Edits to 'https://fairsharing.org/FAIRsharing.s22qdj' by 'The FAIRsharing Team' at 09:47, 17 Apr 2020 (approved):
'onto_disciplines' has been modified:
Before:
Comparative Genomics
Life Science
Proteomics
Transcriptomics
After:
Comparative Genomics
Immunology
Life Science
Microbiology
Proteomics
Transcriptomics
Added:
Immunology
Microbiology
Removed:
Edits to 'https://fairsharing.org/FAIRsharing.s22qdj' by 'BrianLee' at 18:49, 16 Apr 2020 (approved):
'publications' has been modified:
Before:
The UCSC Genome Browser database: extensions and updates 2013|Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, et al.|Nucleic Acids Res|2013
The UCSC Table Browser data retrieval tool|Karolchik D., Hinrichs AS., Furey TS., Roskin KM., Sugnet CW., Haussler D., Kent WJ., |Nucleic Acids Res.|2004
The human genome browser at UCSC|Kent WJ., Sugnet CW., Furey TS., Roskin KM., Pringle TH., Zahler AM., Haussler D., |Genome Res.|2002
ENCODE data in the UCSC Genome Browser: year 5 update|Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ|Nucleic Acids Res.|2013
BLAT--the BLAST-like alignment tool.|Kent WJ., |Genome Res.|2002
Exploring relationships and mining data with the UCSC Gene Sorter|Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D|Genome Res.|2005
The UCSC Genome Browser|Karolchik D, Hinrichs AS, Kent WJ|Curr Protoc Bioinformatics|2012
Initial sequencing and analysis of the human genome|Lander ES., Linton LM., Birren B., Nusbaum C., Zody MC., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., Funke R. et al.|Nature|2001
Assembly of the working draft of the human genome with GigAssembler.|Kent WJ., Haussler D., |Genome Res.|2001
The UCSC Genome Browser database: 2016 update.|Speir ML,Zweig AS,Rosenbloom KR,Raney BJ,Paten B,Nejad P,Lee BT,Learned K,Karolchik D,Hinrichs AS,Heitner S,Harte RA,Haeussler M,Guruvadoo L,Fujita PA,Eisenhart C,Diekhans M,Clawson H,Casper J,Barber GP,Haussler D,Kuhn RM,Kent WJ|Nucleic Acids Res|2015
The UCSC Genome Browser database: 2015 update.|Rosenbloom KR,Armstrong J,Barber GP,Casper J,Clawson H,Diekhans M,Dreszer TR,Fujita PA,Guruvadoo L,Haeussler M,Harte RA,Heitner S,Hickey G,Hinrichs AS,Hubley R,Karolchik D,Learned K,Lee BT,Li CH,Miga KH,Nguyen N,Paten B,Raney BJ,Smit AF,Speir ML,Zweig AS,Haussler D,Kuhn RM,Kent WJ|Nucleic Acids Res|2014
The UCSC Genome Browser database: 2017 update.|Tyner C,Barber GP,Casper J,Clawson H,Diekhans M,Eisenhart C,Fischer CM,Gibson D,Gonzalez JN,Guruvadoo L,Haeussler M,Heitner S,Hinrichs AS,Karolchik D,Lee BT,Lee CM,Nejad P,Raney BJ,Rosenbloom KR,Speir ML,Villarreal C,Vivian J,Zweig AS,Haussler D,Kuhn RM,Kent WJ|Nucleic Acids Res|2016
UCSC Genome Browser enters 20th year.|Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, Powell CC, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Zweig AS, Haussler D, Haeussler M, Kuhn RM, Kent WJ.|Nucleic Acids Res.|2020
After:
The UCSC Genome Browser database: extensions and updates 2013|Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, et al.|Nucleic Acids Res|2013
The UCSC Table Browser data retrieval tool|Karolchik D., Hinrichs AS., Furey TS., Roskin KM., Sugnet CW., Haussler D., Kent WJ., |Nucleic Acids Res.|2004
