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pmid:31114675

pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.

Saket Choudhary

F1000Research · 2019 doi:10.12688/f1000research.18676.1

Paper

complete

Experiment

complete

Data

partial

Analysis

absent

Execution

absent

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
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pmid:31114675
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science-record
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2026-11-01T15:40:45Z
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2026-11-01T18:50:50Z
generator object · 2 fields
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paper object · 10 fields
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title
pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.
doi
10.12688/f1000research.18676.1
pmid
31114675
authors array · 1 item
[0]
Saket Choudhary
journal
F1000Research
year
2019
abstract
The NCBI Sequence Read Archive (SRA) is the primary archive of next-generation sequencing datasets. SRA makes metadata and raw sequencing data available to the research community to encourage reproducibility and to provide avenues for testing novel hypotheses on publicly available data. However, methods to programmatically access this data are limited. We introduce the Python package, pysradb, which provides a collection of command line methods to query and download metadata and data from SRA, utilizing the curated metadata database available through the SRAdb project. We demonstrate the utility of pysradb on multiple use cases for searching and downloading SRA datasets. It is available freely at https://github.com/saketkc/pysradb.
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sections[14] "Underlying data" paragraph 2
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Dataset from DDBJ Sequence Read Archive, Accession number DRP003075: https://identifiers.org/ insdc.sra/DRP003075
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The claim, method and evidence span published with the source article.
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The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.
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the source data with its repository provenance
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Apply the paper's statistical method to the resolved series and compare the result with the published target.
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20301
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Homo sapiens
title
Widespread translational remodeling during human neuronal differentiation
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2026-11-01T15:39:54Z
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Homo sapiens
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Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human Embryonic Stem cells
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2026-11-01T15:39:54Z
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null
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Dataset from DDBJ Sequence Read Archive, Accession number DRP003075: https://identifiers.org/ insdc.sra/DRP003075
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GEO
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9138
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Homo sapiens
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Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human Embryonic Stem cells (part 2)
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2026-11-01T15:39:54Z
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Dataset from DDBJ Sequence Read Archive, Accession number DRP003075: https://identifiers.org/ insdc.sra/DRP003075
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GEO accession URL
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null
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14844;15749;16133;10669;14954;11002;13112
taxon
Bos taurus; Mus musculus; Rattus norvegicus; Gallus gallus; Macaca mulatta
title
Evolutionary dynamics of gene and isoform regulation in mammalian tissues
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2026-11-01T15:39:54Z
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false
