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

pmid:30846902

An online global database of Hemiptera-Phytoplasma-Plant biological interactions.

Valeria Trivellone

Biodiversity data journal · 2019 doi:10.3897/BDJ.7.e32910

Paper

complete

Experiment

partial

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
id
pmid:30846902
kind
science-record
content_hash
sha256:d1bf671ab08bf78110e9da68d4a7e27c34e136465cd566fb382b84a1bdb72e0f
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:43Z
updated_at
2026-11-01T18:50:34Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
An online global database of Hemiptera-Phytoplasma-Plant biological interactions.
doi
10.3897/BDJ.7.e32910
pmid
30846902
authors array · 1 item
[0]
Valeria Trivellone
journal
Biodiversity data journal
year
2019
abstract
BACKGROUND: Phytoplasmas are phloem-limited plant pathogenic bacteria in the class Mollicutes transmitted by sap-feeding insect vectors of the Order Hemiptera. Vectors still have not yet been identified for about half of the 33 known phytoplasma groups and this has greatly hindered efforts to control the spread of diseases affecting important crops. Extensive gaps of knowledge on actual phytoplasma vectors and on the plant disease epidemiology prevent our understanding of the basic underlying biological mechanisms that facilitate interactions between insects, phytoplasmas and their host plants. NEW INFORMATION: This paper presents a complete online database of Hemiptera-Phytoplasma-Plant (HPP) biological interactions worldwide, searchable via an online interface. The raw data are available through Zenodo at https://doi.org/10.5281/zenodo.2532738. The online database search interface was created using the 3I software (Dmitriev 2006) which enhances data usability by providing a customised web interface (http://trivellone.speciesfile.org/) that provides an overview of the recorded biological interactions and ability to discover particular interactions by searching for one or more phytoplasma, insect or plant taxa. The database will facilitate synthesis of all available and relevant data on the observed associations between phytoplasmas and their insect and plant hosts and will provide useful data to generate and test ecological and evolutionary hypotheses.
claims array · 1 item
[0] object · 6 fields
id
claim-data-access
statement
The raw data are available through Zenodo at https://doi.org/10.5281/zenodo.2532738.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:30846902
locator
sections[0] "Abstract" paragraph 2
quote
The raw data are available through Zenodo at https://doi.org/10.5281/zenodo.2532738.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
partial
objective
null
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:30846902
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 · 5 items
[0] object · 15 fields
id
source:pmid:30846902
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.3897/BDJ.7.e32910
sha256
sha256:87b000843b6989616e826ab57a1c3fd043fa306765a95393b6e281c5316e136c
bytes
16817
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.3897/BDJ.7.e32910
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
PMC6400871
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 16 fields
id
asset:table:pmid:30846902:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:8e7d40de26558000f8518f84f68cdcdfdb1424f1ed29855aab8724e0602d9782
bytes
1010
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[28]/table-wrap[1]#DS1
version
null
note
Data set 1.
structure object · 5 fields
pmcid
PMC6400871
section_index
8
section_title
Description
row_count
9
column_count
2
table object · 8 fields
label
Data set 1.
caption
null
rows array · 9 items
[0] array · 2 items
[0]
Column label
[1]
Column description
[1] array · 2 items
[0]
record_id
[1]
record identifier
[2] array · 2 items
[0]
phytoplasma
[1]
Phytoplasma 16Sr groups and subgroups detected in the insect or plant host. The "not detected" entry means that phytoplasma was not detected in the host analysed and the "not characterised" entry means that it was not defined the 16Sr group for the detected phytoplasma as reported in the reference source
[3] array · 2 items
[0]
host_group
[1]
The group (insect or plant) to which the host belongs
[4] array · 2 items
[0]
host_family
[1]
Family name of the insect or plant host
[5] array · 2 items
[0]
host_species
[1]
Species name of the insect or plant host
[6] array · 2 items
[0]
country
[1]
Country where the biological association was detected or searched as reported in the reference source
[7] array · 2 items
[0]
reference_id
[1]
Short reference identifier for the biological interaction
[8] array · 2 items
[0]
full_reference
[1]
Full reference source for the biological interaction
locator
section[28]/table-wrap[1]#DS1
[2] object · 16 fields
id
asset:table:pmid:30846902:2
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:8e7d40de26558000f8518f84f68cdcdfdb1424f1ed29855aab8724e0602d9782
bytes
1010
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[28]/table-wrap[1]#DS1
