v26_4

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DOCS.md

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+---
+title: "Binding Scores"
+description: "Schema reference for computed binding score tables"
+---
+
+These are the computed outputs of the data labeling pipeline.
+
+---
+
+## Binding Scores
+
+**File:** `binding-scores-YYYYMMDD.parquet`
+
+Aggregated binding scores per candidate and antigen pair. Replicate binding scores are averaged across replicates and pivoted so that each antigen concentration becomes its own column.
+
+**Grain:** one row per unique `(candidate_id, sino_catalog_id)`.
+
+### Fixed Columns
+
+| Column | Type | Description |
+| :--- | :--- | :--- |
+| `candidate_library_id` | `string` | Identifier of the candidate library consumed by this sample. |
+| `candidate_name` | `string` | Customer-provided sequence name. |
+| `candidate_id` | `string` | Blake-3 content digest of the reference sequence. |
+| `candidate_sequence` | `string` | The candidate amino acid sequence. |
+| `variant_id` | `string` | Blake-3 content digest of the variant sequence. |
+| `variant_sequence` | `string` | The variant sequence. |
+| `sino_catalog_id` | `string` | Sino catalog identifier for the antigen used in the binding assay. |
+| `antigen_gene_name` | `string` | Gene name of the antigen. |
+| `antigen_sequence` | `string` | Amino acid sequence of the antigen. |
+| `targeting` | `boolean` | Whether the candidate was designed to target this antigen. |
+| `is_expressed` | `boolean` | Whether the candidate is expressed in at least one sample. |
+
+### Dynamic Concentration Columns
+
+<Note>
+In addition to the fixed columns above, this table contains **dynamic columns** for each antigen concentration used in the experiment. The column names follow the pattern `binding_score_{conc}nM` and `binding_score_{conc}nM_std`.
+</Note>
+
+For our standard workflow, you will see these additional columns:
+
+| Column | Type | Description |
+| :--- | :--- | :--- |
+| `binding_score_5nM` | `float` | Mean log binding score at 5 nM. |
+| `binding_score_5nM_std` | `float` | Standard error of the log binding score at 5 nM. |
+| `binding_score_50nM` | `float` | Mean log binding score at 50 nM. |
+| `binding_score_50nM_std` | `float` | Standard error of the log binding score at 50 nM. |
+| `binding_score_500nM` | `float` | Mean log binding score at 500 nM. |
+| `binding_score_500nM_std` | `float` | Standard error of the log binding score at 500 nM. |
+
+---
+
+## Replicate Binding Scores
+
+**File:** `replicate-binding-scores-YYYYMMDD.parquet`
+
+Per-replicate binding scores unrolled across antigen concentrations. Each row represents a single candidate measured in a specific expression/binding sample pair at a specific antigen concentration. Use this table to inspect replicate-level variation and per-sample UMI counts.
+
+**Grain:** one row per `(candidate_id, binding_sample_id, antigen_concentration_nM)`.
+
+| Column | Type | Nullable | Description |
+| :--- | :--- | :--- | :--- |
+| `candidate_library_id` | `string` | no | Identifier of the candidate library consumed by this sample. |
+| `expression_sample_id` | `string` | no | Sample identifier for the expression (base) sample. |
+| `binding_sample_id` | `string` | no | Sample identifier for the binding (dose) sample. |
+| `candidate_name` | `string` | no | Customer-provided sequence name. |
+| `candidate_id` | `string` | no | Blake-3 content digest of the reference sequence. |
+| `candidate_sequence` | `string` | no | The candidate amino acid sequence. |
+| `variant_id` | `string` | no | Blake-3 content digest of the variant sequence. |
+| `variant_sequence` | `string` | no | The variant sequence. |
+| `sino_catalog_id` | `string` | no | Sino catalog identifier for the antigen. |
+| `antigen_gene_name` | `string` | no | Gene name of the antigen. |
+| `antigen_sequence` | `string` | no | Amino acid sequence of the antigen. |
+| `antigen_concentration_nM` | `float` | no | Antigen concentration in nanomolar. |
+| `targeting` | `boolean` | no | Whether the candidate was designed to target this antigen. |
+| `is_expressed` | `boolean` | no | Whether the candidate is expressed. |
+| `binding_score` | `float` | yes | Log binding score. Null when UMI count thresholds are not met. |
+| `expression_umi_count` | `integer` | yes | UMI count from the expression (base) sample. |
+| `binding_umi_count` | `integer` | yes | UMI count from the binding (dose) sample. |
+
+**Key relationships:**
+- `expression_sample_id` and `binding_sample_id` both correspond to `dim_samples.sample_id`.
+- `candidate_id` is the shared candidate key across all tables.
+- `variant_id` is the shared variant key across all tables.
+
+## Specificity Scores
+
+**File:** `specificity-scores-YYYYMMDD.parquet`
+
+Aggregated specificity scores per candidate and antigen pair. Replicate specificity scores are averaged across replicates and pivoted so that each antigen concentration becomes its own column.
+
+**Grain:** one row per unique `(candidate_id, sino_catalog_id)`.
+
+### Fixed Columns
+
+| Column | Type | Description |
+| :--- | :--- | :--- |
+| `candidate_library_id` | `string` | Identifier of the candidate library consumed by this sample. |
+| `candidate_name` | `string` | Customer-provided sequence name. |
+| `candidate_id` | `string` | Blake-3 content digest of the reference sequence. |
+| `candidate_sequence` | `string` | The candidate amino acid sequence. |
+| `variant_id` | `string` | Blake-3 content digest of the variant sequence. |
+| `variant_sequence` | `string` | The variant sequence. |
+| `sino_catalog_id` | `string` | Sino catalog identifier for the antigen used in the binding assay. |