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2026-10-31T18:35:43Z
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Dataset from DDBJ Sequence Read Archive, Accession number DRP003075: https://identifiers.org/ insdc.sra/DRP003075
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GEO
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GEO accession URL
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Dataset from DDBJ Sequence Read Archive, Accession number DRP003075: https://identifiers.org/ insdc.sra/DRP003075
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repository_route_statement
sample_accessions array · 0 items
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2026-10-31T18:35:43Z
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false
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asset:table:pmid:31114675:1
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PMC6505635
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6
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Search
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9
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DRP003075
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[0]
DRP003075
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[0]
DRP003075
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[0]
DRP003075
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[0]
DRP003075
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[3]
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[0]
DRP003075
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[0]
DRP003075
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[0]
ERP013565
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ERR1190989
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section[6]/table-wrap[1]#T1
[8] object · 16 fields
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asset:table:pmid:31114675:2
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jats-table
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PMC6505635
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Getting metadata for a SRA project
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SRP010679
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SRP010679
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SRP010679
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[0]
SRP010679
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[3]
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SRP010679
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[2]
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[0]
SRP010679
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SRS290864
[3]
SRR403892
[12] array · 4 items
[0]
SRP010679
[1]
SRX118296
[2]
SRS290865
[3]
SRR403893
locator
section[7]/table-wrap[1]#T2
[9] object · 16 fields
id
asset:table:pmid:31114675:3
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:a735e99196e90d8d54f351fb26a1a893885512bce0c30dc62c9df58d89eee90f
bytes
923
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[7]/table-wrap[2]#T3
version
null
note
null
structure object · 5 fields
pmcid
PMC6505635
section_index
7
section_title
Getting metadata for a SRA project
row_count
5
column_count
5
table object · 8 fields
label
null
caption
null
rows array · 5 items
[0] array · 5 items
[0]
study_accession
[1]
experiment_accession
[2]
sample_accession
[3]
run_accession
[4]
sample_attribute
[1] array · 5 items
[0]
SRP010679
[1]
SRX118285
[2]
SRS290854
[3]
SRR403882
[4]
source_name: PC3 human prostate cancer cells || cell line: PC3 || sample type: polyA RNA || treatment: vehicle
[2] array · 5 items
[0]
SRP010679
[1]
SRX118286
[2]
SRS290855
[3]
SRR403883
[4]
source_name: PC3 human prostate cancer cells || cell line: PC3 || sample type: ribosome protected RNA || treatment: vehicle
[3] array · 5 items
[0]
SRP010679
[1]
SRX118287
[2]
SRS290856
[3]
SRR403884
[4]
source_name: PC3 human prostate cancer cells || cell line: PC3 || sample type: polyA RNA || treatment: rapamycin
[4] array · 5 items
[0]
SRP010679
[1]
SRX118288
[2]
SRS290857
[3]
SRR403885
[4]
source_name: PC3 human prostate cancer cells || cell line: PC3 || sample type: ribosome protected RNA || treatment: rapamycin
locator
section[7]/table-wrap[2]#T3
[10] object · 16 fields
id
asset:table:pmid:31114675:4
