Corpus Engine Towards a reproducible .science file.
← All .science files

pmid:37094819

smalldisco, a pipeline for siRNA discovery and 3' tail identification.

Ian V Caldas · Leanne H Kelley · Yasir H Ahmed-Braimah · Eleanor M Maine

G3 (Bethesda, Md.) · 2023 doi:10.1093/g3journal/jkad092

Paper

complete

Experiment

partial

Data

partial

Analysis

complete

Execution

absent

Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
id
pmid:37094819
kind
science-record
content_hash
sha256:ada0332e855b282cffba5743942ba7a92caa3fc09e6c9096700ec24b64e4d5bf
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T19:01:46Z
updated_at
2026-11-01T22:09:20Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
smalldisco, a pipeline for siRNA discovery and 3' tail identification.
doi
10.1093/g3journal/jkad092
pmid
37094819
authors array · 4 items
[0]
Ian V Caldas
[1]
Leanne H Kelley
[2]
Yasir H Ahmed-Braimah
[3]
Eleanor M Maine
journal
G3 (Bethesda, Md.)
year
2023
abstract
Capturing and sequencing small RNAs is standard practice; however, identification of a group of these small RNAs-small interfering RNAs (siRNAs)-has been more difficult. We present smalldisco, a command-line tool for small interfering RNA discovery and annotation from small RNA-seq datasets. smalldisco can distinguish short reads that map antisense to an annotated genomic feature (e.g. exons or mRNAs), annotate these siRNAs, and quantify their abundance. smalldisco also uses the program Tailor to quantify 3' nontemplated nucleotides of siRNAs or any small RNA species. smalldisco and supporting documentation are available for download from GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621).
claims array · 2 items
[0] object · 6 fields
id
claim-data-access
statement
smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621). Supplemental material available at G3 online.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:37094819
locator
sections[7] "Data availability" paragraphs 1-3
quote
smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621). Supplemental material available at G3 online.
state
complete
[1] object · 6 fields
id
claim-target-result
statement
First, smalldisco analyzed our sample input dataset in ∼2.5 hours, whereas segmentSeq required ∼2.5 weeks.
kind
qualitative
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:37094819
locator
sections[3] "Results and discussion" paragraph 6
quote
First, smalldisco analyzed our sample input dataset in ∼2.5 hours, whereas segmentSeq required ∼2.5 weeks.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
partial
objective
First, smalldisco analyzed our sample input dataset in ∼2.5 hours, whereas segmentSeq required ∼2.5 weeks.
steps array · 3 items
[0] object · 13 fields
id
read_published_estimate
order
1
name
Read the published estimate from the source
kind
other
state
complete
blocked_on
null
description
The claim, method and evidence span published with the source article.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:37094819
outputs array · 1 item
[0]
the published estimate and its evidence
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
id
obtain_source_data
order
2
name
Obtain the source data from the named repository
kind
data-preparation
state
blocked
blocked_on
data:accession_unresolved
description
The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:PRJNA123485
outputs array · 1 item
[0]
the source data with its repository provenance
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
id
run_analysis
order
3
name
Run the published analysis
kind
analysis
state
complete
blocked_on
null
description
Apply the paper's statistical method to the resolved series and compare the result with the published target.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:PRJNA123485
outputs array · 1 item
[0]
the replicated result and its comparison
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 1 item
[0]
step:obtain_source_data blocked on data:accession_unresolved
data object · 3 fields
state
partial
assets array · 5 items
[0] object · 15 fields
id
source:pmid:37094819
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1093/g3journal/jkad092
sha256
sha256:62abec4cf5466de12e6ed08af43382349a01fa80fd39dfc968113fb8d9bbdc5c
bytes
24958
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1093/g3journal/jkad092
version
null
note
Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.
structure object · 4 fields
pmcid
PMC10234390
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:PRJNA123485
role
raw
format
geo-series
media_type
application/vnd.ncbi.geo-series+json
uri
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PRJNA123485
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
PRJNA123485
version
null
note
smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621). Supplemental material available at G3 online.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621). Supplemental material available at G3 online.
access_statement_kind
data_availability_statement
sample_accessions array · 0 items
sample_count
null
group_sizes
null
group_sizes_basis
null
platform
null
taxon
null
title
null
resolution_checked_at
2026-11-01T18:46:43Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 15 fields
id
data:geo:PRJNA398116
role
raw
format
geo-series
media_type
application/vnd.ncbi.geo-series+json
uri
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PRJNA398116
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
PRJNA398116
version
