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Sifts Table creation now makes chain case sensitive #38
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,46 +1,46 @@ | ||
| -- Given a PDB ID and chain, and a canonical uniprot_acc, this table provides the SIFTS-supplied | ||
| -- sequence alignments between PDB residues (including insertion codes) and transcript | ||
| -- position numbers | ||
| -- | ||
| -- PDB files are full of all kinds of troubles, from misisng residues, to inserted residues, | ||
| -- to residues in descending order. The detailed SIFTS xml file mapping is the essential | ||
| -- glue that the pdbmap needs to effectively mate pdb 3D structures to the often purer | ||
| -- transcript sequences which those structures depict | ||
| -- | ||
| -- The above reasons justify prefering curated SIFTS alignments to on-the-fly alignment | ||
| -- algorithsm. | ||
| -- | ||
| -- Not all PDB residues will be aligned to transcript positions. | ||
| -- Often, transcript positions will not align to PDB residues | ||
| -- | ||
| -- This alignment does not involve isoform specific uniprot identifiers, and care must be taken | ||
| -- Both 1) to ensure that the uniprot amino acid sequence that has been aligned mathces | ||
| -- your sequence inquestion and 2) that this table is not employed to align non-canonical | ||
| -- uniprot identifers to pdb structures. Those alignments are faciliated by other sifts* | ||
| -- tables generated from the Sifts' Rest API | ||
|
|
||
| CREATE TABLE IF NOT EXISTS sifts_legacy_xml ( | ||
| pdbid varchar(20) NOT NULL COMMENT '4 character rcsb pdb ID', | ||
| pdb_chain varchar(20) NOT NULL COMMENT 'chain. Ex A/B/Z/1/d etc', | ||
| PDBe_dbResNum int(11) NOT NULL COMMENT 'The unique PDBe sourced incrementing dbResNum for indexing', | ||
| pdb_resnum int(11) DEFAULT NULL COMMENT 'pdb residue number, null if missing from .pdb', | ||
| pdb_icode varchar(10) NOT NULL COMMENT 'pdb insertion code, usually blank - sometimes single Alpha', | ||
| pdb_resname varchar(20) DEFAULT NULL COMMENT 'pdb residue name', | ||
| uniprot_acc varchar(50) DEFAULT NULL COMMENT 'Ex: O12345-2 6 character uniprot ID and isoform specific id', | ||
| uniprot_resnum int(11) DEFAULT NULL COMMENT 'The 1-starting index into the isoform-specific transcript', | ||
| uniprot_resname varchar(50) DEFAULT NULL COMMENT 'transcript residue. May vary from pdb', | ||
| ncbi varchar(50) DEFAULT NULL, | ||
| pfam varchar(100) DEFAULT NULL, | ||
| cath varchar(100) DEFAULT NULL, | ||
| scop varchar(100) DEFAULT NULL, | ||
| interpro varchar(200) DEFAULT NULL, | ||
| sscode varchar(50) DEFAULT NULL, | ||
| ssname varchar(50) DEFAULT NULL, | ||
| sft_id BIGINT NOT NULL AUTO_INCREMENT, | ||
| PRIMARY KEY (pdbid,pdb_chain,PDBe_dbResNum), | ||
| KEY (pdbid,pdb_chain,pdb_resnum,pdb_icode,uniprot_acc), | ||
| KEY (sft_id), | ||
| KEY (uniprot_acc,pdb_resnum,pdbid) -- This is NOT a unique key. One uniprot ID can be represented in many pdbs | ||
| ) | ||
| CHARACTER SET utf8mb4 COLLATE utf8mb4_general_ci | ||
|
|
||
| -- Given a PDB ID and chain, and a canonical uniprot_acc, this table provides the SIFTS-supplied | ||
| -- sequence alignments between PDB residues (including insertion codes) and transcript | ||
| -- position numbers | ||
| -- | ||
| -- PDB files are full of all kinds of troubles, from misisng residues, to inserted residues, | ||
| -- to residues in descending order. The detailed SIFTS xml file mapping is the essential | ||
| -- glue that the pdbmap needs to effectively mate pdb 3D structures to the often purer | ||
