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Sameer Velankar http://msd.ebi.ac.uk

Formats of Structural data. Sameer Velankar http://msd.ebi.ac.uk. Data Format. ‘A precise specification of how to write data to a file’ E.g. PDB: ATOM 230 C GLY A 34 23.947 85.223 129.533 1.00 14.43 C Data Formats can be hard to change once made

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Sameer Velankar http://msd.ebi.ac.uk

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  1. Formats of Structural data Sameer Velankar http://msd.ebi.ac.uk

  2. Data Format ‘A precise specification of how to write data to a file’ E.g. PDB: ATOM 230 C GLY A 34 23.947 85.223 129.533 1.00 14.43 C Data Formats can be hard to change once made You can convert between formats provided the underlying data model is the same

  3. Formats appear and disappear like meteoroids even before we hear about them. We have (enough!) standards. We are happy and proud of the formats we use now and we do not understand why others do not like them!!

  4. New data from: NMR spectroscopy, X-ray crystallography Electron microscopy XML HTML Flat-files Harvesting ‘Manual’ Data Delivery Data capture Data Storage Relational Database Clean-up CORBA Oracle Legacy data (old PDB)

  5. New data from: NMR spectroscopy, X-ray crystallography Electron microscopy XML HTML Flat-files Harvesting ‘Manual’ Data Delivery Data capture Data Storage Relational Database Clean-up CORBA Oracle Legacy data (old PDB)

  6. New data from: NMR spectroscopy, X-ray crystallography Electron microscopy XML HTML Flat-files Harvesting ‘Manual’ Data Delivery Data capture Data Storage Relational Database CleanUp CORBA Oracle Legacy data (old PDB)

  7. Annotated PDB entry HEADER HEADER OUTER MEMBRANE 29-JUN-99 1QJP TITLE HIGH RESOLUTION STRUCTURE OF THE OUTER MEMBRANE PROTEIN A TITLE 2 (OMPA) TRANSMEMBRANE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER MEMBRANE PROTEIN A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TRANSMEMBRANE DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 STRAIN: BL21DE3; SOURCE 4 PLASMID: PET3B-171; SOURCE 5 GENE: OMPA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET3B-171 KEYWDS OUTER MEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR A.PAUTSCH,G.E.SCHULZ REVDAT 1 30-JUN-00 1QJP 0 JRNL AUTH A.PAUTSCH,G.E.SCHULZ JRNL TITL HIGH RESOLUTION STRUCTURE OF THE OMPA MEMBRANE JRNL TITL 2 DOMAIN JRNL REF J.MOL.BIOL. V. 298 273 2000 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836

  8. Annotated PDB entry HEADER REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 29702 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : NULL

  9. Annotated PDB entry HEADER REMARK 200 – Information about the experiment REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-1998 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 300/350 – Assembly information REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 300 REMARK 300 BIOLOGICAL_UNIT: MONOMER REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000

  10. Annotated PDB entry HEADER DBREF 1QJP A 1 171 SWS P02934 OMPA_ECOLI 22 192 SEQADV 1QJP PHE A 23 SWS P02934 LEU 44 ENGINEERED MUTATION SEQADV 1QJP LYS A 34 SWS P02934 GLN 55 ENGINEERED MUTATION SEQADV 1QJP TYR A 107 SWS P02934 LYS 128 ENGINEERED MUTATION SEQRES 1 A 171 ALA PRO LYS ASP ASN THR TRP TYR THR GLY ALA LYS LEU SEQRES 2 A 171 GLY TRP SER GLN TYR HIS ASP THR GLY LEU ILE ASN ASN SEQRES 3 A 171 ASN GLY PRO THR HIS GLU ASN LYS LEU GLY ALA GLY ALA SEQRES 4 A 171 PHE GLY GLY TYR GLN VAL ASN PRO TYR VAL GLY PHE GLU SEQRES 5 A 171 MET GLY TYR ASP TRP LEU GLY ARG MET PRO TYR LYS GLY SEQRES 6 A 171 SER VAL GLU ASN GLY ALA TYR LYS ALA GLN GLY VAL GLN SEQRES 7 A 171 LEU THR ALA LYS LEU GLY TYR PRO ILE THR ASP ASP LEU SEQRES 8 A 171 ASP ILE TYR THR ARG LEU GLY GLY MET VAL TRP ARG ALA SEQRES 9 A 171 ASP THR TYR SER ASN VAL TYR GLY LYS ASN HIS ASP THR SEQRES 10 A 171 GLY VAL SER PRO VAL PHE ALA GLY GLY VAL GLU TYR ALA SEQRES 11 A 171 ILE THR PRO GLU ILE ALA THR ARG LEU GLU TYR GLN TRP SEQRES 12 A 171 THR ASN ASN ILE GLY ASP ALA HIS THR ILE GLY THR ARG SEQRES 13 A 171 PRO ASP ASN GLY MET LEU SER LEU GLY VAL SER TYR ARG SEQRES 14 A 171 PHE GLY