null
note
smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621). Supplemental material available at G3 online.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621). Supplemental material available at G3 online.
access_statement_kind
data_availability_statement
sample_accessions array · 0 items
sample_count
null
group_sizes
null
group_sizes_basis
null
platform
null
taxon
null
title
null
resolution_checked_at
2026-11-01T18:46:43Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[3] object · 15 fields
id
data:geo:PRJNA447866
role
raw
format
geo-series
media_type
application/vnd.ncbi.geo-series+json
uri
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PRJNA447866
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
PRJNA447866
version
null
note
smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621). Supplemental material available at G3 online.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621). Supplemental material available at G3 online.
access_statement_kind
data_availability_statement
sample_accessions array · 0 items
sample_count
null
group_sizes
null
group_sizes_basis
null
platform
null
taxon
null
title
null
resolution_checked_at
2026-11-01T18:46:43Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[4] object · 15 fields
id
data:geo:PRJNA624174
role
raw
format
geo-series
media_type
application/vnd.ncbi.geo-series+json
uri
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PRJNA624174
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
PRJNA624174
version
null
note
smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621). Supplemental material available at G3 online.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621). Supplemental material available at G3 online.
access_statement_kind
data_availability_statement
sample_accessions array · 0 items
sample_count
null
group_sizes
null
group_sizes_basis
null
platform
null
taxon
null
title
null
resolution_checked_at
2026-11-01T18:46:43Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 8 items
[0]
asset:data:geo:PRJNA123485 not downloaded
[1]
asset:data:geo:PRJNA123485 licence not read
[2]
asset:data:geo:PRJNA398116 not downloaded
[3]
asset:data:geo:PRJNA398116 licence not read
[4]
asset:data:geo:PRJNA447866 not downloaded
[5]
asset:data:geo:PRJNA447866 licence not read
[6]
asset:data:geo:PRJNA624174 not downloaded
[7]
asset:data:geo:PRJNA624174 licence not read
analysis object · 4 fields
state
complete
methods array · 1 item
[0] object · 10 fields
id
method-1
family
sequence_alignment
specific
read_mapping
label
Sequence alignment / homology
dsl_operations array · 2 items
[0]
sequence_align
[1]
alignment_identity
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
sequence_records
evidence object · 3 fields
score
0.8
band
high
quote
HISAT2
targets array · 0 items
gaps array · 0 items
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
blocked_on
data:accession_absent
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 2 items
[0]
sequence_align
[1]
alignment_identity
missing_operations array · 0 items
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: read_mapping.
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
R4
reachable
false
accessions array · 4 items
[0]
PRJNA447866
[1]
PRJNA123485
[2]
PRJNA624174
[3]
PRJNA398116
resolved_accessions array · 0 items
statements array · 1 item
[0]
smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621). Supplemental material available at G3 online.
basis
The paper names PRJNA447866, PRJNA123485, PRJNA624174, PRJNA398116, but the accession does not resolve in the repository (not_in_ncbi_bioproject, not_in_ncbi_bioproject, not_in_ncbi_bioproject, not_in_ncbi_bioproject), so the data cannot be reached from here. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 2 items
[0]
sequence_align
[1]
alignment_identity
assets array · 2 items
[0]
source:pmid:37094819
[1]
data:geo:PRJNA123485
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:PRJNA123485
gaps array · 1 item
[0]
data:accession_absent
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
2026-11-01T18:37:40Z
independence
single_reader
evidence_check object · 2 fields
method
null
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
8355
completion_tokens
2022
cached_tokens
264
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:37094819
type
paper
label
pmid:37094819
[1] object · 3 fields
id
source:pmid:37094819
type
manuscript
label
PMID 37094819 full text
[2] object · 3 fields
id
data:geo:PRJNA123485
type
dataset
label
GEO PRJNA123485
activities array · 3 items
[0] object · 4 fields
id
activity-reading-sci-2026-11-01
type
classification
used array · 3 items
[0] object · 3 fields
id
pmid:37094819
type
paper
label
pmid:37094819
[1] object · 3 fields
id
source:pmid:37094819
type
manuscript
label
PMID 37094819 full text
[2] object · 3 fields
id
data:geo:PRJNA123485
type
dataset
label
GEO PRJNA123485
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-37094819
type
extraction
used array · 1 item
[0]
source:pmid:37094819
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-PRJNA123485
type
accession_resolution
used array · 1 item
[0]
data:geo:PRJNA123485
agent
agent:corpus-assay-engine
agents array · 2 items
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
[1] object · 3 fields
id
agent:minimax-reader
type
software
label
MiniMax literature reader
source_run_id
reading-sci-2026-11-01
dsl_catalogue_fingerprint
343fb30756ba6ec3
capability_table_fingerprint
2cb3e42f047d2ecf
