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README.md
CHANGED
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@@ -3,9 +3,342 @@ pretty_name: Observed Antibody Dataset
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license: cc-by-4.0
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configs:
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- config_name: default
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| 6 |
data_files: paired/*.csv
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- config_name: paired
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| 8 |
data_files: paired/*.csv
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---
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-
# OPIG Observed Antibody Dataset (OAS)
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| 3 |
license: cc-by-4.0
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| 4 |
configs:
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| 5 |
- config_name: default
|
| 6 |
+
configs:
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| 7 |
+
- config_name: paired
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+
features:
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+
- name: meta_Run
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+
dtype: string
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+
- name: meta_Link
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+
dtype: string
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- name: meta_Author
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dtype: string
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- name: meta_Species
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dtype: string
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- name: meta_Age
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+
dtype: string
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- name: meta_BSource
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+
dtype: string
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- name: meta_BType
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+
dtype: string
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- name: meta_Vaccine
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+
dtype: string
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- name: meta_Disease
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+
dtype: string
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- name: meta_Subject
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+
dtype: string
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+
- name: meta_Longitudinal
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+
dtype: string
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+
- name: meta_Unique sequences
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+
dtype: int64
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+
- name: meta_Isotype
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+
dtype: string
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+
- name: meta_Chain
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+
dtype: string
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+
- name: source_file
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dtype: string
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+
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+
# Heavy chain fields
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+
- name: sequence_id_heavy
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+
dtype: string
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+
- name: sequence_heavy
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+
dtype: string
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| 45 |
+
- name: locus_heavy
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+
dtype: string
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+
- name: stop_codon_heavy
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+
dtype: string
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+
- name: vj_in_frame_heavy
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+
dtype: string
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| 51 |
+
- name: v_frameshift_heavy
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+
dtype: string
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+
- name: productive_heavy
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+
dtype: string
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+
- name: rev_comp_heavy
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+
dtype: string
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+
- name: complete_vdj_heavy
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+
dtype: string
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+
- name: v_call_heavy
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+
dtype: string
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+
- name: d_call_heavy
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+
dtype: string
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+
- name: j_call_heavy
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+
dtype: string
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+
- name: sequence_alignment_heavy
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+
dtype: string
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+
- name: germline_alignment_heavy
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+
dtype: string
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+
- name: sequence_alignment_aa_heavy
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+
dtype: string
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+
- name: germline_alignment_aa_heavy
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+
dtype: string
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+
- name: v_alignment_start_heavy
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+
dtype: int64
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+
- name: v_alignment_end_heavy
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+
dtype: int64
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+
- name: d_alignment_start_heavy
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+
dtype: float64
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+
- name: d_alignment_end_heavy
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+
dtype: float64
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| 81 |
+
- name: j_alignment_start_heavy
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+
dtype: int64
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+
- name: j_alignment_end_heavy
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+
dtype: int64
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| 85 |
+
- name: v_sequence_alignment_heavy
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+
dtype: string
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+
- name: v_sequence_alignment_aa_heavy
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+
dtype: string
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| 89 |
+
- name: v_germline_alignment_heavy
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+
dtype: string
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+
- name: v_germline_alignment_aa_heavy
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+
dtype: string
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+
- name: d_sequence_alignment_heavy
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+
dtype: string
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+
- name: d_sequence_alignment_aa_heavy
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+
dtype: string
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| 97 |
+
- name: d_germline_alignment_heavy
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+
dtype: string
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+
- name: d_germline_alignment_aa_heavy
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dtype: string
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+
- name: j_sequence_alignment_heavy
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+
dtype: string
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+
- name: j_sequence_alignment_aa_heavy
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dtype: string
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- name: j_germline_alignment_heavy
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+
dtype: string
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- name: j_germline_alignment_aa_heavy
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+
dtype: string
