo1.maven.org: org.opencb.cellbase:cellbase-core

CellBase projects integrates several biological databases into a NoSQL database plus many WS to query

  • Versions: 79
  • Dependent Packages: 9
  • Dependent Repositories: 6
  • Docker Downloads: 15,170
Rankings
Dependent packages count: 8.3%
Dependent repos count: 9.9%
Average: 17.6%
Forks count: 23.4%
Stargazers count: 28.6%
Last synced: 11 months ago
repo1.maven.org: org.opencb.cellbase:cellbase-client

CellBase projects integrates several biological databases into a NoSQL database plus many WS to query

  • Versions: 73
  • Dependent Packages: 8
  • Dependent Repositories: 3
  • Docker Downloads: 15,184
Rankings
Dependent packages count: 9.6%
Dependent repos count: 13.7%
Average: 18.8%
Forks count: 23.4%
Stargazers count: 28.6%
Last synced: 11 months ago
repo1.maven.org: org.opencb.hpg-bigdata:hpg-bigdata-core

HPG BigData project aims to provide tools for processing genomic big data in a Hadoop cluster

  • Versions: 8
  • Dependent Packages: 3
  • Dependent Repositories: 2
Rankings
Dependent repos count: 16.0%
Dependent packages count: 17.3%
Average: 21.3%
Forks count: 23.4%
Stargazers count: 28.6%
Last synced: 10 months ago
repo1.maven.org: org.opencb.hpg:hpg-bigdata-tools

HPG Big data project aims to manage genomic big data in a Hadoop-based cluster

  • Versions: 1
  • Dependent Packages: 4
  • Dependent Repositories: 1
Rankings
Dependent packages count: 13.8%
Dependent repos count: 20.6%
Average: 21.6%
Forks count: 23.4%
Stargazers count: 28.6%
Last synced: 11 months ago
repo1.maven.org: org.opencb.hpg:hpg-bigdata-core

HPG Big data project aims to manage genomic big data in a Hadoop-based cluster

  • Versions: 1
  • Dependent Packages: 4
  • Dependent Repositories: 1
Rankings
Dependent packages count: 13.8%
Dependent repos count: 20.6%
Average: 21.6%
Forks count: 23.4%
Stargazers count: 28.6%
Last synced: 11 months ago
repo1.maven.org: org.opencb.cellbase:cellbase-lib

CellBase projects integrates several biological databases into a NoSQL database plus many WS to query

  • Versions: 73
  • Dependent Packages: 3
  • Dependent Repositories: 1
  • Docker Downloads: 14
Rankings
Dependent packages count: 17.3%
Dependent repos count: 20.6%
Average: 22.5%
Forks count: 23.4%
Stargazers count: 28.6%
Last synced: 11 months ago
repo1.maven.org: org.opencb.cellbase:cellbase-mongodb

CellBase projects integrates several biological databases into a NoSQL database plus many WS to query

  • Versions: 6
  • Dependent Packages: 4
  • Dependent Repositories: 0
Rankings
Dependent packages count: 13.4%
Average: 22.7%
Dependent repos count: 32.0%
Last synced: 11 months ago
repo1.maven.org: org.opencb.cellbase:cellbase-grpc

CellBase projects integrates several biological databases into a NoSQL database plus many WS to query

  • Versions: 2
  • Dependent Packages: 2
  • Dependent Repositories: 0
Rankings
Forks count: 16.8%
Stargazers count: 20.7%
Dependent packages count: 22.4%
Average: 23.0%
Dependent repos count: 32.0%
Last synced: 10 months ago
repo1.maven.org: org.opencb.cellbase:cellbase-server

CellBase projects integrates several biological databases into a NoSQL database plus many WS to query

  • Versions: 74
  • Dependent Packages: 2
  • Dependent Repositories: 1
Rankings
Dependent repos count: 20.6%
Dependent packages count: 22.9%
Forks count: 23.4%
Average: 23.9%
Stargazers count: 28.6%
Last synced: 11 months ago
repo1.maven.org: org.opencb.hpg-bigdata:hpg-bigdata-analysis

HPG BigData project aims to provide tools for processing genomic big data in a Hadoop cluster

  • Versions: 3
  • Dependent Packages: 2
  • Dependent Repositories: 1
  • Docker Downloads: 14
Rankings
Dependent repos count: 20.6%
Dependent packages count: 22.9%
Forks count: 23.4%
Average: 23.9%
Stargazers count: 28.6%
Last synced: 11 months ago
repo1.maven.org: org.opencb.hpg-bigdata:hpg-bigdata-tools

HPG BigData project aims to provide tools for processing genomic big data in a Hadoop cluster