  11. Annotated PDB entry HEADER HET C8E 181 21 HET C8E 182 21 HET C8E 183 21 HET C8E 184 21 HET C8E 185 21 HET C8E 186 21 HETNAM C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE HETSYN C8E N-OCTYL TETRAOXYETHYLENE FORMUL 2 C8E 6(C16 H34 O5) FORMUL 3 HOH *66(H2 O1) SHEET 1 A 9 LYS A 34 GLN A 44 0 SHEET 2 A 9 THR A 6 SER A 16 -1 N SER A 16 O LYS A 34 SHEET 3 A 9 MET A 161 ARG A 169 -1 N TYR A 168 O THR A 9 SHEET 4 A 9 ILE A 135 THR A 144 -1 N GLN A 142 O MET A 161 SHEET 5 A 9 LYS A 113 THR A 132 -1 N THR A 132 O ILE A 135 SHEET 6 A 9 LEU A 91 TYR A 107 -1 N THR A 106 O ASN A 114 SHEET 7 A 9 TYR A 72 PRO A 86 -1 N TYR A 85 O ILE A 93 SHEET 8 A 9 VAL A 49 ARG A 60 -1 N LEU A 58 O ALA A 74 SHEET 9 A 9 LYS A 34 ASN A 46 -1 N ASN A 46 O VAL A 49

  12. Annotated PDB entry ATOMS ATOM 1 N ALA A 1 40.685 9.235 39.250 1.00 41.73 N ANISOU 1 N ALA A 1 5189 5244 5422 1517 -755 251 N ATOM 2 CA ALA A 1 40.437 10.616 39.731 1.00 34.21 C ANISOU 2 CA ALA A 1 3852 5690 3456 978 203 -95 C ATOM 3 C ALA A 1 41.700 11.455 39.655 1.00 33.90 C ANISOU 3 C ALA A 1 2833 5874 4172 1554 210 -15 C ATOM 4 O ALA A 1 42.811 10.921 39.582 1.00 34.80 O ANISOU 4 O ALA A 1 3211 5948 4064 1990 418 301 O ATOM 5 CB ALA A 1 40.003 10.537 41.194 1.00 35.34 C ANISOU 5 CB ALA A 1 4077 5523 3827 28 458 466 C ATOM 6 N PRO A 2 41.565 12.766 39.609 1.00 32.57 N ANISOU 6 N PRO A 2 2775 5735 3866 1145 240 252 N ATOM 7 CA PRO A 2 42.672 13.694 39.684 1.00 32.36 C ANISOU 7 CA PRO A 2 2759 6152 3384 1006 460 57 C ATOM 8 C PRO A 2 43.515 13.362 40.915 1.00 35.79 C ANISOU 8 C PRO A 2 3145 6418 4037 443 30 714 C

  13. Components of PDB file • HEADER RECORDS • COORDINATE RECORDS

  14. Header Records The PDB format does not enforce multiple relationships between the records e.g. in COMPND record the CHAIN names do not always match those in SEQRES, SITE, TURN, or even ATOM records

  15. What is the SOLUTION? New format??

  16. New proposal for – mmcif (1991)

  17. A new emerging universal format for STRUCTURED data – XML (Extensible Markup Language)

  18. WHAT IS XML? • XML is a markup language for documents containing structured information. • Structured information contains both content (COMPND,SOURCE,ATOM) and some indication of what role that content plays (for example, SOURCE record gives information about source of the molecule, expression system etc.) • A markup language is a mechanism to identify structures in a document. The XML specification defines a standard way to add markup to documents.