| -- transcript sequences which those structures depict | ||
| -- | ||
| -- The above reasons justify prefering curated SIFTS alignments to on-the-fly alignment | ||
| -- algorithsm. | ||
| -- | ||
| -- Not all PDB residues will be aligned to transcript positions. | ||
| -- Often, transcript positions will not align to PDB residues | ||
| -- | ||
| -- This alignment does not involve isoform specific uniprot identifiers, and care must be taken | ||
| -- Both 1) to ensure that the uniprot amino acid sequence that has been aligned mathces | ||
| -- your sequence inquestion and 2) that this table is not employed to align non-canonical | ||
| -- uniprot identifers to pdb structures. Those alignments are faciliated by other sifts* | ||
| -- tables generated from the Sifts' Rest API | ||
|
|
||
| CREATE TABLE IF NOT EXISTS sifts_legacy_xml ( | ||
| pdbid varchar(20) NOT NULL COMMENT '4 character rcsb pdb ID', | ||
| pdb_chain varchar(20) NOT NULL COLLATE utf8mb4_bin COMMENT 'case sensitive chain. Ex A/B/Z/1/d etc', | ||
| PDBe_dbResNum int(11) NOT NULL COMMENT 'The unique PDBe sourced incrementing dbResNum for indexing', | ||
| pdb_resnum int(11) DEFAULT NULL COMMENT 'pdb residue number, null if missing from .pdb', | ||
| pdb_icode varchar(10) NOT NULL COMMENT 'pdb insertion code, usually blank - sometimes single Alpha', | ||
| pdb_resname varchar(20) DEFAULT NULL COMMENT 'pdb residue name', | ||
| uniprot_acc varchar(50) DEFAULT NULL COMMENT 'Ex: O12345-2 6 character uniprot ID and isoform specific id', | ||
| uniprot_resnum int(11) DEFAULT NULL COMMENT 'The 1-starting index into the isoform-specific transcript', | ||
| uniprot_resname varchar(50) DEFAULT NULL COMMENT 'transcript residue. May vary from pdb', | ||
| ncbi varchar(50) DEFAULT NULL, | ||
| pfam varchar(100) DEFAULT NULL, | ||
| cath varchar(100) DEFAULT NULL, | ||
| scop varchar(100) DEFAULT NULL, | ||
| interpro varchar(200) DEFAULT NULL, | ||
| sscode varchar(50) DEFAULT NULL, | ||
| ssname varchar(50) DEFAULT NULL, | ||
| sft_id BIGINT NOT NULL AUTO_INCREMENT, | ||
| PRIMARY KEY (pdbid,pdb_chain,PDBe_dbResNum), | ||
| KEY (pdbid,pdb_chain,pdb_resnum,pdb_icode,uniprot_acc), | ||
| KEY (sft_id), | ||
| KEY (uniprot_acc,pdb_resnum,pdbid) -- This is NOT a unique key. One uniprot ID can be represented in many pdbs | ||
| ) | ||
| CHARACTER SET utf8mb4 COLLATE utf8mb4_general_ci | ||
|
|
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,75 +1,75 @@ | ||
| -- Given either a PDB ID or uniprot ID, this table returns allows reconstruction of the dictionary | ||
| -- as returned by the source rest API documented: https://www.ebi.ac.uk/pdbe/api/doc/sifts.html | ||
| -- and as example would be: https://www.ebi.ac.uk/pdbe/api/mappings/all_isoforms/6cet | ||
| -- | ||
| -- This mapping supplements the legacy xml, which is detailed by residue but lacks isoform | ||
| -- specific uniprot identifiers | ||
|
|
||
| CREATE TABLE IF NOT EXISTS sifts_mappings_pdb_uniprot_all_isoforms ( | ||
| -- { | ||
| -- "6cet": { | ||
| -- "UniProt": { | ||
| -- "O75140": { | ||
| pdbid varchar(20) NOT NULL COMMENT '4 character rcsb pdb ID', | ||
| uniprot_acc varchar(50) DEFAULT NULL COMMENT 'Ex: O12345-2 6 character uniprot ID and isoform specific id', | ||
|
|
||
| -- "identifier": "NPRL3_HUMAN", | ||
| -- "name": "NPRL3_HUMAN", | ||
| identifier varchar(50) DEFAULT NULL COMMENT 'id for the uniprot_acc. Example: DEPD5_HUMAN', | ||
| name varchar(100) DEFAULT NULL COMMENT 'name associated with the uniprot_acc. Example: DEPD5_HUMAN', | ||
|
|
||
| -- "mappings": [ | ||
