From 7ca825bde0d5df843e398e210793c51edac463de Mon Sep 17 00:00:00 2001 From: Claude Date: Tue, 20 Oct 2026 20:46:12 -0500 Subject: [PATCH] Drop the C2/C3 contract labels; name ParsedPaper and CoordinateParse Description text only; models regenerated. Co-Authored-By: Claude Sonnet 5.5 --- README.md | 10 +++++----- src/study_schema/linkml/neuroimaging-paper-parse.yaml | 4 ++-- .../linkml/neuroimaging-paper-parse/coordinates.yaml | 2 +- .../linkml/neuroimaging-paper-parse/paper.yaml | 2 +- .../linkml/neuroimaging-paper-parse/parse_enums.yaml | 4 ++-- src/study_schema/models/paper_parse.py | 4 ++-- 6 files changed, 13 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index 9e52237..3fb883c 100644 --- a/README.md +++ b/README.md @@ -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. diff --git a/src/study_schema/linkml/neuroimaging-paper-parse.yaml b/src/study_schema/linkml/neuroimaging-paper-parse.yaml index f538d69..0187709 100644 --- a/src/study_schema/linkml/neuroimaging-paper-parse.yaml +++ b/src/study_schema/linkml/neuroimaging-paper-parse.yaml @@ -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. diff --git a/src/study_schema/linkml/neuroimaging-paper-parse/coordinates.yaml b/src/study_schema/linkml/neuroimaging-paper-parse/coordinates.yaml index bb0be1d..62a4078 100644 --- a/src/study_schema/linkml/neuroimaging-paper-parse/coordinates.yaml +++ b/src/study_schema/linkml/neuroimaging-paper-parse/coordinates.yaml @@ -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/ diff --git a/src/study_schema/linkml/neuroimaging-paper-parse/paper.yaml b/src/study_schema/linkml/neuroimaging-paper-parse/paper.yaml index b949f8c..c1b300f 100644 --- a/src/study_schema/linkml/neuroimaging-paper-parse/paper.yaml +++ b/src/study_schema/linkml/neuroimaging-paper-parse/paper.yaml @@ -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/ diff --git a/src/study_schema/linkml/neuroimaging-paper-parse/parse_enums.yaml b/src/study_schema/linkml/neuroimaging-paper-parse/parse_enums.yaml index db0dcc1..deb482d 100644 --- a/src/study_schema/linkml/neuroimaging-paper-parse/parse_enums.yaml +++ b/src/study_schema/linkml/neuroimaging-paper-parse/parse_enums.yaml @@ -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: >- diff --git a/src/study_schema/models/paper_parse.py b/src/study_schema/models/paper_parse.py index dad99f3..0a65b1d 100644 --- a/src/study_schema/models/paper_parse.py +++ b/src/study_schema/models/paper_parse.py @@ -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. """