version
null
note
Data set 1.
structure object · 5 fields
pmcid
PMC6400871
section_index
10
section_title
Description
row_count
9
column_count
2
table object · 8 fields
label
Data set 1.
caption
null
rows array · 9 items
[0] array · 2 items
[0]
Column label
[1]
Column description
[1] array · 2 items
[0]
record_id
[1]
record identifier
[2] array · 2 items
[0]
phytoplasma
[1]
Phytoplasma 16Sr groups and subgroups detected in the insect or plant host. The "not detected" entry means that phytoplasma was not detected in the host analysed and the "not characterised" entry means that it was not defined the 16Sr group for the detected phytoplasma as reported in the reference source
[3] array · 2 items
[0]
host_group
[1]
The group (insect or plant) to which the host belongs
[4] array · 2 items
[0]
host_family
[1]
Family name of the insect or plant host
[5] array · 2 items
[0]
host_species
[1]
Species name of the insect or plant host
[6] array · 2 items
[0]
country
[1]
Country where the biological association was detected or searched as reported in the reference source
[7] array · 2 items
[0]
reference_id
[1]
Short reference identifier for the biological interaction
[8] array · 2 items
[0]
full_reference
[1]
Full reference source for the biological interaction
locator
section[28]/table-wrap[1]#DS1
[3] object · 16 fields
id
asset:table:pmid:30846902:3
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:482eddd1691eb58de92e743e50cc7b670b5ae03420cac2ec8e41df014f07ffce
bytes
295
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[11]/table-wrap[1]#taxonomic_coverage
version
null
note
null
structure object · 5 fields
pmcid
PMC6400871
section_index
11
section_title
Taxa included
row_count
4
column_count
3
table object · 8 fields
label
null
caption
null
rows array · 4 items
[0] array · 3 items
[0]
Rank
[1]
Scientific Name
[2]
[1] array · 3 items
[0]
order
[1]
Hemiptera
[2]
[2] array · 3 items
[0]
phylum
[1]
Tracheophyta
[2]
Vascular plant
[3] array · 3 items
[0]
class
[1]
Mollicutes
[2]
Phytoplasma
locator
section[11]/table-wrap[1]#taxonomic_coverage
[4] object · 16 fields
id
asset:table:pmid:30846902:4
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:8e7d40de26558000f8518f84f68cdcdfdb1424f1ed29855aab8724e0602d9782
bytes
1010
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[28]/table-wrap[1]#DS1
version
null
note
Data set 1.
structure object · 5 fields
pmcid
PMC6400871
section_index
28
section_title
Description
row_count
9
column_count
2
table object · 8 fields
label
Data set 1.
caption
null
rows array · 9 items
[0] array · 2 items
[0]
Column label
[1]
Column description
[1] array · 2 items
[0]
record_id
[1]
record identifier
[2] array · 2 items
[0]
phytoplasma
[1]
Phytoplasma 16Sr groups and subgroups detected in the insect or plant host. The "not detected" entry means that phytoplasma was not detected in the host analysed and the "not characterised" entry means that it was not defined the 16Sr group for the detected phytoplasma as reported in the reference source
[3] array · 2 items
[0]
host_group
[1]
The group (insect or plant) to which the host belongs
[4] array · 2 items
[0]
host_family
[1]
Family name of the insect or plant host
[5] array · 2 items
[0]
host_species
[1]
Species name of the insect or plant host
[6] array · 2 items
[0]
country
[1]
Country where the biological association was detected or searched as reported in the reference source
[7] array · 2 items
[0]
reference_id
[1]
Short reference identifier for the biological interaction
[8] array · 2 items
[0]
full_reference
[1]
Full reference source for the biological interaction
locator
section[28]/table-wrap[1]#DS1
gaps array · 0 items
analysis object · 4 fields
state
absent
methods array · 0 items
targets array · 0 items
gaps array · 2 items
[0]
method
[1]
operations
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
blocked
tier
R4
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 (not named), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
basis
The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.
data object · 6 fields
tier
R4
reachable
false
accessions array · 0 items
resolved_accessions array · 0 items
statements array · 1 item
[0]
The raw data are available through Zenodo at https://doi.org/10.5281/zenodo.2532738.
basis
The paper names no accession to its source data, so the data has to come from the authors.
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 5 items
[0]
source:pmid:30846902
[1]
asset:table:pmid:30846902:1
[2]
asset:table:pmid:30846902:2
[3]
asset:table:pmid:30846902:3
[4]
asset:table:pmid:30846902:4
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
2026-10-31T18:14:04Z
independence
single_reader
evidence_check object · 2 fields
method
null
availability
verbatim
calls
3
usage object · 3 fields
prompt_tokens
13071
completion_tokens
1017
cached_tokens
649
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:30846902
type
paper
label
pmid:30846902
[1] object · 3 fields
id
source:pmid:30846902
type
manuscript
label
PMID 30846902 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:30846902
