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

pmid:35858951

Proteins, possibly human, found in World War II concentration camp artifact.

Heyi Yang · Erin Butler · Samantha A Monier · Donald Siegel

Scientific reports · 2022 doi:10.1038/s41598-022-16192-5

Paper

complete

Experiment

partial

Data

partial

Analysis

partial

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:35858951
kind
science-record
content_hash
sha256:8216196ffe103ee393c071cd0af47ca5f5e85d1c18840aa088b0594378a61156
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T18:14:56Z
updated_at
2026-11-01T21:28:26Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Proteins, possibly human, found in World War II concentration camp artifact.
doi
10.1038/s41598-022-16192-5
pmid
35858951
authors array · 4 items
[0]
Heyi Yang
[1]
Erin Butler
[2]
Samantha A Monier
[3]
Donald Siegel
journal
Scientific reports
year
2022
abstract
Museums displaying artifacts of the human struggle against oppression are often caught in their own internal struggle between presenting factual and unbiased descriptions of their collections, or relying on testament of survivors. Often this quandary is resolved in favor of what can be verified, not what is remembered. However, with improving instrumentation, methods and informatic approaches, science can help uncover evidence able to reconcile memory and facts. Following World War II, thousands of small, cement-like disks with numbers impressed on one side were found at concentration camps throughout Europe. Survivors claimed these disks were made of human cremains; museums erred on the side of caution-without documentation of the claims, was it justifiable to present them as fact? The ability to detect species relevant biological material in these disks could help resolve this question. Proteomic mass spectrometry of five disks revealed all contained proteins, including collagens and hemoglobins, suggesting they were made, at least in part, of animal remains. A new protein/informatics approach to species identification showed that while human was not always identified as the top contributor, human was the most likely explanation for one disk. To our knowledge, this is the first demonstration of protein recovery from cremains. Data are available via ProteomeXchange with identifier PXD035267.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
For species identification of the disks, the spectra species-assignment method3 was used.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:35858951
locator
sections[2] "Proteins in species identification" paragraph 2
quote
For species identification of the disks, the spectra species-assignment method3 was used.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE42 partner repository with the dataset identifier PXD035267 and 10.6019/PXD035267.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:35858951
locator
sections[17] "Data availability" paragraph 2
quote
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE42 partner repository with the dataset identifier PXD035267 and 10.6019/PXD035267.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
partial
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:35858951
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_absent
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 · 0 items
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 · 0 items
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_absent
data object · 3 fields
state
partial
assets array · 1 item
[0] object · 15 fields
id
source:pmid:35858951
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1038/s41598-022-16192-5
sha256
sha256:e0390914cb5813337205e394d30007cfe2a098cf68c397700600dadd45cd75f3
bytes
41426
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1038/s41598-022-16192-5
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
PMC9300652
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
gaps array · 0 items
analysis object · 4 fields
state
partial
methods array · 1 item
[0] object · 10 fields
id
method-1
family
null
specific
null
label
spectra species-assignment method
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
evidence object · 3 fields
score
1
band
verbatim
quote
For species identification of the disks, the spectra species-assignment method3 was used.
targets array · 0 items
gaps array · 1 item
[0]
method.reader_named_unmapped
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
R4
expressible
false
required_operations array · 0 items
missing_operations array · 0 items
basis
The reader quoted the method the paper names (spectra species-assignment method), 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
R4
reachable
false
accessions array · 1 item
[0]
PXD035267 and 10.6019/PXD035267
resolved_accessions array · 0 items
statements array · 1 item
[0]
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE42 partner repository with the dataset identifier PXD035267 and 10.6019/PXD035267.
basis
The paper names PXD035267 and 10.6019/PXD035267, but the accession does not resolve in the repository (no reason recorded), 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 · 0 items
assets array · 1 item
[0]
source:pmid:35858951
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:None
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
2026-11-01T17:56:07Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
11839
completion_tokens
898
cached_tokens
128
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:35858951
type
paper
label
pmid:35858951
[1] object · 3 fields
id
source:pmid:35858951
type
manuscript
label
PMID 35858951 full text
[2] object · 3 fields
id
data:geo:None
type
dataset
label
GEO None
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:35858951
type
paper
label
pmid:35858951
[1] object · 3 fields
id
source:pmid:35858951
type
manuscript
label
PMID 35858951 full text
[2] object · 3 fields
id
data:geo:None
type
dataset
label
GEO None
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-35858951
type
extraction
used array · 1 item
[0]
source:pmid:35858951
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-None
type
accession_resolution
used array · 1 item
[0]
data:geo:None
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:35858951
parent_hash