  • Versions: 5
  • Dependent Packages: 2
  • Dependent Repositories: 1
Rankings
Dependent repos count: 20.6%
Dependent packages count: 22.9%
Forks count: 23.4%
Average: 23.9%
Stargazers count: 28.6%
Last synced: 11 months ago
repo1.maven.org: org.opencb.cellbase:cellbase-build

CellBase projects integrates several biological databases into a NoSQL database plus many WS to query

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Forks count: 16.8%
Stargazers count: 20.7%
Average: 29.6%
Dependent repos count: 32.0%
Dependent packages count: 48.9%
Last synced: 10 months ago
repo1.maven.org: org.opencb.hpg-bigdata:hpg-bigdata

HPG BigData project aims to provide tools for processing genomic big data in a Hadoop cluster

  • Versions: 8
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 32.0%
Average: 40.4%
Dependent packages count: 48.9%
Last synced: 11 months ago
repo1.maven.org: org.opencb.cellbase:cellbase

CellBase projects integrates several biological databases into a NoSQL database plus many WS to query

  • Versions: 79
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 32.0%
Average: 40.4%
Dependent packages count: 48.9%
Last synced: 10 months ago
repo1.maven.org: org.opencb.hpg:hpg-bigdata

HPG Big data project aims to manage genomic big data in a Hadoop-based cluster

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 32.0%
Average: 40.4%
Dependent packages count: 48.9%
Last synced: 10 months ago
repo1.maven.org: org.opencb.hpg:hpg-bigdata-app

HPG Big data project aims to manage genomic big data in a Hadoop-based cluster

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 32.0%
Average: 40.4%
Dependent packages count: 48.9%
Last synced: 11 months ago
repo1.maven.org: org.opencb.hpg-bigdata:hpg-bigdata-app

HPG BigData project aims to provide tools for processing genomic big data in a Hadoop cluster

  • Versions: 8
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 32.0%
Average: 40.4%
Dependent packages count: 48.9%
Last synced: 11 months ago
repo1.maven.org: org.opencb.cellbase:cellbase-app

CellBase projects integrates several biological databases into a NoSQL database plus many WS to query

  • Versions: 78
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 32.0%
Average: 40.4%
Dependent packages count: 48.9%
Last synced: 10 months ago