type
paper
label
pmid:30846902
[1] object · 3 fields
id
source:pmid:30846902
type
manuscript
label
PMID 30846902 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-30846902
type
extraction
used array · 1 item
[0]
source:pmid:30846902
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:30846902
parent_hash
sha256:e6e814e1138b56d32f53564c0240f24a781ed6d4825d26aa0d8cbe5a72c1599d
fork_of
null
gaps array · 7 items
[0]
execution.not_run
[1]
method
[2]
operations
[3]
review.human_critique
[4]
review.independent_reader
[5]
review.machine_critique
[6]
step:obtain_source_data blocked on data:accession_absent
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30846902", "kind": "science-record", "revision": 3, "content_hash": "sha256:d1bf671ab08bf78110e9da68d4a7e27c34e136465cd566fb382b84a1bdb72e0f", "created_at": "2026-11-01T15:40:43Z", "updated_at": "2026-11-01T18:50:34Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "An online global database of Hemiptera-Phytoplasma-Plant biological interactions.", "doi": "10.3897/BDJ.7.e32910", "pmid": "30846902", "authors": ["Valeria Trivellone"], "journal": "Biodiversity data journal", "year": 2019, "abstract": "BACKGROUND: Phytoplasmas are phloem-limited plant pathogenic bacteria in the class Mollicutes transmitted by sap-feeding insect vectors of the Order Hemiptera. Vectors still have not yet been identified for about half of the 33 known phytoplasma groups and this has greatly hindered efforts to control the spread of diseases affecting important crops. Extensive gaps of knowledge on actual phytoplasma vectors and on the plant disease epidemiology prevent our understanding of the basic underlying biological mechanisms that facilitate interactions between insects, phytoplasmas and their host plants.\nNEW INFORMATION: This paper presents a complete online database of Hemiptera-Phytoplasma-Plant (HPP) biological interactions worldwide, searchable via an online interface. The raw data are available through Zenodo at https://doi.org/10.5281/zenodo.2532738. The online database search interface was created using the 3I software (Dmitriev 2006) which enhances data usability by providing a customised web interface (http://trivellone.speciesfile.org/) that provides an overview of the recorded biological interactions and ability to discover particular interactions by searching for one or more phytoplasma, insect or plant taxa. The database will facilitate synthesis of all available and relevant data on the observed associations between phytoplasmas and their insect and plant hosts and will provide useful data to generate and test ecological and evolutionary hypotheses.", "claims": [{"id": "claim-data-access", "statement": "The raw data are available through Zenodo at https://doi.org/10.5281/zenodo.2532738.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30846902", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The raw data are available through Zenodo at https://doi.org/10.5281/zenodo.2532738."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "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:30846902"], "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:30846902", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3897/BDJ.7.e32910", "sha256": "sha256:87b000843b6989616e826ab57a1c3fd043fa306765a95393b6e281c5316e136c", "bytes": 16817, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3897/BDJ.7.e32910", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6400871", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:30846902:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8e7d40de26558000f8518f84f68cdcdfdb1424f1ed29855aab8724e0602d9782", "bytes": 1010, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[28]/table-wrap[1]#DS1", "version": null, "note": "Data set 1.", "structure": {"pmcid": "PMC6400871", "section_index": 8, "section_title": "Description", "row_count": 9, "column_count": 2}, "table": {"label": "Data set 1.", "caption": null, "rows": [["Column label", "Column description"], ["record_id", "record identifier"], ["phytoplasma", "Phytoplasma 16Sr groups and subgroups detected in the insect or plant host. The \"not detected\" entry means that phytoplasma was not detected in the host analysed and the \"not characterised\" entry means that it was not defined the 16Sr group for the detected phytoplasma as reported in the reference source"], ["host_group", "The group (insect or plant) to which the host belongs"], ["host_family", "Family name of the insect or plant host"], ["host_species", "Species name of the insect or plant host"], ["country", "Country where the biological association was detected or searched as reported in the reference source"], ["reference_id", "Short reference identifier for the biological interaction"], ["full_reference", "Full reference source for the biological interaction"]], "row_count": 9, "column_count": 2, "numeric_cells": 1, "header_rows": 1, "locator": "section[28]/table-wrap[1]#DS1"}}, {"id": "asset:table:pmid:30846902:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8e7d40de26558000f8518f84f68cdcdfdb1424f1ed29855aab8724e0602d9782", "bytes": 