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:068c166813e1323b53718020c7cf7eb1a8781754493bf7bcd504b91c3e27bc01
bytes
1225
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[7]/table-wrap[3]#T4
version
null
note
null
structure object · 5 fields
pmcid
PMC6505635
section_index
7
section_title
Getting metadata for a SRA project
row_count
14
column_count
5
table object · 8 fields
label
null
caption
null
rows array · 14 items
[0] array · 1 item
[0]
... [truncated]
[1] array · 5 items
[0]
run_accession
[1]
cell_line
[2]
sample_type
[3]
source_name
[4]
treatment
[2] array · 5 items
[0]
SRR403882
[1]
pc3
[2]
polya rna
[3]
pc3 human prostate cancer cells
[4]
vehicle
[3] array · 5 items
[0]
SRR403883
[1]
pc3
[2]
ribosome protected rna
[3]
pc3 human prostate cancer cells
[4]
vehicle
[4] array · 5 items
[0]
SRR403884
[1]
pc3
[2]
polya rna
[3]
pc3 human prostate cancer cells
[4]
rapamycin
[5] array · 5 items
[0]
SRR403885
[1]
pc3
[2]
ribosome protected rna
[3]
pc3 human prostate cancer cells
[4]
rapamycin
[6] array · 5 items
[0]
SRR403886
[1]
pc3
[2]
polya rna
[3]
pc3 human prostate cancer cells
[4]
pp242
[7] array · 5 items
[0]
SRR403887
[1]
pc3
[2]
ribosome protected rna
[3]
pc3 human prostate cancer cells
[4]
pp242
[8] array · 5 items
[0]
SRR403888
[1]
pc3
[2]
polya rna
[3]
pc3 human prostate cancer cells
[4]
vehicle
[9] array · 5 items
[0]
SRR403889
[1]
pc3
[2]
ribosome protected rna
[3]
pc3 human prostate cancer cells
[4]
vehicle
[10] array · 5 items
[0]
SRR403890
[1]
pc3
[2]
polya rna
[3]
pc3 human prostate cancer cells
[4]
rapamycin
[11] array · 5 items
[0]
SRR403891
[1]
pc3
[2]
ribosome protected rna
[3]
pc3 human prostate cancer cells
[4]
rapamycin
[12] array · 5 items
[0]
SRR403892
[1]
pc3
[2]
polya rna
[3]
pc3 human prostate cancer cells
[4]
pp242
[13] array · 5 items
[0]
SRR403893
[1]
pc3
[2]
ribosome protected rna
[3]
pc3 human prostate cancer cells
[4]
pp242
locator
section[7]/table-wrap[3]#T4
[11] object · 16 fields
id
asset:table:pmid:31114675:5
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:0465cfdf71d913dff07de151282a2b5474b745d3429f070ee5ed58a491e37cef
bytes
233
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[7]/table-wrap[4]#T5
version
null
note
null
structure object · 5 fields
pmcid
PMC6505635
section_index
7
section_title
Getting metadata for a SRA project
row_count
5
column_count
2
table object · 8 fields
label
null
caption
null
rows array · 5 items
[0] array · 2 items
[0]
999
[1]
Bisulfite-Seq
[1] array · 2 items
[0]
768
[1]
ChIP-Seq
[2] array · 2 items
[0]
121
[1]
OTHER
[3] array · 2 items
[0]
353
[1]
RNA-Seq
[4] array · 2 items
[0]
28
[1]
WGS
locator
section[7]/table-wrap[4]#T5
[12] object · 16 fields
id
asset:table:pmid:31114675:6
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:27948e036be34abd5e28610b62e70242f87740c569ce12701819a98eef28ddc0
bytes
227
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[8]/table-wrap[1]#T6
version
null
note
null
structure object · 5 fields
pmcid
PMC6505635
section_index
8
section_title
Getting SRPs from GSE
row_count
3
column_count
2
table object · 8 fields
label
null
caption
null
rows array · 3 items
[0] array · 2 items
[0]
study_alias
[1]
study_accession
[1] array · 2 items
[0]
GSE24355
[1]
SRP003870
[2] array · 2 items
[0]
GSE25842
[1]
SRP005378
locator
section[8]/table-wrap[1]#T6
[13] object · 16 fields
id
asset:table:pmid:31114675:7
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:76d15db0151d2dc7b6fc446d70b71bda0de8725b4df507d10f505780e3afebbc
bytes
957
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[8]/table-wrap[2]#T7
version
null
note
null
structure object · 5 fields
pmcid
PMC6505635
section_index
8
section_title
Getting SRPs from GSE
row_count
10
column_count
6
table object · 8 fields
label
null
caption
null
rows array · 10 items
[0] array · 6 items
[0]
study_alias
[1]
study_accession
[2]
experiment_accession
[3]
sample_accession
[4]
experiment_alias
[5]
sample_alias
[1] array · 6 items
[0]
GSE100007
[1]
SRP109126
[2]
SRX2916198
[3]
SRS2282390
[4]
GSM2667747
[5]
GSM2667747
[2] array · 6 items
[0]
GSE100007
[1]
SRP109126
[2]
SRX2916199
[3]
SRS2282391
[4]
GSM2667748
[5]
GSM2667748
[3] array · 6 items
[0]
GSE100007
[1]
SRP109126
[2]
SRX2916200
[3]
SRS2282392
[4]
GSM2667749
[5]
GSM2667749
[4] array · 6 items
[0]
GSE100007
[1]
SRP109126
[2]
SRX2916201
[3]
SRS2282393
[4]
GSM2667750
[5]
GSM2667750