| mapping_entity_id varchar(50) DEFAULT NULL COMMENT 'molecule number in mmcif-speak, but rcsb says it need not be an integer', | ||
|
|
||
| -- "start": { | ||
| -- "author_residue_number": null, | ||
| -- "author_insertion_code": "", | ||
| -- "residue_number": 1 | ||
| -- }, | ||
| mapping_start_author_residue_number int(11) DEFAULT NULL COMMENT 'First residue: last residue number in pdb addressing scheme', | ||
| mapping_start_author_insertion_code varchar(10) DEFAULT NULL COMMENT 'First residue: PDB-style residue insertion code - often NULL', | ||
| mapping_start_residue_number int(11) DEFAULT NULL COMMENT 'First residue: mmcif style residue index', | ||
|
|
||
|
|
||
| -- "end": { | ||
| -- "author_residue_number": null, | ||
| -- "author_insertion_code": "", | ||
| -- "residue_number": 380 | ||
| -- }, | ||
| mapping_end_author_residue_number int(11) DEFAULT NULL COMMENT 'Last residue: last residue number in pdb addressing scheme', | ||
| mapping_end_author_insertion_code varchar(10) DEFAULT NULL COMMENT 'Last residue: PDB-style residue insertion code - often NULL', | ||
| mapping_end_residue_number int(11) DEFAULT NULL COMMENT 'Last residue: mmcif style residue index', | ||
|
|
||
| -- "chain_id": "N", | ||
| -- "unp_start": 1, | ||
| -- "unp_end": 380, | ||
| -- "pdb_start": 1, | ||
| -- "pdb_end": 380, | ||
| -- "struct_asym_id": "A", | ||
| -- "identity": 1 | ||
| mapping_pdb_chain varchar(20) NOT NULL COMMENT 'chain in pdb. Ex A/B/Z etc', | ||
| mapping_struct_asym_id varchar(20) NOT NULL COMMENT 'chain in mmcif.', | ||
|
|
||
| mapping_pdb_start int(11) NOT NULL COMMENT 'First residue: pdb number', | ||
| mapping_pdb_start_insertion_code varchar(10) DEFAULT NULL COMMENT 'First residue: pdb insertion code if seen', | ||
| mapping_pdb_end int(11) NOT NULL COMMENT 'Last residue: pdb residue number', | ||
| mapping_pdb_end_insertion_code varchar(10) DEFAULT NULL COMMENT 'Last residue: pdb insertion code if seen', | ||
|
|
||
| mapping_unp_start int(11) NOT NULL COMMENT 'First residue: index of uniprot residue', | ||
| mapping_unp_end int(11) NOT NULL COMMENT 'Last residue: index of uniprot residue', | ||
|
|
||
| mapping_seq_identity float not null COMMENT 'sequence identity calculated by ue: PDB-style residue insertion code - often NULL', | ||
|
|
||
| PRIMARY KEY (pdbid,uniprot_acc,mapping_pdb_chain,mapping_pdb_start), | ||
| KEY (uniprot_acc,pdbid,mapping_unp_start,mapping_pdb_chain) | ||
| ) CHARACTER SET utf8mb4 COLLATE utf8mb4_general_ci | ||
|
|
||
|
|
||
| -- The best isoforms from sifts come in identical format | ||
| -- but it is sanity-saving to keep separate source resources | ||
| -- separated in our tables, rather than having an additional "best isoform" column | ||
| -- in the above table | ||
| CREATE TABLE IF NOT EXISTS sifts_mappings_pdb_uniprot_best_isoforms | ||
| (PRIMARY KEY (pdbid,uniprot_acc,mapping_pdb_chain,mapping_pdb_start), | ||
| KEY (uniprot_acc,pdbid,mapping_unp_start,mapping_pdb_chain)) | ||
| AS SELECT * FROM sifts_mappings_pdb_uniprot_all_isoforms where 1=2 | ||
| -- Given either a PDB ID or uniprot ID, this table returns allows reconstruction of the dictionary | ||
| -- as returned by the source rest API documented: https://www.ebi.ac.uk/pdbe/api/doc/sifts.html | ||
| -- and as example would be: https://www.ebi.ac.uk/pdbe/api/mappings/all_isoforms/6cet | ||
| -- | ||
| -- This mapping supplements the legacy xml, which is detailed by residue but lacks isoform | ||
| -- specific uniprot identifiers | ||
|
|
||
| CREATE TABLE IF NOT EXISTS sifts_mappings_pdb_uniprot_all_isoforms ( | ||
| -- { | ||
| -- "6cet": { | ||
| -- "UniProt": { | ||
