← All .science files
pmid:37999519
Structural Similarities, in Relation with the Cross-Reactivity, of Hymenoptera Allergenic Dipeptidyl Peptidases IV-An Overall Comparison Including a New Dipeptidyl Peptidase IV Sequence from Vespa velutina.
Rafael I Monsalve · Manuel Lombardero · Lars H Christensen · Beatriz Núñez-Acevedo · David González-de-Olano · Miriam Sobrino-García · Rosita M Castillo-Loja · Susana B Bravo · Manuela Alonso-Sampedro · Carmen Vidal
Toxins · 2023 doi:10.3390/toxins15110656
Paper
complete
Experiment
complete
Data
partial
Analysis
absent
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 · 10 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 · 0 items
data object · 3 fields
assets array · 2 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 0 items
gaps array · 2 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 · 0 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 0 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 · 8 items
assays array · 1 item
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37999519", "kind": "science-record", "revision": 2, "content_hash": "sha256:6fa6945bc2747a3f0d4e9a70dba4065ec467adf565a58eb3621a459f84bf5a10", "created_at": "2026-11-01T19:02:55Z", "updated_at": "2026-11-01T19:19:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Structural Similarities, in Relation with the Cross-Reactivity, of Hymenoptera Allergenic Dipeptidyl Peptidases IV-An Overall Comparison Including a New Dipeptidyl Peptidase IV Sequence from Vespa velutina.", "doi": "10.3390/toxins15110656", "pmid": "37999519", "authors": ["Rafael I Monsalve", "Manuel Lombardero", "Lars H Christensen", "Beatriz Núñez-Acevedo", "David González-de-Olano", "Miriam Sobrino-García", "Rosita M Castillo-Loja", "Susana B Bravo", "Manuela Alonso-Sampedro", "Carmen Vidal"], "journal": "Toxins", "year": 2023, "abstract": "(1) Background: Dipeptidyl Peptidases IV (DPPIVs), present in many organisms, are minor components in the venoms of Hymenoptera, where they have been identified as cross-reactive allergenic molecules. Considering that the structure of homologous DPPIVs is well characterized, we aimed to explain which regions have higher similarity among these proteins and present a comparison among them, including a new Vespa velutina DPPIV sequence. Moreover, two cases of sensitization to DPPIVs in wasp- and honeybee-sensitized patients are presented. (2) Methods: Proteomic analyses have been performed on the venom of the Asian hornet Vespa velutina to demonstrate the sequence of its DPPIV (allergen named Vesp v 3, with sequence accession number P0DRB8, and with the proteomic data available via ProteomeXchange with the identifier PXD046030). A comparison performed through their alignments and analysis of the three-dimensional structure showed a region with higher similarity among Hymenoptera DPPIVs. Additionally, ImmunoCAP™ determinations (including specific inhibition experiments), as well as IgE immunoblotting, are performed to demonstrate the allergenicity of Api m 5 and Ves v 3. (3) Results and Conclusions: The data presented demonstrate that the similarities among Hymenoptera DPPIVs are most likely localized at the C-terminal region of these enzymes. In addition, a higher similarity of the Vespa/Vespula DPPIVs is shown. The clinical cases analyzed demonstrated the allergenicity of Api m 5 and Ves v 3 in the sera of the allergic patients, as well as the presence of this minor component in the preparations used in venom immunotherapy.", "claims": [{"id": "claim-data-access", "statement": "The data presented in this work were made public by the authors by explicitly making public the new Vespa velutina sequence (UniProtKB database accession number P0DRB8), publishing the raw data in the Supplementary Material files and depositing the proteomic data generated into the PRIDE partner repository with the dataset identifier PXD046030.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37999519", "locator": "sections[22] \"Data Availability Statement\" paragraph 2", "quote": "The data presented in this work were made public by the authors by explicitly making public the new Vespa velutina sequence (UniProtKB database accession number P0DRB8), publishing the raw data in the Supplementary Material files and depositing the proteomic data generated into the PRIDE partner repository with the dataset identifier PXD046030."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The data presented demonstrate that the similarities among Hymenoptera DPPIVs are most likely localized at the C-terminal region of these enzymes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37999519", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data presented demonstrate that the similarities among Hymenoptera DPPIVs are most likely localized at the C-terminal region of these enzymes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The data presented demonstrate that the similarities among Hymenoptera DPPIVs are most likely localized at the C-terminal region of these enzymes.", "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:37999519"], "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": "complete", "blocked_on": null, "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:PXD046030"], "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:PXD046030"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37999519", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/toxins15110656", "sha256": "sha256:227ef9a39f67fd32ecf291249319c114c9ee231a56fe3818c797ae73acba9309", "bytes": 55362, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/toxins15110656", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10675595", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD046030", "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=PXD046030", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD046030", "version": null, "note": "The data presented in this work were made public by the authors by explicitly making public the new Vespa velutina sequence (UniProtKB database accession number P0DRB8), publishing the raw data in the Supplementary Material files and depositing the proteomic data generated into the PRIDE partner repository with the dataset identifier PXD046030.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data presented in this work were made public by the authors by explicitly making public the new Vespa velutina sequence (UniProtKB database accession number P0DRB8), publishing the raw data in the Supplementary Material files and depositing the proteomic data generated into the PRIDE partner repository with the dataset identifier PXD046030.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Structural Similarities on Hymenoptera Allergenic Dipeptidyl Peptidases IV (DPPIVs). Overall comparison also including a new DPPIV sequence from Vespa velutina.", "resolution_checked_at": "2026-11-01T19:09:50Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD046030 not downloaded", "asset:data:geo:PXD046030 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "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": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "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": {"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": "R1", "reachable": true, "accessions": ["PXD046030"], "resolved_accessions": ["PXD046030"], "statements": ["The data presented in this work were made public by the authors by explicitly making public the new Vespa velutina sequence (UniProtKB database accession number P0DRB8), publishing the raw data in the Supplementary Material files and depositing the proteomic data generated into the PRIDE partner repository with the dataset identifier PXD046030."], "basis": "The paper names PXD046030 in PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:37999519", "data:geo:PXD046030"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD046030"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:00:00Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 16552, "completion_tokens": 1418, "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:37999519", "type": "paper", "label": "pmid:37999519"}, {"id": "source:pmid:37999519", "type": "manuscript", "label": "PMID 37999519 full text"}, {"id": "data:geo:PXD046030", "type": "dataset", "label": "GEO PXD046030"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37999519", "type": "paper", "label": "pmid:37999519"}, {"id": "source:pmid:37999519", "type": "manuscript", "label": "PMID 37999519 full text"}, {"id": "data:geo:PXD046030", "type": "dataset", "label": "GEO PXD046030"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37999519", "type": "extraction", "used": ["source:pmid:37999519"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD046030", "type": "accession_resolution", "used": ["data:geo:PXD046030"], "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:37999519", "parent_hash": "sha256:9de6679379c71a54b4df896206ae5db95063257b441464396815d2a5ac770829", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:PXD046030 licence not read", "asset:data:geo:PXD046030 not downloaded", "execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ific inhibition experiments), as well as IgE immunoblotting, are performed to demonstrate the allergenic", "5 was clearly shown in the SDS-PAGE and IgE-immunoblot (Figure 6), being barely visible in the Apis", "ained bands around 17 kDa). SDS-PAGE and IgE immunoblotting of patients’ sera against Apis mellifera and", "and Vespula spp. extracts. SDS-PAGE and IgE immunoblotting show the results of testing for 15 µg of Api"], "order_basis": "paper_text_order:1261", "id": "assay:1"}]}