2016 Summer - Araport Project Overview Leaflet
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Araport is an open-source data platform established by the NSF and BBSRC to provide plant scientists access to Arabidopsis genomic data. It houses various types of data through components like ThaleMine, JBrowse, and Science Apps. The latest release, Araport11, contains revised gene annotations from RNA-seq data and contributions from various groups. ThaleMine allows users to access expression, ortholog, interaction and other data, analyze gene lists, and share queries. JBrowse hosts over 100 tracks including Araport11 updates and RNA-seq data for browsing. Araport also features apps and a developer community to expand its resources and analyses.
![Araport is an initiative funded by the NSF and the BBSRC,
and was established after a series of community
workshops [1] to give Arabidopsis and plant scientists
direct access to a new generation web-based data
platform. Users can browse and analyze a wide array of
data already available through Araport, and publish their
own data modules for community sharing and building
analysis workflows. The Araport data platform consists of
three major components: ThaleMine, JBrowse, and
Science Apps [2, 3]. Find out more at,
https://www.araport.org.
Araport has completed comprehensive updates to both
structural and functional annotation of the Col-0
genome as Araport11that has been officially released by
NCBI as of June 2016. Araport11 contains revisions to
gene structures and isoforms derived from 113 publicly
available RNA-seq datasets, as well as non-coding
genes, upstream ORFs, pseudogenes, along with
annotation contributions from NCBI, UniProt, and
individual research groups. The Araport11 data release
is available through ThaleMine, JBrowse, Science Apps,
and FTP download. Find out more at,
https://www.araport.org/data/araport11.
n
ThaleMine is based on the popular model organism data
warehouse GMOD InterMine. ThaleMine currently
houses a widearray of Arabidopsis genomic information
including RNA-seq expression (NCBI SRA), array
expression (BAR), coexpression (ATTED), orthologs
(Phytozome, Panther), protein interactions (IntAct,
BioGrid), pathways (KEGG), publications (NCBI, UniProt),
etc. Germplasm and phenotypes (ABRC/TAIR) havealso
been integrated into the Gene Report page. Users can
browse Gene Reports, analyze gene lists for feature
enrichment, run data queries (prebuilt or customized),
export data tables, and save/share. gene lists and data
queries. Find out more at
https://apps.araport.org/thalemine.
The GMOD JBrowse is a next generation fast response
genome browser. The Araport JBrowse hosts a
collection of over 100 data tracks of which some data
sources are accessed in real-time. Data tracks include
the latest Araport11 gene structure updates and over
100 RNA-seq datasets used in the Araport genome
reannotation effort, TDNA-seq (Ecker lab), population
variants (1001 Genomes Project), epigenetic marks
(EPIC-CoGe), chromatin states (Gutierrez lab), sequence
conservation (VISTA) plots (Phytozome), and more. In
addition to the large collection of data tracks from which
to choose, users can also upload and view their own
sequence alignments (e.g. BAM files) or genomic
features (e.g. GFF files) for side-by-side comparison with
the reference genome annotation. New mechanisms for
community users to easily publish persistent data tracks
for public sharing are being developed. Find out more
at, https://apps.araport.org/jbrowse.
Categories TAIR10 Araport11
(A) Protein-coding gene
Number of loci 27,416 27,655
Number of transcripts 35,386 48,359
Number of loci with >=2 splice variants 5,804 (18%) 10,696 (39%)
(B) Noncoding gene
Long intergenic noncoding RNA (lincRNA) 36 2,444
Natural antisense transcript (NAT) 223 1,115
MicroRNA (miRNA) 177 325
Small nucleolar RNA (snoRNA) 71 287
Small nuclear RNA (snRNA) 13 82
tRNA 689 689
rRNA 15 15
Other RNA 394 221
(C) Genomic feature
Small RNA 35,846
Novel transcribed region 508
Upstream open reading frame 58 84
Obsolete loci with short coding sequence 388
The Arabidopsis Information Portal
Araport11 Genome Annotation
ThaleMine Data Warehouse
JBrowse Genome Browser](https://image.slidesharecdn.com/araport-trifold-june-160627154410/85/2016-Summer-Araport-Project-Overview-Leaflet-1-320.jpg)
![A growing collection of modules providing data or
analysis capabilities will serve as building blocks for
creating discovery workflows. Themodules will be built
and shared by the research community for
interoperability and reuse. Users can review the currently
available set of Science Apps, and provide comments
and feedback on what modules they would like to see or
contribute. More at,
https://www.araport.org/apps/catalog.
Araport is an open source science resource and
maintains an active GitHub repository. The community
is not only invited to contribute and expand
functionalities, but is also empowered to do so. Araport
developers exploit cutting edge technologies such as
CyVerse/iPlant, Agave, Adama, git, jQuery, Bootstrap,
Docker, and Swagger. Araport hosts developer
workshops, and hack-a-thons to help the community
enrich and exploit this resource. Find out more at,
https://www.araport.org/devzone.
[1] International Arabidopsis Informatics Consortium.
(2012). Taking the next step: building an Arabidopsis
information portal. The Plant Cell, 24(6), 2248-2256.
PMID: 22751211
[2] Krishnakumar et al. (2014). Araport: the Arabidopsis
Information Portal. Nucl. Acids Res., 43(D1), D1003-
D1009. PMID: 25414324
[3] Hanlon et al. (2015). Araport: an application platform
for data discovery. Concurrency Computat.: Pract.Exper.,
doi: 10.1002/cpe.3542.