The human genome browser at UCSC|Kent WJ., Sugnet CW., Furey TS., Roskin KM., Pringle TH., Zahler AM., Haussler D., |Genome Res.|2002
ENCODE data in the UCSC Genome Browser: year 5 update|Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ|Nucleic Acids Res.|2013
BLAT--the BLAST-like alignment tool.|Kent WJ., |Genome Res.|2002
Exploring relationships and mining data with the UCSC Gene Sorter|Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D|Genome Res.|2005
The UCSC Genome Browser|Karolchik D, Hinrichs AS, Kent WJ|Curr Protoc Bioinformatics|2012
Initial sequencing and analysis of the human genome|Lander ES., Linton LM., Birren B., Nusbaum C., Zody MC., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., Funke R. et al.|Nature|2001
Assembly of the working draft of the human genome with GigAssembler.|Kent WJ., Haussler D., |Genome Res.|2001
The UCSC Genome Browser database: 2016 update.|Speir ML,Zweig AS,Rosenbloom KR,Raney BJ,Paten B,Nejad P,Lee BT,Learned K,Karolchik D,Hinrichs AS,Heitner S,Harte RA,Haeussler M,Guruvadoo L,Fujita PA,Eisenhart C,Diekhans M,Clawson H,Casper J,Barber GP,Haussler D,Kuhn RM,Kent WJ|Nucleic Acids Res|2015
The UCSC Genome Browser database: 2015 update.|Rosenbloom KR,Armstrong J,Barber GP,Casper J,Clawson H,Diekhans M,Dreszer TR,Fujita PA,Guruvadoo L,Haeussler M,Harte RA,Heitner S,Hickey G,Hinrichs AS,Hubley R,Karolchik D,Learned K,Lee BT,Li CH,Miga KH,Nguyen N,Paten B,Raney BJ,Smit AF,Speir ML,Zweig AS,Haussler D,Kuhn RM,Kent WJ|Nucleic Acids Res|2014
The UCSC Genome Browser database: 2017 update.|Tyner C,Barber GP,Casper J,Clawson H,Diekhans M,Eisenhart C,Fischer CM,Gibson D,Gonzalez JN,Guruvadoo L,Haeussler M,Heitner S,Hinrichs AS,Karolchik D,Lee BT,Lee CM,Nejad P,Raney BJ,Rosenbloom KR,Speir ML,Villarreal C,Vivian J,Zweig AS,Haussler D,Kuhn RM,Kent WJ|Nucleic Acids Res|2016
UCSC Genome Browser enters 20th year.|Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, Powell CC, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Zweig AS, Haussler D, Haeussler M, Kuhn RM, Kent WJ.|Nucleic Acids Res.|2020
The UCSC Genome Browser database: 2019 update|Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, Gibson D, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ.|Nucleic Acids Res.|2019
The UCSC Genome Browser database: 2018 update.|Casper J, Zweig AS, Villarreal C, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Karolchik D, Hinrichs AS, Haeussler M, Guruvadoo L, Navarro Gonzalez J, Gibson D, Fiddes IT, Eisenhart C, Diekhans M, Clawson H, Barber GP, Armstrong J, Haussler D, Kuhn RM, Kent WJ. |Nucleic Acids Res.|2018
Added:
The UCSC Genome Browser database: 2019 update|Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, Gibson D, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ.|Nucleic Acids Res.|2019
The UCSC Genome Browser database: 2018 update.|Casper J, Zweig AS, Villarreal C, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Karolchik D, Hinrichs AS, Haeussler M, Guruvadoo L, Navarro Gonzalez J, Gibson D, Fiddes IT, Eisenhart C, Diekhans M, Clawson H, Barber GP, Armstrong J, Haussler D, Kuhn RM, Kent WJ. |Nucleic Acids Res.|2018