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+
- name: fwr1_heavy
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+
dtype: string
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- name: fwr1_aa_heavy
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+
dtype: string
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+
- name: cdr1_heavy
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+
dtype: string
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- name: cdr1_aa_heavy
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+
dtype: string
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- name: fwr2_heavy
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+
dtype: string
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- name: fwr2_aa_heavy
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+
dtype: string
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- name: cdr2_heavy
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+
dtype: string
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| 123 |
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- name: cdr2_aa_heavy
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+
dtype: string
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| 125 |
+
- name: fwr3_heavy
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+
dtype: string
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| 127 |
+
- name: fwr3_aa_heavy
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+
dtype: string
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| 129 |
+
- name: fwr4_heavy
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| 130 |
+
dtype: string
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| 131 |
+
- name: fwr4_aa_heavy
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+
dtype: string
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| 133 |
+
- name: cdr3_heavy
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| 134 |
+
dtype: string
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| 135 |
+
- name: cdr3_aa_heavy
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| 136 |
+
dtype: string
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| 137 |
+
- name: junction_heavy
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+
dtype: string
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- name: junction_length_heavy
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+
dtype: float64
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+
- name: junction_aa_heavy
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+
dtype: string
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| 143 |
+
- name: junction_aa_length_heavy
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+
dtype: float64
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+
- name: v_score_heavy
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| 146 |
+
dtype: float64
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+
- name: d_score_heavy
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+
dtype: float64
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| 149 |
+
- name: j_score_heavy
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+
dtype: float64
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+
- name: v_cigar_heavy
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+
dtype: string
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- name: d_cigar_heavy
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+
dtype: string
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| 155 |
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- name: j_cigar_heavy
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+
dtype: string
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- name: v_support_heavy
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| 158 |
+
dtype: float64
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| 159 |
+
- name: d_support_heavy
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| 160 |
+
dtype: float64
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| 161 |
+
- name: j_support_heavy
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| 162 |
+
dtype: float64
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| 163 |
+
- name: v_identity_heavy
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| 164 |
+
dtype: float64
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| 165 |
+
- name: d_identity_heavy
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| 166 |
+
dtype: float64
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| 167 |
+
- name: j_identity_heavy
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| 168 |
+
dtype: float64
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| 169 |
+
- name: v_sequence_start_heavy
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| 170 |
data_files: paired/*.csv
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- config_name: paired
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+
configs:
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| 173 |
+
- config_name: paired
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| 174 |
+
features:
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+
- name: meta_Run
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| 176 |
+
dtype: string
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| 177 |
+
- name: meta_Link
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| 178 |
+
dtype: string
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| 179 |
+
- name: meta_Author
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| 180 |
+
dtype: string
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| 181 |
+
- name: meta_Species
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| 182 |
+
dtype: string
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| 183 |
+
- name: meta_Age
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| 184 |
+
dtype: string
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| 185 |
+
- name: meta_BSource
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| 186 |
+
dtype: string
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| 187 |
+
- name: meta_BType
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| 188 |
+
dtype: string
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| 189 |
+
- name: meta_Vaccine
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| 190 |
+
dtype: string
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| 191 |
+
- name: meta_Disease
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| 192 |
+
dtype: string
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| 193 |
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- name: meta_Subject
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| 194 |
+
dtype: string
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| 195 |
+
- name: meta_Longitudinal
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| 196 |
+
dtype: string
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| 197 |
+
- name: meta_Unique sequences
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| 198 |
+
dtype: int64
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| 199 |
+
- name: meta_Isotype
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| 200 |
+
dtype: string
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| 201 |
+
- name: meta_Chain
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| 202 |
+
dtype: string
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| 203 |
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- name: source_file
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| 204 |
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dtype: string
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| 205 |
+
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| 206 |
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# Heavy chain fields
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| 207 |
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- name: sequence_id_heavy
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| 208 |
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dtype: string
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| 209 |
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- name: sequence_heavy
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| 210 |
+
dtype: string
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| 211 |
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- name: locus_heavy
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| 212 |
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dtype: string
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| 213 |
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- name: stop_codon_heavy
