www.gigadb.org

– revolutionizing data dissemination, organization and use.

Tam SneddonBGI-Hong Kong

Now taking submissions…

OverviewIntroduction

/

What is ,why we want your data and why you should submit to us?

Data Publishing

DOIs

Published datasets

New database features

Future tools: Galaxy/Cloud

www.gigasciencejournal.com www.gigadb.org

Reproducibility/Reuse

Utility/Usability

Standards/Searchability/Sharing

Data publishing/DOI

DataCite goal: “increase acceptance of research as legitimate, citable contributions to the scholarly record”

PlantsChinese cabbageCucumber, domesticFoxtail milletPigeonpeaPotatoSorghum

MicrobesE. Coli O104:H4 TY-2482T2D gut metagenome

Cell-linesChinese Hamster Ovary

- Crab-eatingMinipigMouse methylomesNaked mole rat Penguin - Adelie penguin - Emperor penguinPigeon, domesticPolar bearSheep, domesticTibetan antelope

InvertebratesAnt - Florida carpenter ant- Jerdon’s jumping ant- Leaf-cutter antRoundwormSchistosoma haematobiumSilkworm, domestic and wild

Humans Ancient DNA- Aboriginal Australian- Saqqaq Eskimo Asian individual (YH) - DNA methylome - Genome assembly- TranscriptomeCancer- Hepatocellular carcinoma- Single-cell bladderHuman exome – chronic hepatitis B infection predisposing variants

VertebratesDarwin finchGiant panda Macaque - Chinese rhesus

Currently: 36 public datasets

PlantsChinese cabbageCucumber, domesticFoxtail milletPigeonpeaPotatoSorghum

MicrobesE. Coli O104:H4 TY-2482T2D gut metagenome

Cell-linesChinese Hamster Ovary

- Crab-eatingMinipigMouse methylomesNaked mole rat Penguin - Adelie penguin - Emperor penguinPigeon, domesticPolar bearSheep, domesticTibetan antelope

InvertebratesAnt - Florida carpenter ant- Jerdon’s jumping ant- Leaf-cutter antRoundwormSchistosoma haematobiumSilkworm, domestic and wild

Humans Ancient DNA- Aboriginal Australian- Saqqaq Eskimo Asian individual (YH) - DNA methylome - Genome assembly- TranscriptomeCancer- Hepatocellular carcinoma- Single-cell bladderHuman exome – chronic hepatitis B infection predisposing variants

VertebratesDarwin finchGiant panda Macaque - Chinese rhesus

Currently: 36 public datasets

*14TB*

PlantsChinese cabbageCucumber, domesticFoxtail milletPigeonpeaPotatoSorghum

MicrobesE. Coli O104:H4 TY-2482T2D gut metagenome

Cell-linesChinese Hamster Ovary

- Crab-eatingMinipigMouse methylomesNaked mole rat Penguin - Adelie penguin - Emperor penguinPigeon, domesticPolar bearSheep, domesticTibetan antelope

InvertebratesAnt - Florida carpenter ant- Jerdon’s jumping ant- Leaf-cutter antRoundwormSchistosoma haematobiumSilkworm, domestic and wild

Humans Ancient DNA- Aboriginal Australian- Saqqaq Eskimo Asian individual (YH) - DNA methylome - Genome assembly- TranscriptomeCancer- Hepatocellular carcinoma- Single-cell bladder cancerHuman exome – chronic hepatitis B infection predisposing variants

VertebratesDarwin finchGiant panda Macaque - Chinese rhesus

Currently: 36 public datasets***15 pre-publication***

PlantsChinese cabbageCucumber, domesticFoxtail milletPigeonpeaPotato*Sorghum*

MicrobesE. Coli O104:H4 TY-2482T2D gut metagenome

Cell-linesChinese Hamster Ovary

- Crab-eatingMinipig*Mouse methylomes*Naked mole rat Penguin - Adelie penguin - Emperor penguinPigeon, domestic*Polar bear*Sheep, domesticTibetan antelope

InvertebratesAnt - Florida carpenter ant- Jerdon’s jumping ant- Leaf-cutter antRoundwormSchistosoma haematobiumSilkworm, domestic and wild

Humans Ancient DNA- Aboriginal Australian- Saqqaq Eskimo Asian individual (YH) - DNA methylome - Genome assembly- *Transcriptome*Cancer- Hepatocellular carcinoma- *Single-cell bladder cancer*Human exome – chronic hepatitis B infection predisposing variants

VertebratesDarwin finchGiant panda Macaque - Chinese rhesus

Currently: 36 public datasets*5 citations in the references*

PlantsChinese cabbageCucumber, domesticFoxtail milletPigeonpeaPotato*Sorghum*

MicrobesE. Coli O104:H4 TY-2482

Cell-linesChinese Hamster Ovary (CHO)

Currently: 36 public datasets*5 citations in the references*

Humans Ancient DNA- Aboriginal Australian- Saqqaq Eskimo Asian individual (YH) - DNA methylome - Genome assembly- TranscriptomeCancer- Hepatocellular carcinoma- Single-cell bladderHuman exome – chronic hepatitis B infection predisposing variants