1010, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[28]/table-wrap[1]#DS1", "version": null, "note": "Data set 1.", "structure": {"pmcid": "PMC6400871", "section_index": 10, "section_title": "Description", "row_count": 9, "column_count": 2}, "table": {"label": "Data set 1.", "caption": null, "rows": [["Column label", "Column description"], ["record_id", "record identifier"], ["phytoplasma", "Phytoplasma 16Sr groups and subgroups detected in the insect or plant host. The \"not detected\" entry means that phytoplasma was not detected in the host analysed and the \"not characterised\" entry means that it was not defined the 16Sr group for the detected phytoplasma as reported in the reference source"], ["host_group", "The group (insect or plant) to which the host belongs"], ["host_family", "Family name of the insect or plant host"], ["host_species", "Species name of the insect or plant host"], ["country", "Country where the biological association was detected or searched as reported in the reference source"], ["reference_id", "Short reference identifier for the biological interaction"], ["full_reference", "Full reference source for the biological interaction"]], "row_count": 9, "column_count": 2, "numeric_cells": 1, "header_rows": 1, "locator": "section[28]/table-wrap[1]#DS1"}}, {"id": "asset:table:pmid:30846902:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:482eddd1691eb58de92e743e50cc7b670b5ae03420cac2ec8e41df014f07ffce", "bytes": 295, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#taxonomic_coverage", "version": null, "note": null, "structure": {"pmcid": "PMC6400871", "section_index": 11, "section_title": "Taxa included", "row_count": 4, "column_count": 3}, "table": {"label": null, "caption": null, "rows": [["Rank", "Scientific Name", ""], ["order", "Hemiptera", ""], ["phylum", "Tracheophyta", "Vascular plant"], ["class", "Mollicutes", "Phytoplasma"]], "row_count": 4, "column_count": 3, "numeric_cells": 0, "header_rows": 1, "locator": "section[11]/table-wrap[1]#taxonomic_coverage"}}, {"id": "asset:table:pmid:30846902:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8e7d40de26558000f8518f84f68cdcdfdb1424f1ed29855aab8724e0602d9782", "bytes": 1010, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[28]/table-wrap[1]#DS1", "version": null, "note": "Data set 1.", "structure": {"pmcid": "PMC6400871", "section_index": 28, "section_title": "Description", "row_count": 9, "column_count": 2}, "table": {"label": "Data set 1.", "caption": null, "rows": [["Column label", "Column description"], ["record_id", "record identifier"], ["phytoplasma", "Phytoplasma 16Sr groups and subgroups detected in the insect or plant host. The \"not detected\" entry means that phytoplasma was not detected in the host analysed and the \"not characterised\" entry means that it was not defined the 16Sr group for the detected phytoplasma as reported in the reference source"], ["host_group", "The group (insect or plant) to which the host belongs"], ["host_family", "Family name of the insect or plant host"], ["host_species", "Species name of the insect or plant host"], ["country", "Country where the biological association was detected or searched as reported in the reference source"], ["reference_id", "Short reference identifier for the biological interaction"], ["full_reference", "Full reference source for the biological interaction"]], "row_count": 9, "column_count": 2, "numeric_cells": 1, "header_rows": 1, "locator": "section[28]/table-wrap[1]#DS1"}}], "gaps": []}, "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": "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 (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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["The raw data are available through Zenodo at https://doi.org/10.5281/zenodo.2532738."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:30846902", "asset:table:pmid:30846902:1", "asset:table:pmid:30846902:2", "asset:table:pmid:30846902:3", "asset:table:pmid:30846902:4"], "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": "2026-10-31T18:14:04Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 13071, "completion_tokens": 1017, "cached_tokens": 649}}, "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:30846902", "type": "paper", "label": "pmid:30846902"}, {"id": "source:pmid:30846902", "type": "manuscript", "label": "PMID 30846902 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30846902", "type": "paper", "label": "pmid:30846902"}, {"id": "source:pmid:30846902", "type": "manuscript", "label": "PMID 30846902 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30846902", "type": "extraction", "used": ["source:pmid:30846902"], "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:30846902", "parent_hash": "sha256:e6e814e1138b56d32f53564c0240f24a781ed6d4825d26aa0d8cbe5a72c1599d", "fork_of": null, "generation": 2}, "gaps": ["execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"]}