Tam Sneddon: Revolutionizing data dissemination, organization and use.
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Transcript of Tam Sneddon: Revolutionizing data dissemination, organization and use.
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www.gigadb.org
– revolutionizing data dissemination, organization and use.
Tam SneddonBGI-Hong Kong
Now taking submissions…
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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
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www.gigasciencejournal.com www.gigadb.org
Reproducibility/Reuse
Utility/Usability
Standards/Searchability/Sharing
Data publishing/DOI
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DataCite goal: “increase acceptance of research as legitimate, citable contributions to the scholarly record”
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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
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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*
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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***
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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*
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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 }
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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
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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
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- 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
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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)
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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)
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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)
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Related DOIs:10.5524/100013 (is supplemented by)10.5524/100014 (is supplemented by)
http://dx.doi.org/10.5524/100015http://gigadb.org/100015
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Galaxy for GigaScience
BioinformaticsDevelopment PublishingBiomedical and bioinformatics research
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Thanks to:
[email protected]@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