File size: 11,069 Bytes
06d6d7e 33565e1 06d6d7e 33565e1 06d6d7e 33565e1 06d6d7e 33565e1 06d6d7e 33565e1 06d6d7e 33565e1 06d6d7e 33565e1 06d6d7e 33565e1 06d6d7e 33565e1 06d6d7e 33565e1 06d6d7e 33565e1 06d6d7e 33565e1 06d6d7e 33565e1 06d6d7e 33565e1 06d6d7e 33565e1 06d6d7e 977a72b 06d6d7e 977a72b 06d6d7e c812115 06d6d7e | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 | ---
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.
|