| -- "O75140": { | ||
| pdbid varchar(20) NOT NULL COMMENT '4 character rcsb pdb ID', | ||
| uniprot_acc varchar(50) DEFAULT NULL COMMENT 'Ex: O12345-2 6 character uniprot ID and isoform specific id', | ||
|
|
||
| -- "identifier": "NPRL3_HUMAN", | ||
| -- "name": "NPRL3_HUMAN", | ||
| identifier varchar(50) DEFAULT NULL COMMENT 'id for the uniprot_acc. Example: DEPD5_HUMAN', | ||
| name varchar(100) DEFAULT NULL COMMENT 'name associated with the uniprot_acc. Example: DEPD5_HUMAN', | ||
|
|
||
| -- "mappings": [ | ||
| mapping_entity_id varchar(50) DEFAULT NULL COMMENT 'molecule number in mmcif-speak, but rcsb says it need not be an integer', | ||
|
|
||
| -- "start": { | ||
| -- "author_residue_number": null, | ||
| -- "author_insertion_code": "", | ||
| -- "residue_number": 1 | ||
| -- }, | ||
| mapping_start_author_residue_number int(11) DEFAULT NULL COMMENT 'First residue: last residue number in pdb addressing scheme', | ||
| mapping_start_author_insertion_code varchar(10) DEFAULT NULL COMMENT 'First residue: PDB-style residue insertion code - often NULL', | ||
| mapping_start_residue_number int(11) DEFAULT NULL COMMENT 'First residue: mmcif style residue index', | ||
|
|
||
|
|
||
| -- "end": { | ||
| -- "author_residue_number": null, | ||
| -- "author_insertion_code": "", | ||
| -- "residue_number": 380 | ||
| -- }, | ||
| mapping_end_author_residue_number int(11) DEFAULT NULL COMMENT 'Last residue: last residue number in pdb addressing scheme', | ||
| mapping_end_author_insertion_code varchar(10) DEFAULT NULL COMMENT 'Last residue: PDB-style residue insertion code - often NULL', | ||
| mapping_end_residue_number int(11) DEFAULT NULL COMMENT 'Last residue: mmcif style residue index', | ||
|
|
||
| -- "chain_id": "N", | ||
| -- "unp_start": 1, | ||
| -- "unp_end": 380, | ||
| -- "pdb_start": 1, | ||
| -- "pdb_end": 380, | ||
| -- "struct_asym_id": "A", | ||
| -- "identity": 1 | ||
| mapping_pdb_chain varchar(20) NOT NULL COLLATE utf8mb4_bin COMMENT 'case sensitive chain. Ex A/B/Z/1/d etc', | ||
| mapping_struct_asym_id varchar(20) NOT NULL COMMENT 'chain in mmcif.', | ||
|
|
||
| mapping_pdb_start int(11) NOT NULL COMMENT 'First residue: pdb number', | ||
| mapping_pdb_start_insertion_code varchar(10) DEFAULT NULL COMMENT 'First residue: pdb insertion code if seen', | ||
| mapping_pdb_end int(11) NOT NULL COMMENT 'Last residue: pdb residue number', | ||
| mapping_pdb_end_insertion_code varchar(10) DEFAULT NULL COMMENT 'Last residue: pdb insertion code if seen', | ||
|
|
||
| mapping_unp_start int(11) NOT NULL COMMENT 'First residue: index of uniprot residue', | ||
| mapping_unp_end int(11) NOT NULL COMMENT 'Last residue: index of uniprot residue', | ||
|
|
||
| mapping_seq_identity float not null COMMENT 'sequence identity calculated by ue: PDB-style residue insertion code - often NULL', | ||
|
|
||
| PRIMARY KEY (pdbid,uniprot_acc,mapping_pdb_chain,mapping_pdb_start), | ||
| KEY (uniprot_acc,pdbid,mapping_unp_start,mapping_pdb_chain) | ||
| ) CHARACTER SET utf8mb4 COLLATE utf8mb4_general_ci | ||
|
|
||
|
|
||
| -- The best isoforms from sifts come in identical format | ||
| -- but it is sanity-saving to keep separate source resources | ||
| -- separated in our tables, rather than having an additional "best isoform" column | ||
| -- in the above table | ||
| CREATE TABLE IF NOT EXISTS sifts_mappings_pdb_uniprot_best_isoforms | ||
| (PRIMARY KEY (pdbid,uniprot_acc,mapping_pdb_chain,mapping_pdb_start), | ||
| KEY (uniprot_acc,pdbid,mapping_unp_start,mapping_pdb_chain)) | ||
| AS SELECT * FROM sifts_mappings_pdb_uniprot_all_isoforms where 1=2 |