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| 214 |
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dtype: string
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| 215 |
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- name: vj_in_frame_heavy
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| 216 |
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dtype: string
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| 217 |
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- name: v_frameshift_heavy
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| 218 |
+
dtype: string
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| 219 |
+
- name: productive_heavy
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| 220 |
+
dtype: string
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| 221 |
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- name: rev_comp_heavy
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| 222 |
+
dtype: string
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| 223 |
+
- name: complete_vdj_heavy
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| 224 |
+
dtype: string
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| 225 |
+
- name: v_call_heavy
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| 226 |
+
dtype: string
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| 227 |
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- name: d_call_heavy
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| 228 |
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dtype: string
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| 229 |
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- name: j_call_heavy
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| 230 |
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dtype: string
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| 231 |
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- name: sequence_alignment_heavy
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| 232 |
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dtype: string
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| 233 |
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- name: germline_alignment_heavy
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| 234 |
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dtype: string
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| 235 |
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- name: sequence_alignment_aa_heavy
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| 236 |
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dtype: string
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| 237 |
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- name: germline_alignment_aa_heavy
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| 238 |
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dtype: string
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| 239 |
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- name: v_alignment_start_heavy
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| 240 |
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dtype: int64
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| 241 |
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- name: v_alignment_end_heavy
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| 242 |
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dtype: int64
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| 243 |
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- name: d_alignment_start_heavy
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| 244 |
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dtype: float64
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| 245 |
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- name: d_alignment_end_heavy
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| 246 |
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dtype: float64
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| 247 |
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- name: j_alignment_start_heavy
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| 248 |
+
dtype: int64
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| 249 |
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- name: j_alignment_end_heavy
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| 250 |
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dtype: int64
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| 251 |
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- name: v_sequence_alignment_heavy
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| 252 |
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dtype: string
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| 253 |
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- name: v_sequence_alignment_aa_heavy
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| 254 |
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dtype: string
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| 255 |
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- name: v_germline_alignment_heavy
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| 256 |
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dtype: string
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| 257 |
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- name: v_germline_alignment_aa_heavy
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| 258 |
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dtype: string
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| 259 |
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- name: d_sequence_alignment_heavy
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| 260 |
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dtype: string
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| 261 |
+
- name: d_sequence_alignment_aa_heavy
|
| 262 |
+
dtype: string
|
| 263 |
+
- name: d_germline_alignment_heavy
|
| 264 |
+
dtype: string
|
| 265 |
+
- name: d_germline_alignment_aa_heavy
|
| 266 |
+
dtype: string
|
| 267 |
+
- name: j_sequence_alignment_heavy
|
| 268 |
+
dtype: string
|
| 269 |
+
- name: j_sequence_alignment_aa_heavy
|
| 270 |
+
dtype: string
|
| 271 |
+
- name: j_germline_alignment_heavy
|
| 272 |
+
dtype: string
|
| 273 |
+
- name: j_germline_alignment_aa_heavy
|
| 274 |
+
dtype: string
|
| 275 |
+
- name: fwr1_heavy
|
| 276 |
+
dtype: string
|
| 277 |
+
- name: fwr1_aa_heavy
|
| 278 |
+
dtype: string
|
| 279 |
+
- name: cdr1_heavy
|
| 280 |
+
dtype: string
|
| 281 |
+
- name: cdr1_aa_heavy
|
| 282 |
+
dtype: string
|
| 283 |
+
- name: fwr2_heavy
|
| 284 |
+
dtype: string
|
| 285 |
+
- name: fwr2_aa_heavy
|
| 286 |
+
dtype: string
|
| 287 |
+
- name: cdr2_heavy
|
| 288 |
+
dtype: string
|
| 289 |
+
- name: cdr2_aa_heavy
|
| 290 |
+
dtype: string
|
| 291 |
+
- name: fwr3_heavy
|
| 292 |
+
dtype: string
|
| 293 |
+
- name: fwr3_aa_heavy
|
| 294 |
+
dtype: string
|
| 295 |
+
- name: fwr4_heavy
|
| 296 |
+
dtype: string
|
| 297 |
+
- name: fwr4_aa_heavy
|
| 298 |
+
dtype: string
|
| 299 |
+
- name: cdr3_heavy
|
| 300 |
+
dtype: string
|
| 301 |
+
- name: cdr3_aa_heavy
|
| 302 |
+
dtype: string
|
| 303 |
+
- name: junction_heavy
|
| 304 |
+
dtype: string
|
| 305 |
+
- name: junction_length_heavy
|
| 306 |
+
dtype: float64
|
| 307 |
+
- name: junction_aa_heavy
|
| 308 |
+
dtype: string
|
| 309 |
+
- name: junction_aa_length_heavy
|
| 310 |
+
dtype: float64
|
| 311 |
+
- name: v_score_heavy
|
| 312 |
+
dtype: float64
|
| 313 |
+
- name: d_score_heavy
|
| 314 |
+
dtype: float64
|
| 315 |
+
- name: j_score_heavy
|
| 316 |
+
dtype: float64
|
| 317 |
+
- name: v_cigar_heavy
|
| 318 |
+
dtype: string
|
| 319 |
+
- name: d_cigar_heavy
|
| 320 |
+
dtype: string
|
| 321 |
+
- name: j_cigar_heavy
|
| 322 |
+
dtype: string
|
| 323 |
+
- name: v_support_heavy
|
| 324 |
+
dtype: float64
|
| 325 |
+
- name: d_support_heavy
|
| 326 |
+
dtype: float64
|
| 327 |
+
- name: j_support_heavy
|
| 328 |
+
dtype: float64
|
| 329 |
+
- name: v_identity_heavy
|
| 330 |
+
dtype: float64
|
| 331 |
+
- name: d_identity_heavy
|
| 332 |
+
dtype: float64
|
| 333 |
+
- name: j_identity_heavy
|
| 334 |
+
dtype: float64
|
| 335 |
+
- name: v_sequence_start_heavy
|
| 336 |
data_files: paired/*.csv
|
| 337 |
---
|
| 338 |
|
| 339 |
+
# OPIG Observed Antibody Dataset (OAS)
|
| 340 |
+
|
| 341 |
+
## Filtering
|
| 342 |
+
|
| 343 |
+
If you know you only want a subset of this dataset, you can load a filtered subset like this:
|
| 344 |
+
`ds = load_dataset('OPIG/OAS', streaming=streaming, filters=[("meta_Species", "==", "human")]`.
|