Replies: 3 comments
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speaking with alejandro: What we want to extract from analyses (after coordinate parsing):
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propose analysis extraction schema Coordinate-Reporting Analysis Extraction SchemaStandalone schema for extracting coordinate-reporting neuroimaging results from paper text, prompt-appended analyses.jsonl rows, and optional source-table context. One entry corresponds to one coordinate-generating reported effect or statistical map. In this JSON schema, use null where the human-readable rubric would otherwise use N/A or an applicable-but-not-reported placeholder. Schema ID: Root Object
Definition:
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| Field | Type | Required | Description |
|---|---|---|---|
lines |
array of integer | Yes | 1-based line numbers from the analyses.jsonl content provided in the prompt input. |
mapping |
string | Yes | Relationship between this extracted entry and the provided analyses.jsonl row(s). |
Definition: jsonlRefSkipped
| Field | Type | Required | Description |
|---|---|---|---|
lines |
array of integer | Yes | 1-based line numbers from the analyses.jsonl content provided in the prompt input. |
mapping |
string | Yes | This analyses.jsonl row is being skipped because it is not a usable inferential coordinate-reporting entry. |
Definition: stringOrNull
Nullable string field.
Type: string or null
Definition: stringArrayOrNull
Type: array of string or null
Definition: sampleSizes
Type: object or null
Definition: coordinate
| Field | Type | Required | Description |
|---|---|---|---|
x |
number | Yes | |
y |
number | Yes | |
z |
number | Yes | |
label |
string or null | No | Optional short label if needed to disambiguate a coordinate or explain why the coordinate is included. |
Definition: inferenceScheme
| Field | Type | Required | Description |
|---|---|---|---|
primary_threshold |
string or null (stringOrNull) |
Yes | Primary or test-forming threshold. Use null if there is no meaningful primary threshold. |
correction_method |
string or null (stringOrNull) |
Yes | Actual significance logic should be recorded here, especially for threshold-free or non-cluster inference. |
extent_rule |
string or null (stringOrNull) |
Yes | Cluster or extent rule, or null if not used / not applicable. |
Definition: usedEntry
| Field | Type | Required | Description |
|---|---|---|---|
status |
string | Yes | This entry is an inferential coordinate-reporting result. |
jsonl_ref |
object (jsonlRefUsed) |
Yes | Structured reference to the analyses.jsonl row(s) that support this extracted used entry. |
label |
string | Yes | Human-readable name for the real analysis or reported effect. This does not need to match the parser's original row name. |
seed_region |
string or null (stringOrNull) |
Yes | Seed, anchor, or named component that defines the analysis focus. This may be an anatomical seed, atlas seed, network anchor, or ICA component name. Use null if the analysis is not anchored to a seed, ROI, or named component. |
search_space |
string | Yes | Controlled class describing where inference was allowed to occur. This should reflect the governing inferential domain, using the narrowest applicable search space. |
search_space_detail |
string or null (stringOrNull) |
Yes | Specific identity of the search space when the controlled class is too coarse by itself (for example, 'right BA4 iM1', 'ICA component: default mode network', or 'inclusive mask from one-sample hippocampal FC map'). |
software |
array of string or null | Yes | Software used to model the coordinate-generating analysis. Do not include preprocessing-only software unless it is also part of the modeling step. |
model_type |
string | Yes | Broad statistical family for the coordinate-generating result. Use the allowed values defined by the rubric's precedence rule. |
model_summary |
string | Yes | Concise description of the coordinate-generating result. It should identify the map type, search space, group structure, what was tested, and repeated-measures / within-subject / longitudinal structure if present. |
sample_sizes |
object or null | Yes | Subject counts for the actual coordinate-generating model. Use null if the paper does not report enough information for a reliable count. |
covariates |
array of string or null | Yes | Adjustment or nuisance terms included in the inferential model. List only covariates used in the reported model itself, not the main categorical contrast or continuous effect. |
conditions |
array of string | Yes | The groups, task states, or intervention stages entering the model. This lists the design cells or model inputs, not the tested direction of effect. |
contrast |
string or null (stringOrNull) |
Yes | The focal categorical comparison or direction of effect (for example, group comparison, task contrast, or condition contrast). Use this for tested categorical effects only, not for listing model inputs. Set null if not used, unresolved, or omnibus. (e.g., 'A > B') |
regression |
string or null (stringOrNull) |
Yes | The focal continuous predictor or association being tested (for example, age, symptom score, or behavior correlation), ideally including direction when known. Use this for tested continuous effects only, not for nuisance covariates. Set null if not used, unresolved, or omnibus. |
inference_scheme |
object (inferenceScheme) |
Yes | Structured summary of the inferential logic used to declare the reported coordinates significant. |
stereotaxic_space |
string or null (stringOrNull) |
Yes | Reporting space for the coordinates (for example, MNI or Talairach), not just the normalization target. |
smoothing |
string or null (stringOrNull) |
Yes | Reported smoothing kernel or method, usually in mm FWHM. |
coordinates |
array of object (coordinate) or null |
Yes | Use null for exact clean matches. Use an explicit list only when split/merged/complex. |
coordinate_representation |
string | Yes | How the inferential coordinates are represented in the paper (for example cluster peaks, subpeaks, node centers, or component peaks). |
notes |
string or null (stringOrNull) |
Yes | Free-text notes for parser errors, unresolved ambiguity, split/merge rationale, threshold mismatches, or other important caveats. |
Definition: skippedEntry
| Field | Type | Required | Description |
|---|---|---|---|
status |
string | Yes | This entry is not a usable inferential coordinate-reporting result. |
jsonl_ref |
object (jsonlRefSkipped) |
Yes | Structured reference to the analyses.jsonl row(s) being skipped. |
label |
string | Yes | Short description of what the skipped coordinates represent. |
coordinate_representation |
string | Yes | Type of non-inferential coordinate-like content represented by this skipped entry. |
stereotaxic_space |
string or null (stringOrNull) |
Yes | Reported coordinate space if obvious from the supplied input; otherwise null. |
skip_reason |
string | Yes | Explanation of why the supplied row should not be treated as an inferential coordinate-reporting analysis. |
notes |
string or null (stringOrNull) |
Yes | Optional clarifying context for the skipped entry. |
Definition: entry
Type: object (usedEntry) or object (skippedEntry)
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example output: example prompt: |
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Treating it like a graph
2 benchmarks:
https://arxiv.org/html/2602.14743v1
https://arxiv.org/html/2602.12247v1
more reading:
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