+| `antigen_gene_name` | `string` | Gene name of the antigen. |
+| `antigen_sequence` | `string` | Amino acid sequence of the antigen. |
+| `is_expressed` | `boolean` | Whether the candidate is expressed in at least one sample. |
+
+### Dynamic Concentration Columns
+
+<Note>
+In addition to the fixed columns above, this table contains **dynamic columns** for each antigen concentration used in the experiment. The column names follow the pattern `log_specificity_score_{conc}nM` and `log_specificity_score_{conc}nM_std`.
+</Note>
+
+For our standard workflow, you will see these additional columns:
+
+| Column | Type | Description |
+| :--- | :--- | :--- |
+| `log_specificity_score_5nM` | `float` | Mean log specificity score at 5 nM. |
+| `log_specificity_score_5nM_std` | `float` | Standard error of the log specificity score at 5 nM. |
+| `log_specificity_score_50nM` | `float` | Mean log specificity score at 50 nM. |
+| `log_specificity_score_50nM_std` | `float` | Standard error of the log specificity score at 50 nM. |
+| `log_specificity_score_500nM` | `float` | Mean log specificity score at 500 nM. |
+| `log_specificity_score_500nM_std` | `float` | Standard error of the log specificity score at 500 nM. |
+
+---
+
+## Replicate Specificity Scores
+
+**File:** `replicate-specificity-scores-YYYYMMDD.parquet`
+
+Per-replicate specificity scores unrolled across antigen concentrations. Each row represents a single candidate measured in a specific expression/binding sample pair at a specific antigen concentration. Use this table to inspect replicate-level variation.
+
+**Grain:** one row per `(candidate_id, binding_sample_id, antigen_concentration_nM)`.
+
+| Column | Type | Nullable | Description |
+| :--- | :--- | :--- | :--- |
+| `candidate_library_id` | `string` | no | Identifier of the candidate library consumed by this sample. |
+| `expression_sample_id` | `string` | no | Sample identifier for the expression (base) sample. |
+| `binding_sample_id` | `string` | no | Sample identifier for the binding (dose) sample. |
+| `candidate_name` | `string` | no | Customer-provided sequence name. |
+| `candidate_id` | `string` | no | Blake-3 content digest of the reference sequence. |
+| `candidate_sequence` | `string` | no | The candidate amino acid sequence. |
+| `variant_id` | `string` | no | Blake-3 content digest of the variant sequence. |
+| `variant_sequence` | `string` | no | The variant sequence. |
+| `sino_catalog_id` | `string` | no | Sino catalog identifier for the antigen. |
+| `antigen_gene_name` | `string` | no | Gene name of the antigen. |
+| `antigen_sequence` | `string` | no | Amino acid sequence of the antigen. |
+| `antigen_concentration_nM` | `float` | no | Antigen concentration in nanomolar. |
+| `is_expressed` | `boolean` | no | Whether the candidate is expressed. |
+| `log_specificity_score` | `float` | yes | Log specificity score. Null when UMI count thresholds are not met. |
+
+**Key relationships:**
+- `expression_sample_id` and `binding_sample_id` both correspond to `dim_samples.sample_id`.
+- `candidate_id` is the shared candidate key across all tables.
+- `variant_id` is the shared variant key across all tables.
+
+## Expression Scores
+
+**File:** `expression-scores-YYYYMMDD.parquet`
+
+Aggregated expression scores per candidate. Expression scores are averaged across replicates.
+
+**Grain:** one row per unique `(candidate_id, variant_id)`.
+
+### Fixed Columns
+
+| Column | Type | Description |
+| :--- | :--- | :--- |
+| `candidate_library_id` | `string` | Identifier of the candidate library consumed by this sample. |
+| `candidate_name` | `string` | Customer-provided sequence name. |
+| `candidate_id` | `string` | Blake-3 content digest of the reference sequence. |
+| `candidate_sequence` | `string` | The candidate amino acid sequence. |
+| `variant_id` | `string` | Blake-3 content digest of the variant sequence. |
+| `variant_sequence` | `string` | The variant sequence. |
+| `is_expressed` | `boolean` | Whether the candidate is expressed in at least one sample. |
+| `expression_score` | `float` | Mean expression score across all samples. |
+| `expression_score_std` | `float` | Standard error of the expression score across all samples. |
+
+---
+
+## Replicate Expression Scores
+
+**File:** `replicate-expression-scores-YYYYMMDD.parquet`
+
+Per-replicate expression scores unrolled across different biological replicates. Use this table to inspect replicate-level variation.
+
+**Grain:** one row per `(expression_sample_id, candidate_id, variant_id)`.
+
+| Column | Type | Nullable | Description |
+| :--- | :--- | :--- | :--- |
+| `candidate_library_id` | `string` | no | Identifier of the candidate library consumed by this sample. |
+| `expression_sample_id` | `string` | no | Sample identifier for the expression (base) sample. |
+| `candidate_name` | `string` | no | Customer-provided sequence name. |
+| `candidate_id` | `string` | no | Blake-3 content digest of the reference sequence. |
+| `candidate_sequence` | `string` | no | The candidate amino acid sequence. |
+| `variant_id` | `string` | no | Blake-3 content digest of the variant sequence. |
+| `variant_sequence` | `string` | no | The variant sequence. |
+| `is_expressed` | `boolean` | no | Whether the candidate is expressed. |
+| `expression_score` | `float` | yes | Expression score derived from the log enrichment from synthesis to expression. Null when UMI count thresholds are not met. |
+
+**Key relationships:**
+- `expression_sample_id` corresponds to `dim_samples.sample_id`.
+- `candidate_id` is the shared candidate key across all tables.
+- `variant_id` is the shared variant key across all tables.

