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EMBL-EBI Integration of Sequence and 3D structure Databases.

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Presentation on theme: "EMBL-EBI Integration of Sequence and 3D structure Databases."— Presentation transcript:

1 EMBL-EBI Integration of Sequence and 3D structure Databases


3 EMBL-Bank DNA sequences EnsEMBL Human Genome Gene Annotation Uniprot Protein Sequences EMSD Macromolecular Structure Data Array-Express Microarray Expression Data

4 EMBL-EBI  Integration With Uniprot  eFamily Project  Future Plans

5 EMBL-EBI UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. Integration With UniProt

6 EMBL-EBI MSD / UniProt: UniProtMSD Agreed common mechanism for exchange of information. Services Two Different Database Systems “One of the major benefits of using databases for data storage is for data sharing”

7 EMBL-EBI  Collaboration between MSD (Sameer Velankar, Phil McNeil) and UniProt (Virginie Mittard, Daniel Barrell) groups  Depends upon  Clean UniProt (UNP) cross references in the DBREF records for each chain (where possible)  Clean taxonomy ids for each PDB chain  Taxonomy for PDB Source and UniProt OS must be the same MSD/Uniprot Collaboration

8 EMBL-EBI  Cleanup of the DBREF records in the PDB entries  Cleanup of the UniProt cross references in PDB entries  Cleanup of Source Information  NCBI Taxonomy IDs  Cleanup of the Reference information  Update UniProt entries  Source, Reference, Secondary structure information  Supply Additional Information  revision date, experimental method, resolution, R-factor  Residue-by-residue mapping between MSD and UniProt enables chimaeras to be handled correctly

9 EMBL-EBI Sequence Schema


11 EMBL-EBI Display of Mappings



14  IntEnz is the name for the Integrated relational Enzyme database and is the most up-to-date version of the Enzyme Nomenclature.  The IntEnz relational database implemented and supported by the EBI is the master copy of the Enzyme Nomenclature data.  MSD uses the UniProt accession code(s) mapped to each chain to link to the IntEnz EC number  This done directly via the MSD and IntEnz Oracle relational databases Integration With IntEnz

15 EMBL-EBI eFamily The eFamily project is designed to integrate the information contained in five of the major protein databases.

16 EMBL-EBI  To integrate the information contained in the five major protein databases.  The member databases (CATH, SCOP, MSD, Interpro, and Pfam) contain information describing protein domains.  For SCOP, CATH and MSD the data is primarily concerned with 3D structures  In InterPro and Pfam the focus is mainly on the sequences.  It is often difficult for biologists to navigate from protein sequence to protein structure and back again.  eFamily aims to provide the scientific community with a coherent and rich view of protein families that allow users seamlessly to navigate between the worlds of protein structure and protein sequence, by improved data resources and integration via grid technologies. eFamily Core Activities

17 EMBL-EBI UniProt GO InterPro GO PROSITE SCOP Pfam CATH GO Curated Common Domains definition HMM prediction Curated Mapping & curation Mapping per residue Mapping start – end MSD mapping Residues/Sequence DATA INTEGRATION

18 EMBL-EBI InterPro-UniProt(s) UniProt-PDBCHAIN(S) CATH/SCOP DOMAIN PDBCHAIN(S) InterPro-CATH/SCOP CATH/SCOP DOMAIN UniProt Complexity of Mappings  An InterPro entry is a collection of one or more UniProt entries  Unlike PDB concept of CHAIN does not exist in UniProt  UniProt entry is always numbered from 1 to N  PDB SEQRES Residue numbering is from 1 to N  PDB CHAIN (ATOM Records) Residue numbering is not necessarily 1 to N  UniProt to PDB Mapping can be one to many  PDB CHAIN to UniProt Mapping can be one to many

19 EMBL-EBI SCOP Domain PDB Residue Range Chains Swiss-Prot Residue Range MSD-SCOP Mapping for 1cbw

20 EMBL-EBI MSD-CATH Mapping for 1cbw CATH Domains PDB Residue Range Chains Swiss-Prot Residue Range

21 EMBL-EBI MSD-Pfam Mapping for 1cbw Pfam DomainPDB Residue Range Chains Swiss-Prot Residue Range

22 EMBL-EBI Practical Applications of Database Integration

23 EMBL-EBI Mappings Used in Pfam  Pfam now uses UniProt to structure mapping from MSD Search Database  Saves duplication of effort and weeks of compute  Use mapping for annotation of alignments Pfam domains highlighted on structure of RuBisCo (8ruc)

24 EMBL-EBI Mappings Used in Interpro

25 EMBL-EBI Mappings Used in SCOP

26 EMBL-EBI Comparison of SCOP, CATH and Pfam Domains SCOP, CATH and Pfam have developed web-services for describing their particular domain families. These services can be queried with a protein identifier, protein accession or PDB identifier. The databases use the MSD/UniProt mapping to translate between the sequence and structure domains

27 EMBL-EBI XML & Web Services The eFamily project has developed a XML schema to describe:  Domains  Annotation  Sequence Alignments  Structure Alignments This will be used to provide web-services as part of the eFamily project. More information about the XML schema is available at - We are also developing a perl based API for the eFamily XML which will be available from eFamily site as well as via bio-perl. The MSD residue-by-residue mapping is made available in XML format based on the eFamily schema.

28 EMBL-EBI Mapping Annotation

29 EMBL-EBI Future Plans

30 EMBL-EBI Integration of IntAct database- IntAct provides a freely available, open source database system and analysis tools for protein interaction data.

31 EMBL-EBI  Makes use of cleaned-up cross-reference & taxonomy data, SEQRES and ATOM/HETATM records from the PDB and the sequence from the UniProt entry to align and map each residue.  Makes connected segments from the PDB ATOM/HETATM records for each chain  These are then aligned against the SEQRES records and all the alignments for the segments are merged to get the SEQRES-ATOM alignment  This enables any unobserved residues to be considered Residue Mapping Program 1

32 EMBL-EBI  A similar operation is performed on the UniProt sequence and connected segments from the ATOM/HETATM records to get the UNP-ATOM alignment  The SEQRES-ATOM and UNP-ATOM alignments are then merged to get the final alignment  This is repeated for each chain in the PDB archive (with a UNP cross-reference  The mapping is loaded into the MSD relational database and validated Residue Mapping Program 2

33 EMBL-EBI Integrating data from MSD into CATH  Protocols have been developed for regular imports of a subset of MSD data warehouse into a local CATH database set up in ORACLE 9i  For example, information on the biological unit and on protein-ligand interactions will be integrated to increase functional annotations for CATH domain families

34 EMBL-EBI Two step process of data synchronisation  Data are moved from the MSD search database to the CATH-UCL site using a combination of Oracle Export/Import and SQL*Loader utilities  Subsequent updates in the MSD database are pushed to the CATH site using an incremental replication mechanism.  Data from the CATH site are pushed to the MSD site, using the same two step process  The two databases are synchronised MSD & CATH Data Exchange

35 EMBL-EBI  Structure  SCOP  CATH  Sequence  UniProt (neé Swiss-Prot /Trembl/PIR), InterPro, Go, Pfam  Function  IntEnz  Literature  Medline

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