snapshot_id
ba34b49490d9bfaf
lineage object · 4 fields
parent_id
pmid:37094819
parent_hash
sha256:d0e82a861ca38637284e39fe3e34a283143e01ab9071f758ceea7bdf086a3ca2
fork_of
null
gaps array · 13 items
[0]
asset:data:geo:PRJNA123485 licence not read
[1]
asset:data:geo:PRJNA123485 not downloaded
[2]
asset:data:geo:PRJNA398116 licence not read
[3]
asset:data:geo:PRJNA398116 not downloaded
[4]
asset:data:geo:PRJNA447866 licence not read
[5]
asset:data:geo:PRJNA447866 not downloaded
[6]
asset:data:geo:PRJNA624174 licence not read
[7]
asset:data:geo:PRJNA624174 not downloaded
[8]
execution.not_run
[9]
review.human_critique
[10]
review.independent_reader
[11]
review.machine_critique
[12]
step:obtain_source_data blocked on data:accession_unresolved
assays array · 3 items
[0] object · 11 fields
role
data_generation
definition_id
transfection
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 4 items
[0]
smalldisco, a pipeline for siRNA discovery and 3' tail identification.
[1]
Fig. 1. smalldisco can be run in two modes: sirna and tail. Overview of the smalldisco pipelin
[2]
iew of the smalldisco pipeline outlining the siRNA discovery and annotation workflows. Two anal
[3]
workflows. Two analysis modes are available: sirna and tail. “Genomic feature” refers to a user
order_basis
paper_text_order:0
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
rna_seq
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.93
evidence array · 1 item
[0]
ring RNA discovery and annotation from small RNA-seq datasets. smalldisco can distinguish short r
order_basis
paper_text_order:301
id
assay:2
[2] object · 11 fields
role
analysis
definition_id
sequence_alignment
definition_version
f2132e96ae6c7a4e
required_operations array · 2 items
[0]
sequence_align
[1]
alignment_identity
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
HISAT2
order_basis
consumes_earlier_output
id
assay:3
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37094819", "kind": "science-record", "revision": 3, "content_hash": "sha256:ada0332e855b282cffba5743942ba7a92caa3fc09e6c9096700ec24b64e4d5bf", "created_at": "2026-11-01T19:01:46Z", "updated_at": "2026-11-01T22:09:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "smalldisco, a pipeline for siRNA discovery and 3' tail identification.", "doi": "10.1093/g3journal/jkad092", "pmid": "37094819", "authors": ["Ian V Caldas", "Leanne H Kelley", "Yasir H Ahmed-Braimah", "Eleanor M Maine"], "journal": "G3 (Bethesda, Md.)", "year": 2023, "abstract": "Capturing and sequencing small RNAs is standard practice; however, identification of a group of these small RNAs-small interfering RNAs (siRNAs)-has been more difficult. We present smalldisco, a command-line tool for small interfering RNA discovery and annotation from small RNA-seq datasets. smalldisco can distinguish short reads that map antisense to an annotated genomic feature (e.g. exons or mRNAs), annotate these siRNAs, and quantify their abundance. smalldisco also uses the program Tailor to quantify 3' nontemplated nucleotides of siRNAs or any small RNA species. smalldisco and supporting documentation are available for download from GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621).", "claims": [{"id": "claim-data-access", "statement": "smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621).\nSupplemental material available at G3 online.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37094819", "locator": "sections[7] \"Data availability\" paragraphs 1-3", "quote": "smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621).\nSupplemental material available at G3 online."}], "state": "complete"}, {"id": "claim-target-result", "statement": "First, smalldisco analyzed our sample input dataset in ∼2.5 hours, whereas segmentSeq required ∼2.5 weeks.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37094819", "locator": "sections[3] \"Results and discussion\" paragraph 6", "quote": "First, smalldisco analyzed our sample input dataset in ∼2.5 hours, whereas segmentSeq required ∼2.5 weeks."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "First, smalldisco analyzed our sample input dataset in ∼2.5 hours, whereas segmentSeq required ∼2.5 weeks.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:37094819"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_unresolved", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PRJNA123485"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PRJNA123485"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_unresolved"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37094819", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1093/g3journal/jkad092", "sha256": "sha256:62abec4cf5466de12e6ed08af43382349a01fa80fd39dfc968113fb8d9bbdc5c", "bytes": 24958, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1093/g3journal/jkad092", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10234390", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PRJNA123485", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PRJNA123485", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA123485", "version": null, "note": "smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621).\nSupplemental material available at G3 online.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621).\nSupplemental material available at G3 online.