Dependencies

.github/workflows/r-release.yml actions
  • actions/checkout v1 composite
  • r-lib/actions/setup-r master composite
cellbase-client/src/main/R/DESCRIPTION cran
  • R >= 3.3 depends
  • RCurl * depends
  • BiocParallel * imports
  • Gviz * imports
  • R.utils * imports
  • Rsamtools * imports
  • data.table * imports
  • doMC * imports
  • doParallel * imports
  • foreach * imports
  • jsonlite * imports
  • methods * imports
  • parallel * imports
  • pbapply * imports
  • tidyr * imports
  • utils * imports
  • BiocStyle * suggests
  • knitr * suggests
  • rmarkdown * suggests
cellbase-app/app/cloud/docker/cellbase-base/Dockerfile docker
  • openjdk 11-jre build
cellbase-app/app/cloud/docker/cellbase-builder/Dockerfile docker
  • opencb/cellbase-base $TAG build
cellbase-app/app/cloud/docker/cellbase-python/Dockerfile docker
  • opencb/cellbase-base $TAG build
cellbase-app/app/cloud/docker/cellbase-rest/Dockerfile docker
  • opencb/cellbase-base $TAG build
cellbase-client/src/main/python/Dockerfile docker
  • ubuntu latest build
cellbase-app/pom.xml maven
  • org.apache.logging.log4j:log4j-core
  • org.opencb.cellbase:cellbase-client 5.3.0-SNAPSHOT
  • org.opencb.cellbase:cellbase-server 5.3.0-SNAPSHOT
  • org.junit.jupiter:junit-jupiter-api test
  • org.junit.jupiter:junit-jupiter-engine test
  • org.junit.platform:junit-platform-engine test
cellbase-client/pom.xml maven
  • org.glassfish.jersey.core:jersey-client
  • org.glassfish.jersey.inject:jersey-hk2
  • org.opencb.cellbase:cellbase-core
  • org.glassfish.jersey.containers:jersey-container-servlet test
  • org.hamcrest:hamcrest-all test
  • org.junit.jupiter:junit-jupiter-api test
  • org.junit.jupiter:junit-jupiter-engine test
  • org.junit.jupiter:junit-jupiter-params test
  • org.junit.platform:junit-platform-engine test
cellbase-core/pom.xml maven
  • com.fasterxml.jackson.core:jackson-core
  • com.fasterxml.jackson.dataformat:jackson-dataformat-yaml
  • org.apache.logging.log4j:log4j-slf4j-impl
  • org.opencb.biodata:biodata-tools
  • org.hamcrest:hamcrest-all test
  • org.junit.jupiter:junit-jupiter-api test
  • org.junit.jupiter:junit-jupiter-engine test
  • org.junit.platform:junit-platform-engine test
cellbase-lib/pom.xml maven
  • org.apache.logging.log4j:log4j-core
  • org.apache.poi:poi-ooxml 4.1.2
  • org.eclipse.jetty:jetty-util-ajax
  • org.glassfish.jersey.core:jersey-client
  • org.opencb.cellbase:cellbase-core
  • org.opencb.commons:commons-datastore-mongodb ${java-common-libs.version}
  • org.hamcrest:hamcrest-all test
  • org.junit.jupiter:junit-jupiter-api test
  • org.junit.jupiter:junit-jupiter-engine test
  • org.junit.platform:junit-platform-engine test
cellbase-client/src/main/python/requirements.txt pypi
  • pyyaml *
  • requests *
  • retrying *
.github/workflows/develop.yml actions
.github/workflows/pull-request-merge.yml actions
.github/workflows/release.yml actions
.github/workflows/task.yml actions
.github/workflows/test-analysis.yml actions
  • actions/checkout v3 composite
  • actions/setup-java v3 composite
  • scacap/action-surefire-report v1 composite
  • supercharge/mongodb-github-action 1.8.0 composite
cellbase-client/src/main/python/setup.py pypi
cellbase-server/pom.xml maven
  • javax.servlet:javax.servlet-api 3.1.0 provided
  • com.fasterxml.jackson.module:jackson-module-jsonSchema
  • io.swagger:swagger-jersey2-jaxrs 1.6.5
  • org.eclipse.jetty:jetty-server
  • org.eclipse.jetty:jetty-webapp
  • org.glassfish.jersey.containers:jersey-container-servlet
  • org.glassfish.jersey.containers:jersey-container-servlet-core
  • org.glassfish.jersey.inject:jersey-hk2
  • org.glassfish.jersey.media:jersey-media-json-jackson
  • org.glassfish.jersey.media:jersey-media-multipart
  • org.opencb.cellbase:cellbase-lib 5.8.0-SNAPSHOT
cellbase-test/pom.xml maven
  • org.fitnesse:fitnesse 20161106
  • smartrics.restfixture:smartrics-RestFixture 4.1
pom.xml maven
  • com.fasterxml.jackson.core:jackson-core 2.11.4
  • com.fasterxml.jackson.core:jackson-databind 2.11.4
  • com.fasterxml.jackson.dataformat:jackson-dataformat-yaml 2.11.4
  • com.fasterxml.jackson.module:jackson-dataformat-protobuf 2.11.4
  • com.fasterxml.jackson.module:jackson-module-jsonSchema 2.11.4
  • io.grpc:grpc-all 1.48.0
  • org.apache.logging.log4j:log4j-core 2.17.2
  • org.apache.logging.log4j:log4j-slf4j-impl 2.17.2
  • org.eclipse.jetty:jetty-server 9.4.17.v20190418
  • org.eclipse.jetty:jetty-util-ajax 9.4.17.v20190418
  • org.eclipse.jetty:jetty-webapp 9.4.17.v20190418
  • org.glassfish.jersey.containers:jersey-container-servlet 2.30.1
  • org.glassfish.jersey.containers:jersey-container-servlet-core 2.30.1
  • org.glassfish.jersey.core:jersey-client 2.30.1
  • org.glassfish.jersey.inject:jersey-hk2 2.30.1
  • org.glassfish.jersey.media:jersey-media-json-jackson 2.30.1
  • org.glassfish.jersey.media:jersey-media-multipart 2.30.1
  • org.opencb.biodata:biodata-tools 2.12.0-SNAPSHOT
  • org.opencb.cellbase:cellbase-core ${project.parent.version}
  • org.opencb.cellbase:cellbase-lib ${project.parent.version}
  • org.opencb.commons:commons-datastore-mongodb 4.12.0-SNAPSHOT
  • org.slf4j:slf4j-api 1.7.32
  • org.hamcrest:hamcrest-all 1.3 test
  • org.junit.jupiter:junit-jupiter-api 5.5.2 test
  • org.junit.jupiter:junit-jupiter-engine 5.5.2 test
  • org.junit.jupiter:junit-jupiter-params 5.5.2 test
  • org.junit.platform:junit-platform-engine 1.5.2 test
environment.yml conda
  • pyyaml
  • requests
  • retrying