  19. Target Data Formats XML : <residue name=“TYR” SEQID=“108”> <atom name=“HB1”> … </atom> … </residue> NMR-STAR (Self-defining Text Archive and Retrieval Format) SQL database

  20. Information related to structure Emergence of new techniques for determining structures or validation of the structure means that the HEADER records need to adapt to integrate the new information. e.g. FREE R VALUE : 0.198 It was not possible to refine structure with anisotropic B factors. May want to include cross references to new databases (GO- gene ontology)

  21. The present archive (PDB style file format) is also difficult to search against for complex queries!!

  22. How do we create a storage mechanism which is flexible enough to adapt to new changes and at the same time can be widely used for complex searches or data mining? New data from: NMR spectroscopy, X-ray crystallography Electron microscopy XML HTML Flat-files Harvesting ‘Manual’ Data Delivery Data capture Data Storage Relational Database Clean-up CORBA Oracle Legacy data (old PDB)

  23. Is it possible to have a storage mechanism which does not have any particular format?

  24. Data Base Tasks • GET DATA • ORGANISE AND STORE DATA • GIVE IT BACK

  25. What does an RDBMS provide? • efficient database management • non-procedural • maintain data in an organised form • reading and writing data to the computer • fast data access mechanisms • reduce or eliminate need for redundant data • ensure integrity and consistency of data

  26. Example Tables and Relationships DEPOSITION * CREATION_DATE REF_CONTACT_NAME * LAST_UPDATE * EMAIL * TITLE * NAME_FAMILY o ACCESSION_CODE o BUILDING o DATE_ALL_ARRIVED_DATE o DEPARTMENT_1 o DEP_PASSWORD o DEPARTMENT_2 o DETAILS_NDB o FAX o HARVEST_PROJECT_NAME o NAME_GIVEN o HOLD_DATE o NAME_INITIALS o HTTP_REFERER o NAME_SUFFIX o HTTP_USER_AGENT o PHONE o IMMUNE_RELATED o TITLE o RELEASE_DATE o URL o VIRUS_FLAG

  27. Example of SQL create table DEP_ENTITY ( DE_ID number(10,0) not null, DEP_DEP_ID number(10,0) not null, ID varchar2(255) not null, NAME varchar2(255) not null, DE_TYPE varchar2(10) not null, SYNTHETIC char(1) default 'N' not null, DETAILS varchar2(2000) null, SYSTEM varchar2(255) null, SYSTEMATIC_NAME varchar2(80) null, COMMON_NAME varchar2(80) null, FORMULA_WGHT number(8,0) null, ENGINEERED varchar2(255) null, MUTANT_FLAG varchar2(255) null, FRAGMENT_FLAG varchar2(255) null, MUTATION_STRING varchar2(40) null, ) ;

  28. Normalised database ~ 410 tables, 2000 attributes deposition data ~ 260 tables, 1300 attributes is used to calculate provides standard values for reference data ~ 130 tables, 500 attributes derived data ~ 20 tables, 200 attributes

  29. New data from: NMR spectroscopy, X-ray crystallography Electron microscopy XML HTML Flat-files Harvesting ‘Manual’ Data capture Data Storage Data Delivery Relational Database Clean-up CORBA Oracle Legacy data (old PDB)

  30. Funding and Partners of the EBI-Macromolecular Structure Database Group (EBI-MSD) CCPNCambridge(UK) Ehrlangen(Germany) Aarhous (Denmark) CCP4Daresbury(UK) Brussels(Belgium) CCP4Daresbury(UK) Nijmegen (NL) Frankfurt(Germany) Uppsala(Sweden) CNBMadrid(Spain) Oxford (UK) York(UK) CNRS(Paris) CNBMadrid(Spain) AUTO-STRUCT EU FPV (0) IIMSEU FPV(1) TEMBLOREU FPV(12) EMBLHamburg(Germany) Nijmegen(NL) MRCCambridge(UK) NMRQUALEU FPV(1) Cambridge (UK) EBI-MSD Group EMBL(4) WT(5) BBSRC(1) CCP4(0.5) Utrecht(NL) EMBLHeidelberg(Germany) RCSBUSA Glaxo Wellcome BMRBUSA CCP4Daresbury(UK) UCLLondon(UK) Zeneca Ltd Azara Ltd BrukerAnalytica Key:Circles represent coordinating partners. Numbers in brackets are the number of staff supported. (e.g. AUTOSTRUCT supports no staff at EBI)RCSB: Research Collaboratory for Structural BioinformaticsBMRB: BioMagResBank EMBL: European Molecular Biology LaboratoryWT: Wellcome TrustBBSRC: UK Biotechnology and Biological Sciences Research CouncilCCP4: UK Collaborative Computational Project 4.EU FPV: European Union, Framework Five.

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