← 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
paper object · 10 fields
authors array · 4 items
claims array · 2 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
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
data object · 3 fields
assets array · 5 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 0 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 0 items
[3] object · 15 fields
structure object · 15 fields
sample_accessions array · 0 items
[4] object · 15 fields
structure object · 15 fields
sample_accessions array · 0 items
gaps array · 8 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 2 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 2 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 4 items
resolved_accessions array · 0 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 2 items
assets array · 2 items
steps array · 1 item
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
gaps array · 1 item
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 13 items
assays array · 3 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[2] object · 11 fields
required_operations array · 2 items
source_hashes object · 1 field
evidence array · 1 item
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"}]}