sha256:e7835edaf9b0448909806635cc8cd426584f092b7a1a9610eb0897eab385952f
fork_of
null
gaps array · 6 items
[0]
execution.not_run
[1]
method.reader_named_unmapped
[2]
review.human_critique
[3]
review.independent_reader
[4]
review.machine_critique
[5]
step:obtain_source_data blocked on data:accession_absent
assays array · 1 item
[0] object · 11 fields
role
data_generation
definition_id
mass_spectrometry
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 3 items
[0]
could help resolve this question. Proteomic mass spectrometry of five disks revealed all contained protein
[1]
/MS grade (Fisher, Fairlawn NJ)Trypsin Gold, Mass Spectrometry Grade (Promega, Madison WI)Urea (Sigma, St.
[2]
hese disks could help resolve this question. Proteomic mass spectrometry of five disks revealed all
order_basis
paper_text_order:934
id
assay:1
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35858951", "kind": "science-record", "revision": 3, "content_hash": "sha256:8216196ffe103ee393c071cd0af47ca5f5e85d1c18840aa088b0594378a61156", "created_at": "2026-11-01T18:14:56Z", "updated_at": "2026-11-01T21:28:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteins, possibly human, found in World War II concentration camp artifact.", "doi": "10.1038/s41598-022-16192-5", "pmid": "35858951", "authors": ["Heyi Yang", "Erin Butler", "Samantha A Monier", "Donald Siegel"], "journal": "Scientific reports", "year": 2022, "abstract": "Museums displaying artifacts of the human struggle against oppression are often caught in their own internal struggle between presenting factual and unbiased descriptions of their collections, or relying on testament of survivors. Often this quandary is resolved in favor of what can be verified, not what is remembered. However, with improving instrumentation, methods and informatic approaches, science can help uncover evidence able to reconcile memory and facts. Following World War II, thousands of small, cement-like disks with numbers impressed on one side were found at concentration camps throughout Europe. Survivors claimed these disks were made of human cremains; museums erred on the side of caution-without documentation of the claims, was it justifiable to present them as fact? The ability to detect species relevant biological material in these disks could help resolve this question. Proteomic mass spectrometry of five disks revealed all contained proteins, including collagens and hemoglobins, suggesting they were made, at least in part, of animal remains. A new protein/informatics approach to species identification showed that while human was not always identified as the top contributor, human was the most likely explanation for one disk. To our knowledge, this is the first demonstration of protein recovery from cremains. Data are available via ProteomeXchange with identifier PXD035267.", "claims": [{"id": "claim-method", "statement": "For species identification of the disks, the spectra species-assignment method3 was used.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35858951", "locator": "sections[2] \"Proteins in species identification\" paragraph 2", "quote": "For species identification of the disks, the spectra species-assignment method3 was used."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE42 partner repository with the dataset identifier PXD035267 and 10.6019/PXD035267.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35858951", "locator": "sections[17] \"Data availability\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE42 partner repository with the dataset identifier PXD035267 and 10.6019/PXD035267."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "", "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:35858951"], "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_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35858951", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-022-16192-5", "sha256": "sha256:e0390914cb5813337205e394d30007cfe2a098cf68c397700600dadd45cd75f3", "bytes": 41426, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-022-16192-5", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9300652", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "spectra species-assignment method", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "For species identification of the disks, the spectra species-assignment method3 was used."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (spectra species-assignment method), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["PXD035267 and 10.6019/PXD035267"], "resolved_accessions": [], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE42 partner repository with the dataset identifier PXD035267 and 10.6019/PXD035267."], "basis": "The paper names PXD035267 and 10.6019/PXD035267, but the accession does not resolve in the repository (no reason recorded), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:35858951"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "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": "2026-11-01T17:56:07Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11839, "completion_tokens": 898, "cached_tokens": 128}}, "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:35858951", "type": "paper", "label": "pmid:35858951"}, {"id": "source:pmid:35858951", "type": "manuscript", "label": "PMID 35858951 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35858951", "type": "paper", "label": "pmid:35858951"}, {"id": "source:pmid:35858951", "type": "manuscript", "label": "PMID 35858951 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35858951", "type": "extraction", "used": ["source:pmid:35858951"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:35858951", "parent_hash": "sha256:e7835edaf9b0448909806635cc8cd426584f092b7a1a9610eb0897eab385952f", "fork_of": null, "generation": 2}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["could help resolve this question. Proteomic mass spectrometry of five disks revealed all contained protein", "/MS grade (Fisher, Fairlawn NJ)Trypsin Gold, Mass Spectrometry Grade (Promega, Madison WI)Urea (Sigma, St.", "hese disks could help resolve this question. Proteomic mass spectrometry of five disks revealed all"], "order_basis": "paper_text_order:934", "id": "assay:1"}]}