[5] array · 6 items
[0]
GSE100007
[1]
SRP109126
[2]
SRX2916202
[3]
SRS2282394
[4]
GSM2667751
[5]
GSM2667751
[6] array · 6 items
[0]
GSE100007
[1]
SRP109126
[2]
SRX2916203
[3]
SRS2282395
[4]
GSM2667752
[5]
GSM2667752
[7] array · 6 items
[0]
GSE100007
[1]
SRP109126
[2]
SRX2916204
[3]
SRS2282396
[4]
GSM2667753
[5]
GSM2667753
[8] array · 6 items
[0]
GSE100007
[1]
SRP109126
[2]
SRX2916205
[3]
SRS2282397
[4]
GSM2667754
[5]
GSM2667754
[9] array · 6 items
[0]
GSE100007
[1]
SRP109126
[2]
SRX2916206
[3]
SRS2282400
[4]
GSM2667755
[5]
GSM2667755
locator
section[8]/table-wrap[2]#T7
[14] object · 16 fields
id
asset:table:pmid:31114675:8
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:931a8963c24dcdfaeaec42e7d5e5ddc1c2967e4c20b48f8e0492ab77e0901b6b
bytes
432
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[9]/table-wrap[1]#T8
version
null
note
null
structure object · 5 fields
pmcid
PMC6505635
section_index
9
section_title
Getting a list of GEO experiments for a GEO study
row_count
10
column_count
2
table object · 8 fields
label
null
caption
null
rows array · 10 items
[0] array · 2 items
[0]
study_alias
[1]
experiment_alias
[1] array · 2 items
[0]
GSE41637
[1]
GSM1020640_1
[2] array · 2 items
[0]
GSE41637
[1]
GSM1020641_1
[3] array · 2 items
[0]
GSE41637
[1]
GSM1020642_1
[4] array · 2 items
[0]
GSE41637
[1]
GSM1020643_1
[5] array · 2 items
[0]
GSE41637
[1]
GSM1020644_1
[6] array · 2 items
[0]
GSE41637
[1]
GSM1020645_1
[7] array · 2 items
[0]
GSE41637
[1]
GSM1020646_1
[8] array · 2 items
[0]
GSE41637
[1]
GSM1020647_1
[9] array · 2 items
[0]
GSE41637
[1]
GSM1020648_1
locator
section[9]/table-wrap[1]#T8
[15] object · 16 fields
id
asset:table:pmid:31114675:9
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:e42c2869c6893e0d16de178df738f7009db11e485e1c20e13364f5bfca3bc393
bytes
1021
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[9]/table-wrap[2]#T9
version
null
note
null
structure object · 5 fields
pmcid
PMC6505635
section_index
9
section_title
Getting a list of GEO experiments for a GEO study
row_count
10
column_count
3
table object · 8 fields
label
null
caption
null
rows array · 10 items
[0] array · 3 items
[0]
study_alias
[1]
experiment_alias
[2]
sample_attribute
[1] array · 3 items
[0]
GSE41637
[1]
GSM1020640_1
[2]
source_name: mouse_brain || strain: DBA/2J || tissue: brain
[2] array · 3 items
[0]
GSE41637
[1]
GSM1020641_1
[2]
source_name: mouse_colon || strain: DBA/2J || tissue: colon
[3] array · 3 items
[0]
GSE41637
[1]
GSM1020642_1
[2]
source_name: mouse_heart || strain: DBA/2J || tissue: heart
[4] array · 3 items
[0]
GSE41637
[1]
GSM1020643_1
[2]
source_name: mouse_kidney || strain: DBA/2J || tissue: kidney
[5] array · 3 items
[0]
GSE41637
[1]
GSM1020644_1
[2]
source_name: mouse_liver || strain: DBA/2J || tissue: liver
[6] array · 3 items
[0]
GSE41637
[1]
GSM1020645_1
[2]
source_name: mouse_lung || strain: DBA/2J || tissue: lung
[7] array · 3 items
[0]
GSE41637
[1]
GSM1020646_1
[2]
source_name: mouse_skm || strain: DBA/2J || tissue: skeletal muscle
[8] array · 3 items
[0]
GSE41637
[1]
GSM1020647_1
[2]
source_name: mouse_spleen || strain: DBA/2J || tissue: spleen
[9] array · 3 items
[0]
GSE41637
[1]
GSM1020648_1
[2]
source_name: mouse_testes || strain: DBA/2J || tissue: testes
locator
section[9]/table-wrap[2]#T9
[16] object · 16 fields
id
asset:table:pmid:31114675:10
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:cec1fea3364d0ddb78e64b7c298adf6efc8b6c585cf5fee685915862b1b4094f
bytes
633
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[9]/table-wrap[3]#T10
version
null
note
null
structure object · 5 fields
pmcid
PMC6505635
section_index
9
section_title
Getting a list of GEO experiments for a GEO study
row_count
8
column_count
5
table object · 8 fields
label
null
caption
null
rows array · 8 items
[0] array · 5 items
[0]
study_alias
[1]
experiment_alias
[2]
source_name
[3]
strain
[4]
tissue
[1] array · 5 items
[0]
GSE41637
[1]
GSM1020640_1
[2]
mouse_brain
[3]
dba/2j
[4]
brain
[2] array · 5 items
[0]
GSE41637
[1]
GSM1020641_1
[2]
mouse_colon
[3]
dba/2j
[4]
colon
[3] array · 5 items
[0]
GSE41637
[1]
GSM1020642_1
[2]
mouse_heart
[3]
dba/2j
[4]
heart
[4] array · 5 items
[0]
GSE41637
[1]
GSM1020643_1
[2]
mouse_kidney
[3]
dba/2j
[4]
kidney
[5] array · 5 items
[0]
GSE41637
[1]
GSM1020644_1
[2]
mouse_liver
[3]
dba/2j
[4]
liver
[6] array · 5 items
[0]
GSE41637
[1]
