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10 changes: 5 additions & 5 deletions README.md
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Expand Up @@ -166,14 +166,14 @@ keeping, since an answer the vocabulary has no slot for is the evidence it is sh
`neuroimaging-paper-parse.yaml` and `neuroimaging-paper-parse/` hold the two artifacts the
ingestion workflow hands downstream, as contracts both sides validate against:

| Contract | Class | Producer | Consumers |
|---|---|---|---|
| C2 | `ParsedPaper`: the text every offset addresses, tables row by row, bibliography, `is_meta_analysis` | ns-pond-ingestion-workflow (extract, metadata, triage) | the workflow's coordinate stages, pondie, neurostore |
| C3 | `CoordinateParse`: points grouped into keyed analyses, with roles and sign splits | ns-pond-ingestion-workflow (analyses, resolve, space); pondie for a revision | pondie, neurostore |
| Class | Producer | Consumers |
|---|---|---|
| `ParsedPaper`: the text every offset addresses, tables row by row, bibliography, `is_meta_analysis` | ns-pond-ingestion-workflow (extract, metadata, triage) | the workflow's coordinate stages, pondie, neurostore |
| `CoordinateParse`: points grouped into keyed analyses, with roles and sign splits | ns-pond-ingestion-workflow (analyses, resolve, space); pondie for a revision | pondie, neurostore |

They live here rather than as a NIMADS extension because the extraction and storage
records point into them: evidence spans address `ParsedPaper.text_sha256`, and
`Analysis.source_table_analysis` names a C3 key. NIMADS stays the meta-analysis
`Analysis.source_table_analysis` names a `CoordinateParse` key. NIMADS stays the meta-analysis
interchange. A `ParsedPoint`'s `coordinates`, `space` and `values` carry NIMADS's names and
meaning, so projecting a parse onto a studyset is a field copy.

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4 changes: 2 additions & 2 deletions src/study_schema/linkml/neuroimaging-paper-parse.yaml
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Expand Up @@ -3,8 +3,8 @@ name: neuroimaging-paper-parse
title: Neuroimaging Paper Parse Schema
description: >-
The two artifacts the ingestion workflow hands downstream before any language model has
read the paper for its study design: the parsed paper (contract C2) and the coordinate
parse (contract C3). The extraction record (neuroimaging-study-extraction) and the
read the paper for its study design: the parsed paper (ParsedPaper) and the coordinate
parse (CoordinateParse). The extraction record (neuroimaging-study-extraction) and the
storage record (neuroimaging-study-storage) both point back into these artifacts --
evidence spans into the parsed paper's text, analyses into the coordinate parse's keys --
so the three schemas live in one repository and are versioned together.
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Expand Up @@ -2,7 +2,7 @@ id: https://neurostuff.org/schemas/neuroimaging-paper-parse/coordinates
name: neuroimaging-paper-parse-coordinates
title: Neuroimaging Paper Parse Coordinates Module
description: >-
Contract C3: a paper's reported coordinates, grouped into analyses, each analysis keyed
A coordinate parse (CoordinateParse): a paper's reported coordinates, grouped into analyses, each analysis keyed
by its name, space and points.
prefixes:
linkml: https://w3id.org/linkml/
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Expand Up @@ -2,7 +2,7 @@ id: https://neurostuff.org/schemas/neuroimaging-paper-parse/paper
name: neuroimaging-paper-parse-paper
title: Neuroimaging Paper Parse Paper Module
description: >-
Contract C2: a downloaded paper, parsed. Written once by the ingestion workflow; read by
A downloaded paper, parsed (ParsedPaper). Written once by the ingestion workflow; read by
its own coordinate stages and by pondie, neither of which writes it.
prefixes:
linkml: https://w3id.org/linkml/
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Expand Up @@ -20,9 +20,9 @@ enums:
description: Which of the two parse artifacts a header belongs to.
permissible_values:
parsed_paper:
description: Contract C2, a ParsedPaper.
description: A ParsedPaper.
coordinate_parse:
description: Contract C3, a CoordinateParse, original or revision.
description: A CoordinateParse, original or revision.

DocumentSource:
description: >-
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4 changes: 2 additions & 2 deletions src/study_schema/models/paper_parse.py
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Expand Up @@ -76,11 +76,11 @@ class ArtifactKind(str, Enum):
"""
parsed_paper = "parsed_paper"
"""
Contract C2, a ParsedPaper.
A ParsedPaper.
"""
coordinate_parse = "coordinate_parse"
"""
Contract C3, a CoordinateParse, original or revision.
A CoordinateParse, original or revision.
"""


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