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T18:46:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PRJNA398116", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PRJNA398116", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA398116", "version": null, "note": "smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621).\nSupplemental material available at G3 online.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621).\nSupplemental material available at G3 online.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T18:46:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PRJNA447866", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PRJNA447866", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA447866", "version": null, "note": "smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621).\nSupplemental material available at G3 online.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621).\nSupplemental material available at G3 online.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T18:46:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PRJNA624174", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PRJNA624174", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA624174", "version": null, "note": "smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621).\nSupplemental material available at G3 online.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621).\nSupplemental material available at G3 online.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T18:46:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PRJNA123485 not downloaded", "asset:data:geo:PRJNA123485 licence not read", "asset:data:geo:PRJNA398116 not downloaded", "asset:data:geo:PRJNA398116 licence not read", "asset:data:geo:PRJNA447866 not downloaded", "asset:data:geo:PRJNA447866 licence not read", "asset:data:geo:PRJNA624174 not downloaded", "asset:data:geo:PRJNA624174 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "sequence_alignment", "specific": "read_mapping", "label": "Sequence alignment / homology", "dsl_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["sequence_records"], "evidence": {"score": 0.8, "band": "high", "quote": "HISAT2"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: read_mapping."}, "capability": {"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": {"tier": "R4", "reachable": false, "accessions": ["PRJNA447866", "PRJNA123485", "PRJNA624174", "PRJNA398116"], "resolved_accessions": [], "statements": ["smalldisco and supporting documentation are available on GitHub (https://github.com/ianvcaldas/smalldisco) and archived in Zenodo (https://doi.org/10.5281/zenodo.7799621).\nSupplemental material available at G3 online."], "basis": "The paper names PRJNA447866, PRJNA123485, PRJNA624174, PRJNA398116, but the accession does not resolve in the repository (not_in_ncbi_bioproject, not_in_ncbi_bioproject, not_in_ncbi_bioproject, not_in_ncbi_bioproject), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["sequence_align", "alignment_identity"], "assets": ["source:pmid:37094819", "data:geo:PRJNA123485"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PRJNA123485"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:37:40Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 8355, "completion_tokens": 2022, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:37094819", "type": "paper", "label": "pmid:37094819"}, {"id": "source:pmid:37094819", "type": "manuscript", "label": "PMID 37094819 full text"}, {"id": "data:geo:PRJNA123485", "type": "dataset", "label": "GEO PRJNA123485"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37094819", "type": "paper", "label": "pmid:37094819"}, {"id": "source:pmid:37094819", "type": "manuscript", "label": "PMID 37094819 full text"}, {"id": "data:geo:PRJNA123485", "type": "dataset", "label": "GEO PRJNA123485"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37094819", "type": "extraction", "used": ["source:pmid:37094819"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PRJNA123485", "type": "accession_resolution", "used": ["data:geo:PRJNA123485"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:37094819", "parent_hash": "sha256:d0e82a861ca38637284e39fe3e34a283143e01ab9071f758ceea7bdf086a3ca2", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:PRJNA123485 licence not read", "asset:data:geo:PRJNA123485 not downloaded", "asset:data:geo:PRJNA398116 licence not read", "asset:data:geo:PRJNA398116 not downloaded", "asset:data:geo:PRJNA447866 licence not read", "asset:data:geo:PRJNA447866 not downloaded", "asset:data:geo:PRJNA624174 licence not read", "asset:data:geo:PRJNA624174 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_unresolved"], "assays": [{"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["smalldisco, a pipeline for siRNA discovery and 3' tail identification.", "Fig. 1. smalldisco can be run in two modes: sirna and tail. Overview of the smalldisco pipelin", "iew of the smalldisco pipeline outlining the siRNA discovery and annotation workflows. Two anal", "workflows. Two analysis modes are available: sirna and tail. “Genomic feature” refers to a user"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ring RNA discovery and annotation from small RNA-seq datasets. smalldisco can distinguish short r"], "order_basis": "paper_text_order:301", "id": "assay:2"}, {"role": "analysis", "definition_id": "sequence_alignment", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["sequence_align", "alignment_identity"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["HISAT2"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}