README.md

@@ -1,29 +1,28 @@
 ---
 configs:
-    - config_name: binding_scores
-      data_files:
-          - split: train
-            path: "binding_scores/**/*.parquet"
-    - config_name: replicate_binding_scores
-      data_files:
-          - split: train
-            path: "replicate_binding_scores/**/*.parquet"
-    - config_name: specificity_scores
-      data_files:
-          - split: train
-            path: "specificity_scores/**/*.parquet"
-    - config_name: replicate_specificity_scores
-      data_files:
-          - split: train
-            path: "replicate_specificity_scores/**/*.parquet"
+- config_name: expression_scores
+  data_files:
+  - split: train
+    path: "expression_scores/**/*.parquet"
+- config_name: replicate_expression_scores
+  data_files:
+  - split: train
+    path: "replicate_expression_scores/**/*.parquet"
+- config_name: binding_scores
+  data_files:
+  - split: train
+    path: "binding_scores/**/*.parquet"
+- config_name: replicate_binding_scores
+  data_files:
+  - split: train
+    path: "replicate_binding_scores/**/*.parquet"
+- config_name: specificity_scores
+  data_files:
+  - split: train
+    path: "specificity_scores/**/*.parquet"
+- config_name: replicate_specificity_scores
+  data_files:
+  - split: train
+    path: "replicate_specificity_scores/**/*.parquet"
 license: mit
 ---
-
-The instance `data-lab-demo` contains example datasets generated using [version 26.3](https://instance.bio/docs/release-notes#26-3-2026-06-30) of the [instance Data Lab](https://instance.bio/docs/dataset-docs/overview) process.
-
-For a more thorough explanation, refer to the [Instance Data Lab](./Instance%20Data%20Lab.pdf) report.
-
-## Dataset Schemas
-
-- [`binding_scores` and `replicate_binding_scores`](https://instance.bio/docs/dataset-docs/binding-scores)
-- [`specificity_scores` and `replicate_specificity_scores`](https://instance.bio/docs/dataset-docs/specificity-scores)

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