Powered by
Funded by
Science Apps
Developer Zone
References
Last modified: June 23, 2016
Science App
Visualization of BARInteraction data
https://www.araport.org
Email: araport@jcvi.org
Twitter: @araport
org
https://www.araport.org](https://image.slidesharecdn.com/araport-trifold-june-160627154410/85/2016-Summer-Araport-Project-Overview-Leaflet-2-320.jpg)
2016 Summer - Araport Project Overview Leaflet
- 1. Araport is an initiative funded by the NSF and the BBSRC, and was established after a series of community workshops [1] to give Arabidopsis and plant scientists direct access to a new generation web-based data platform. Users can browse and analyze a wide array of data already available through Araport, and publish their own data modules for community sharing and building analysis workflows. The Araport data platform consists of three major components: ThaleMine, JBrowse, and Science Apps [2, 3]. Find out more at, https://www.araport.org. Araport has completed comprehensive updates to both structural and functional annotation of the Col-0 genome as Araport11that has been officially released by NCBI as of June 2016. Araport11 contains revisions to gene structures and isoforms derived from 113 publicly available RNA-seq datasets, as well as non-coding genes, upstream ORFs, pseudogenes, along with annotation contributions from NCBI, UniProt, and individual research groups. The Araport11 data release is available through ThaleMine, JBrowse, Science Apps, and FTP download. Find out more at, https://www.araport.org/data/araport11. n ThaleMine is based on the popular model organism data warehouse GMOD InterMine. ThaleMine currently houses a widearray of Arabidopsis genomic information including RNA-seq expression (NCBI SRA), array expression (BAR), coexpression (ATTED), orthologs (Phytozome, Panther), protein interactions (IntAct, BioGrid), pathways (KEGG), publications (NCBI, UniProt), etc. Germplasm and phenotypes (ABRC/TAIR) havealso been integrated into the Gene Report page. Users can browse Gene Reports, analyze gene lists for feature enrichment, run data queries (prebuilt or customized), export data tables, and save/share. gene lists and data queries. Find out more at https://apps.araport.org/thalemine. The GMOD JBrowse is a next generation fast response genome browser. The Araport JBrowse hosts a collection of over 100 data tracks of which some data sources are accessed in real-time. Data tracks include the latest Araport11 gene structure updates and over 100 RNA-seq datasets used in the Araport genome reannotation effort, TDNA-seq (Ecker lab), population variants (1001 Genomes Project), epigenetic marks (EPIC-CoGe), chromatin states (Gutierrez lab), sequence conservation (VISTA) plots (Phytozome), and more. In addition to the large collection of data tracks from which to choose, users can also upload and view their own sequence alignments (e.g. BAM files) or genomic features (e.g. GFF files) for side-by-side comparison with the reference genome annotation. New mechanisms for community users to easily publish persistent data tracks for public sharing are being developed. Find out more at, https://apps.araport.org/jbrowse. Categories TAIR10 Araport11 (A) Protein-coding gene Number of loci 27,416 27,655 Number of transcripts 35,386 48,359 Number of loci with >=2 splice variants 5,804 (18%) 10,696 (39%) (B) Noncoding gene Long intergenic noncoding RNA (lincRNA) 36 2,444 Natural antisense transcript (NAT) 223 1,115 MicroRNA (miRNA) 177 325 Small nucleolar RNA (snoRNA) 71 287 Small nuclear RNA (snRNA) 13 82 tRNA 689 689 rRNA 15 15 Other RNA 394 221 (C) Genomic feature Small RNA 35,846 Novel transcribed region 508 Upstream open reading frame 58 84 Obsolete loci with short coding sequence 388 The Arabidopsis Information Portal Araport11 Genome Annotation ThaleMine Data Warehouse JBrowse Genome Browser
- 2. A growing collection of modules providing data or analysis capabilities will serve as building blocks for creating discovery workflows. Themodules will be built and shared by the research community for interoperability and reuse. Users can review the currently available set of Science Apps, and provide comments and feedback on what modules they would like to see or contribute. More at, https://www.araport.org/apps/catalog. Araport is an open source science resource and maintains an active GitHub repository. The community is not only invited to contribute and expand functionalities, but is also empowered to do so. Araport developers exploit cutting edge technologies such as CyVerse/iPlant, Agave, Adama, git, jQuery, Bootstrap, Docker, and Swagger. Araport hosts developer workshops, and hack-a-thons to help the community enrich and exploit this resource. Find out more at, https://www.araport.org/devzone. [1] International Arabidopsis Informatics Consortium. (2012). Taking the next step: building an Arabidopsis information portal. The Plant Cell, 24(6), 2248-2256. PMID: 22751211 [2] Krishnakumar et al. (2014). Araport: the Arabidopsis Information Portal. Nucl. Acids Res., 43(D1), D1003- D1009. PMID: 25414324 [3] Hanlon et al. (2015). Araport: an application platform for data discovery. Concurrency Computat.: Pract.Exper., doi: 10.1002/cpe.3542. Powered by Funded by Science Apps Developer Zone References Last modified: June 23, 2016 Science App Visualization of BARInteraction data https://www.araport.org Email: araport@jcvi.org Twitter: @araport org https://www.araport.org