| --- |
| 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. |
|
|