Removed:
Edits to 'https://fairsharing.org/FAIRsharing.s22qdj' by 'BrianLee' at 18:46, 16 Apr 2020 (approved):
'publications' has been modified:
Before:
The UCSC Genome Browser database: extensions and updates 2013|Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, et al.|Nucleic Acids Res|2013
The UCSC Table Browser data retrieval tool|Karolchik D., Hinrichs AS., Furey TS., Roskin KM., Sugnet CW., Haussler D., Kent WJ., |Nucleic Acids Res.|2004
The human genome browser at UCSC|Kent WJ., Sugnet CW., Furey TS., Roskin KM., Pringle TH., Zahler AM., Haussler D., |Genome Res.|2002
ENCODE data in the UCSC Genome Browser: year 5 update|Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ|Nucleic Acids Res.|2013
BLAT--the BLAST-like alignment tool.|Kent WJ., |Genome Res.|2002
Exploring relationships and mining data with the UCSC Gene Sorter|Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D|Genome Res.|2005
The UCSC Genome Browser|Karolchik D, Hinrichs AS, Kent WJ|Curr Protoc Bioinformatics|2012
Initial sequencing and analysis of the human genome|Lander ES., Linton LM., Birren B., Nusbaum C., Zody MC., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., Funke R. et al.|Nature|2001
Assembly of the working draft of the human genome with GigAssembler.|Kent WJ., Haussler D., |Genome Res.|2001
The UCSC Genome Browser database: 2016 update.|Speir ML,Zweig AS,Rosenbloom KR,Raney BJ,Paten B,Nejad P,Lee BT,Learned K,Karolchik D,Hinrichs AS,Heitner S,Harte RA,Haeussler M,Guruvadoo L,Fujita PA,Eisenhart C,Diekhans M,Clawson H,Casper J,Barber GP,Haussler D,Kuhn RM,Kent WJ|Nucleic Acids Res|2015
The UCSC Genome Browser database: 2015 update.|Rosenbloom KR,Armstrong J,Barber GP,Casper J,Clawson H,Diekhans M,Dreszer TR,Fujita PA,Guruvadoo L,Haeussler M,Harte RA,Heitner S,Hickey G,Hinrichs AS,Hubley R,Karolchik D,Learned K,Lee BT,Li CH,Miga KH,Nguyen N,Paten B,Raney BJ,Smit AF,Speir ML,Zweig AS,Haussler D,Kuhn RM,Kent WJ|Nucleic Acids Res|2014
The UCSC Genome Browser database: 2017 update.|Tyner C,Barber GP,Casper J,Clawson H,Diekhans M,Eisenhart C,Fischer CM,Gibson D,Gonzalez JN,Guruvadoo L,Haeussler M,Heitner S,Hinrichs AS,Karolchik D,Lee BT,Lee CM,Nejad P,Raney BJ,Rosenbloom KR,Speir ML,Villarreal C,Vivian J,Zweig AS,Haussler D,Kuhn RM,Kent WJ|Nucleic Acids Res|2016
After:
The UCSC Genome Browser database: extensions and updates 2013|Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, et al.|Nucleic Acids Res|2013
The UCSC Table Browser data retrieval tool|Karolchik D., Hinrichs AS., Furey TS., Roskin KM., Sugnet CW., Haussler D., Kent WJ., |Nucleic Acids Res.|2004
The human genome browser at UCSC|Kent WJ., Sugnet CW., Furey TS., Roskin KM., Pringle TH., Zahler AM., Haussler D., |Genome Res.|2002
ENCODE data in the UCSC Genome Browser: year 5 update|Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ|Nucleic Acids Res.|2013
BLAT--the BLAST-like alignment tool.|Kent WJ., |Genome Res.|2002
Exploring relationships and mining data with the UCSC Gene Sorter|Kent WJ, Hsu F, Karolchik D, Kuhn RM, Clawson H, Trumbower H, Haussler D|Genome Res.|2005