VertebratesDarwin finchGiant panda Macaque - Chinese rhesus

- Crab-eatingMinipigMouse methylomesNaked mole rat Penguin - Adelie penguin - Emperor penguinPigeon, domesticPolar bearSheep, domesticTibetan antelope

InvertebratesAnt - Florida carpenter ant- Jerdon’s jumping ant- Leaf-cutter antRoundwormSchistosoma haematobiumSilkworm, domestic and wild

Complemented by data submitted to INSDC databases:- Raw data SRA:SRA046843 - Assemblies of 3 strains Genbank:AHAO00000000-AHAQ00000000 - SNPs dbSNP batch ids:1056306-10563068 - CNVs- InDels dbVAR:nstd63 - SV }

PlantsChinese cabbageCucumber, domesticFoxtail milletPigeonpeaPotatoSorghum

MicrobesE. Coli O104:H4 TY-2482

Cell-linesChinese Hamster Ovary (CHO)

Currently: 36 public datasets*5 citations in the references*

Humans Ancient DNA- Aboriginal Australian- Saqqaq Eskimo Asian individual (YH) - DNA methylome - Genome assembly- *Transcriptome*Cancer- Hepatocellular carcinoma- Single-cell bladderHuman exome – chronic hepatitis B infection predisposing variants

VertebratesDarwin finchGiant panda Macaque - Chinese rhesus

- Crab-eatingMinipigMouse methylomesNaked mole rat Penguin - Adelie penguin - Emperor penguinPigeon, domesticPolar bearSheep, domesticTibetan antelope

InvertebratesAnt - Florida carpenter ant- Jerdon’s jumping ant- Leaf-cutter antRoundwormSchistosoma haematobiumSilkworm, domestic and wild

PlantsChinese cabbageCucumber, domesticFoxtail milletPigeonpeaPotatoSorghum

MicrobesE. Coli O104:H4 TY-2482

Cell-linesChinese Hamster Ovary (CHO)

Currently: 36 public datasets*5 citations in the references*

Humans Ancient DNA- Aboriginal Australian- Saqqaq Eskimo Asian individual (YH) - DNA methylome - Genome assembly- *Transcriptome*Cancer- Hepatocellular carcinoma- Single-cell bladderHuman exome – chronic hepatitis B infection predisposing variants

VertebratesDarwin finchGiant panda Macaque - Chinese rhesus

- Crab-eatingMinipigMouse methylomesNaked mole rat Penguin - Adelie penguin - Emperor penguinPigeon, domestic*Polar bear*Sheep, domesticTibetan antelope

InvertebratesAnt - Florida carpenter ant- Jerdon’s jumping ant- Leaf-cutter antRoundwormSchistosoma haematobiumSilkworm, domestic and wild

- Crab-eatingMinipig*Mouse methylomes*Naked mole rat Penguin - Adelie penguin - Emperor penguinPigeon, domesticPolar bearSheep, domesticTibetan antelope

InvertebratesAnt - Florida carpenter ant- Jerdon’s jumping ant- Leaf-cutter antRoundwormSchistosoma haematobiumSilkworm, domestic and wild

PlantsChinese cabbageCucumber, domesticFoxtail milletPigeonpeaPotatoSorghum

MicrobesE. Coli O104:H4 TY-2482

Cell-linesChinese Hamster Ovary (CHO)

Currently: 36 public datasets*5 citations in the references*

Humans Ancient DNA- Aboriginal Australian- Saqqaq Eskimo Asian individual (YH) - DNA methylome - Genome assembly- TranscriptomeCancer- Hepatocellular carcinoma- *Single-cell bladder cancer*Human exome – chronic hepatitis B infection predisposing variants

VertebratesDarwin finchGiant panda Macaque - Chinese rhesus

GigaDB is a new database integrated with the GigaScience journal to meet the needs of a new generation of biological and biomedical research as it enters the era of “big-data”… (see more)

GigaDB is a new database integrated with the GigaScience journal to meet the needs of a new generation of biological and biomedical research as it enters the era of “big-data”… (see more)

GigaDB is a new database integrated with the GigaScience journal to meet the needs of a new generation of biological and biomedical research as it enters the era of “big-data”… (see more)

Related DOIs:10.5524/100013 (is supplemented by)10.5524/100014 (is supplemented by)

http://dx.doi.org/10.5524/100015http://gigadb.org/100015

Galaxy for GigaScience

BioinformaticsDevelopment PublishingBiomedical and bioinformatics research

Thanks to:

editorial@gigasciencejournal.comdatabase@gigasciencejournal.com

@gigascience

facebook.com/GigaScience

blogs.openaccesscentral.com/blogs/gigablog/

Contact us:

Laurie GoodmanScott EdmondsAlexandra BasfordPeter LiJesse Si Zhe

Follow us:

Shaoguang Liang (BGI-SZ)Tin-Lap Lee (CUHK)Qiong Luo (HKUST)Senghong Wang (HKUST)Yan Zhou (HKUST)Cogini

www.gigadb.org