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Filtering Data Provided by SIFTS

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Zefeng Zhu edited this page Sep 8, 2020 · 2 revisions

Data Provided by REST calls based on SIFTS mappings

Reference: https://www.ebi.ac.uk/pdbe/api/doc/sifts.html

RAW

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{
    "1a01": {
        "UniProt": {
            "P68871": {
                "identifier": "HBB_HUMAN",
                "name": "HBB_HUMAN",
                "mappings": [{
                    "entity_id": 2,
                    "end": {
                        "author_residue_number": 146,
                        "author_insertion_code": "",
                        "residue_number": 146
                    },
                    "chain_id": "B",
                    "pdb_start": 1,
                    "start": {
                        "author_residue_number": 1,
                        "author_insertion_code": "",
                        "residue_number": 1
                    },
                    "unp_end": 147,
                    "pdb_end": 146,
                    "struct_asym_id": "B",
                    "unp_start": 2,
                    "is_canonical": true,
                    "identity": 0.99
                }, {
                    "entity_id": 2,
                    "end": {
                        "author_residue_number": 146,
                        "author_insertion_code": "",
                        "residue_number": 146
                    },
                    "chain_id": "D",
                    "pdb_start": 1,
                    "start": {
                        "author_residue_number": 1,
                        "author_insertion_code": "",
                        "residue_number": 1
                    },
                    "unp_end": 147,
                    "pdb_end": 146,
                    "struct_asym_id": "D",
                    "unp_start": 2,
                    "is_canonical": true,
                    "identity": 0.99
                }]
            },
            "P69905": {
                "identifier": "HBA_HUMAN",
                "name": "HBA_HUMAN",
                "mappings": [{
                    "entity_id": 1,
                    "end": {
                        "author_residue_number": 141,
                        "author_insertion_code": "",
                        "residue_number": 141
                    },
                    "chain_id": "A",
                    "pdb_start": 1,
                    "start": {
                        "author_residue_number": 1,
                        "author_insertion_code": "",
                        "residue_number": 1
                    },
                    "unp_end": 142,
                    "pdb_end": 141,
                    "struct_asym_id": "A",
                    "unp_start": 2,
                    "is_canonical": true,
                    "identity": 1
                }, {
                    "entity_id": 1,
                    "end": {
                        "author_residue_number": 141,
                        "author_insertion_code": "",
                        "residue_number": 141
                    },
                    "chain_id": "C",
                    "pdb_start": 1,
                    "start": {
                        "author_residue_number": 1,
                        "author_insertion_code": "",
                        "residue_number": 1
                    },
                    "unp_end": 142,
                    "pdb_end": 141,
                    "struct_asym_id": "C",
                    "unp_start": 2,
                    "is_canonical": true,
                    "identity": 1
                }]
            }
        }
    }
}

Convert to Tabular Format

UniProt chain_id end entity_id identifier identity is_canonical name pdb_end pdb_id pdb_start start struct_asym_id unp_end unp_start
P68871 B {"author_residue_number":146,"author_insertion_code":"","residue_number":146} 2 HBB_HUMAN 0.99 TRUE HBB_HUMAN 146 1a01 1 {"author_residue_number":1,"author_insertion_code":"","residue_number":1} B 147 2
P68871 D {"author_residue_number":146,"author_insertion_code":"","residue_number":146} 2 HBB_HUMAN 0.99 TRUE HBB_HUMAN 146 1a01 1 {"author_residue_number":1,"author_insertion_code":"","residue_number":1} D 147 2
P69905 A {"author_residue_number":141,"author_insertion_code":"","residue_number":141} 1 HBA_HUMAN 1 TRUE HBA_HUMAN 141 1a01 1 {"author_residue_number":1,"author_insertion_code":"","residue_number":1} A 142 2
P69905 C {"author_residue_number":141,"author_insertion_code":"","residue_number":141} 1 HBA_HUMAN 1 TRUE HBA_HUMAN 141 1a01 1 {"author_residue_number":1,"author_insertion_code":"","residue_number":1} C 142 2

Aggregate Coverage Related Columns and Annotate

UniProt pdb_id entity_id chain_id identity pdb_range unp_range group_info pdb_gap_list unp_gap_list var_list repeated var_0_count unp_gap_0_count unp_pdb_var sifts_range_tag new_unp_range new_pdb_range
Q9NP77 3o2s 2 B 1 ((21,214)) ((1,194)) 1 () () (0) FALSE 1 0 0 Safe ((1,194)) ((21,214))
Q8N2K1-3 2f4w 1 B 0.920398 ((3,187)) ((1,201)) 1 () () (16) FALSE 0 0 16 Deletion ((1,44),(61,201)) ((3,46),(47,187))

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