The UCSC Genome Browser|Karolchik D, Hinrichs AS, Kent WJ|Curr Protoc Bioinformatics|2012
Initial sequencing and analysis of the human genome|Lander ES., Linton LM., Birren B., Nusbaum C., Zody MC., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., Funke R. et al.|Nature|2001
Assembly of the working draft of the human genome with GigAssembler.|Kent WJ., Haussler D., |Genome Res.|2001
The UCSC Genome Browser database: 2016 update.|Speir ML,Zweig AS,Rosenbloom KR,Raney BJ,Paten B,Nejad P,Lee BT,Learned K,Karolchik D,Hinrichs AS,Heitner S,Harte RA,Haeussler M,Guruvadoo L,Fujita PA,Eisenhart C,Diekhans M,Clawson H,Casper J,Barber GP,Haussler D,Kuhn RM,Kent WJ|Nucleic Acids Res|2015
The UCSC Genome Browser database: 2015 update.|Rosenbloom KR,Armstrong J,Barber GP,Casper J,Clawson H,Diekhans M,Dreszer TR,Fujita PA,Guruvadoo L,Haeussler M,Harte RA,Heitner S,Hickey G,Hinrichs AS,Hubley R,Karolchik D,Learned K,Lee BT,Li CH,Miga KH,Nguyen N,Paten B,Raney BJ,Smit AF,Speir ML,Zweig AS,Haussler D,Kuhn RM,Kent WJ|Nucleic Acids Res|2014
The UCSC Genome Browser database: 2017 update.|Tyner C,Barber GP,Casper J,Clawson H,Diekhans M,Eisenhart C,Fischer CM,Gibson D,Gonzalez JN,Guruvadoo L,Haeussler M,Heitner S,Hinrichs AS,Karolchik D,Lee BT,Lee CM,Nejad P,Raney BJ,Rosenbloom KR,Speir ML,Villarreal C,Vivian J,Zweig AS,Haussler D,Kuhn RM,Kent WJ|Nucleic Acids Res|2016
UCSC Genome Browser enters 20th year.|Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, Powell CC, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Zweig AS, Haussler D, Haeussler M, Kuhn RM, Kent WJ.|Nucleic Acids Res.|2020
Added:
UCSC Genome Browser enters 20th year.|Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, Powell CC, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Zweig AS, Haussler D, Haeussler M, Kuhn RM, Kent WJ.|Nucleic Acids Res.|2020
Removed:
Edits to 'https://fairsharing.org/FAIRsharing.s22qdj' by 'BrianLee' at 18:42, 16 Apr 2020 (approved):
'dataProcesses' has been modified:
Before:
daily data releases
data QA
versioning by genome assembly
versioning by individual annotation
access to historical files possible
file download(tab-delimited,XML)
Genome Browser
Table Browser
Gene Sorter
REST API returning JSON data
After:
daily data releases
data QA
versioning by genome assembly
versioning by individual annotation
access to historical files possible
file download(tab-delimited,XML)
Genome Browser
Table Browser
Gene Sorter
REST API returning JSON data
Download Server
MySQL data server
Added:
Download Server
MySQL data server
Removed:
Edits to 'https://fairsharing.org/FAIRsharing.s22qdj' by 'BrianLee' at 18:40, 16 Apr 2020 (approved):
'dataProcesses' has been modified:
Before:
daily data releases
data QA
versioning by genome assembly
versioning by individual annotation
access to historical files possible
file download(tab-delimited,XML)
Genome Browser
Table Browser
Gene Sorter
After:
daily data releases
data QA
versioning by genome assembly
versioning by individual annotation
access to historical files possible
file download(tab-delimited,XML)
Genome Browser
Table Browser
Gene Sorter
REST API returning JSON data
Added:
REST API returning JSON data
Removed:
Edits to 'https://fairsharing.org/FAIRsharing.s22qdj' by 'BrianLee' at 18:36, 16 Apr 2020 (approved):
'tools' has been modified:
Before:
Blat||http://genome.ucsc.edu/cgi-bin/hgBlat
In Silico PCR||http://genome.ucsc.edu/cgi-bin/hgPcr
Genome Graphs||http://genome.ucsc.edu/cgi-bin/hgGenome
VisiGene||http://genome.ucsc.edu/cgi-bin/hgVisiGene
liftOver||http://genome.ucsc.edu/cgi-bin/hgLiftOver
Variant Annotation Integrator (VAI)||http://genome.ucsc.edu/cgi-bin/hgVai
Data Integrator||http://genome.ucsc.edu/cgi-bin/hgIntegrator
Genome Browser in a Box (virtual machine)||http://genome.ucsc.edu/goldenpath/help/gbib.html
After:
Blat||http://genome.ucsc.edu/cgi-bin/hgBlat
In Silico PCR||http://genome.ucsc.edu/cgi-bin/hgPcr
Genome Graphs||http://genome.ucsc.edu/cgi-bin/hgGenome
VisiGene||http://genome.ucsc.edu/cgi-bin/hgVisiGene
liftOver||http://genome.ucsc.edu/cgi-bin/hgLiftOver
Variant Annotation Integrator (VAI)||http://genome.ucsc.edu/cgi-bin/hgVai
Data Integrator||http://genome.ucsc.edu/cgi-bin/hgIntegrator
Genome Browser in a Box (virtual machine)||http://genome.ucsc.edu/goldenpath/help/gbib.html
Genome Browser in the Cloud (installation script)||http://genome.ucsc.edu/goldenpath/help/gbic.html
REST API data interface||http://api.genome.ucsc.edu/
Gene interactions and pathways from curated databases and text-mining ||http://genome.ucsc.edu/cgi-bin/hgGeneGraph
Added:
Genome Browser in the Cloud (installation script)||http://genome.ucsc.edu/goldenpath/help/gbic.html
REST API data interface||http://api.genome.ucsc.edu/
Gene interactions and pathways from curated databases and text-mining ||http://genome.ucsc.edu/cgi-bin/hgGeneGraph
Removed:
Edits to 'https://fairsharing.org/FAIRsharing.s22qdj' by 'BrianLee' at 18:25, 16 Apr 2020 (approved):
'user_defined_tags' has been modified:
Before:
Uniqueness mapping
After:
COVID-19
Uniqueness mapping
Added:
COVID-19
Removed:
'miriam_id' has been modified:
Before: None
After:
Edits to 'https://fairsharing.org/FAIRsharing.s22qdj' by 'The FAIRsharing Team' at 11:17, 21 Nov 2018 (approved):
'domains' has been modified:
Before:
Annotation
Biological regulation
Comparative genomics
DNA microarray
DNA sequence data
DNA structural variation To remove
Deoxyribonucleic acid (DNA)
Disease phenotype
Gene
Gene expression data
Gene prediction
Genetic polymorphism
Genome
Genotype
Indel
Life Science
Messenger RNA (mRNA)
Proteomics
Regulation of gene expression
Regulatory region
Ribonucleic acid (RNA)
Sequence
Sequence alignment
Sequence annotation
Sequence composition, complexity and repeats
Transcriptomics
Uniqueness mapping
After:
Annotation
Biological regulation
Comparative genomics
DNA microarray
DNA sequence data
DNA structural variation
Deoxyribonucleic acid (DNA)
Disease phenotype
Gene
Gene expression data
Gene prediction
Genetic polymorphism
Genome
Genotype
Indel
Life Science
Messenger RNA (mRNA)
Proteomics
Regulation of gene expression
Regulatory region
Ribonucleic acid (RNA)
Sequence
Sequence alignment
Sequence annotation
Sequence composition, complexity and repeats
Transcriptomics
Uniqueness mapping
Added:
DNA structural variation
Removed:
DNA structural variation To remove