GSM1020645_1
[2]
mouse_lung
[3]
dba/2j
[4]
lung
[7] array · 5 items
[0]
GSE41637
[1]
GSM1020646_1
[2]
mouse_skm
[3]
dba/2j
[4]
skeletal muscle
locator
section[9]/table-wrap[3]#T10
[17] object · 16 fields
id
asset:table:pmid:31114675:11
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:3d5d5a4fcf793dd2c1ccb53fe39805f8d135e4230be2aff28bb627edfc9b1d2d
bytes
240
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[10]/table-wrap[1]#T11
version
null
note
null
structure object · 5 fields
pmcid
PMC6505635
section_index
10
section_title
Getting SRR from GSM
row_count
3
column_count
2
table object · 8 fields
label
null
caption
null
rows array · 3 items
[0] array · 2 items
[0]
experiment_alias
[1]
run_accession
[1] array · 2 items
[0]
GSM1020640_1
[1]
SRR594393
[2] array · 2 items
[0]
GSM1020646_1
[1]
SRR594399
locator
section[10]/table-wrap[1]#T11
gaps array · 12 items
[0]
asset:data:geo:GSE100007 not downloaded
[1]
asset:data:geo:GSE100007 licence not read
[2]
asset:data:geo:GSE24355 not downloaded
[3]
asset:data:geo:GSE24355 licence not read
[4]
asset:data:geo:GSE25842 not downloaded
[5]
asset:data:geo:GSE25842 licence not read
[6]
asset:data:geo:GSE41637 not downloaded
[7]
asset:data:geo:GSE41637 licence not read
[8]
asset:data:geo:SRP000941 not downloaded
[9]
asset:data:geo:SRP000941 licence not read
[10]
asset:data:geo:SRP010679 not downloaded
[11]
asset:data:geo:SRP010679 licence not read
analysis object · 4 fields
state
absent
methods array · 0 items
targets array · 0 items
gaps array · 2 items
[0]
method
[1]
operations
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
blocked
tier
R4
blocking_axis
method
blocked_on
method:not_determinable
axes object · 3 fields
method object · 5 fields
tier
R4
expressible
false
required_operations array · 0 items
missing_operations array · 0 items
basis
The reader quoted the method the paper names (not named), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
basis
The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.
data object · 6 fields
tier
R1
reachable
true
accessions array · 6 items
[0]
GSE24355
[1]
GSE25842
[2]
GSE100007
[3]
GSE41637
[4]
SRP010679
[5]
SRP000941
resolved_accessions array · 4 items
[0]
GSE24355
[1]
GSE25842
[2]
GSE100007
[3]
GSE41637
statements array · 1 item
[0]
Dataset from DDBJ Sequence Read Archive, Accession number DRP003075: https://identifiers.org/ insdc.sra/DRP003075
basis
The paper names GSE24355, GSE25842, GSE100007, GSE41637 in Gene Expression Omnibus and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 13 items
[0]
source:pmid:31114675
[1]
data:geo:GSE100007
[2]
asset:table:pmid:31114675:1
[3]
asset:table:pmid:31114675:2
[4]
asset:table:pmid:31114675:3
[5]
asset:table:pmid:31114675:4
[6]
asset:table:pmid:31114675:5
[7]
asset:table:pmid:31114675:6
[8]
asset:table:pmid:31114675:7
[9]
asset:table:pmid:31114675:8
[10]
asset:table:pmid:31114675:9
[11]
asset:table:pmid:31114675:10
[12]
asset:table:pmid:31114675:11
steps array · 1 item
[0]
run_analysis
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:GSE100007
gaps array · 1 item
[0]
method:not_determinable
review object · 5 fields
state
partial
machine_critique object · 5 fields
kind
extraction_review
reader object · 5 fields
model
MiniMax-M3.1-Flash
provider
minimax
provider_family
minimax
read_at
2026-10-31T18:14:48Z
independence
single_reader
evidence_check object · 2 fields
method
null
availability
null
calls
3
usage object · 3 fields
prompt_tokens
15611
completion_tokens
2323
cached_tokens
784
stages array · 1 item
[0] object · 4 fields
id
extraction
state
complete
reader
MiniMax-M3.1-Flash
provider
minimax
gaps array · 3 items
[0]
review.independent_reader
[1]
review.machine_critique
[2]
review.human_critique
execution object · 5 fields
state
absent
status
not_run
mode
null
runs array · 0 items
gaps array · 1 item
[0]
execution.not_run
provenance object · 7 fields
entities array · 3 items
[0] object · 3 fields
id
pmid:31114675
type
paper
label
pmid:31114675
[1] object · 3 fields
id
source:pmid:31114675
type
manuscript
label
PMID 31114675 full text
[2] object · 3 fields
id
data:geo:GSE100007
type
dataset
label
GEO GSE100007
activities array · 3 items
[0] object · 4 fields
id
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pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Ar
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