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AutoDep 4.0 A data deposition and archival system Sameer Velankar.

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Presentation on theme: "AutoDep 4.0 A data deposition and archival system Sameer Velankar."— Presentation transcript:

1 http://www.ebi.ac.uk/msd AutoDep 4.0 A data deposition and archival system Sameer Velankar

2 http://www.ebi.ac.uk/msd PDB Deposition A ‘poor’ cousin of the structure determination process. Low priority and often seen as a necessary evil for facilitating publication of structure. Lack of seamless integration between structure determination to deposition. Low return for time invested for deposition.

3 http://www.ebi.ac.uk/msd Structure Determination/Genomics Pipeline

4 http://www.ebi.ac.uk/msd PDB Deposition AutoDep 4.0 A new generation structure deposition and archival tool developed at the MSD. (http://www.ebi.ac.uk/msd-srv/autodep4/)http://www.ebi.ac.uk/msd-srv/autodep4/

5 http://www.ebi.ac.uk/msd AutoDep 4.0 Interface Architecture Harvesting Annotation/Value added data

6 http://www.ebi.ac.uk/msd Secured with user-provided password. Context dependent page generation. Inline validation of input Data. Multiple deposition options to save time and effort. AutoDep 4.0 (Interface)

7 http://www.ebi.ac.uk/msd AutoDep 4.0 (Interface) Incomplete

8 http://www.ebi.ac.uk/msd AutoDep 4.0 Interface Architecture Harvesting Annotation/Value added data

9 http://www.ebi.ac.uk/msd Based on java/XML technologies. XML dictionaries govern the look of the deposition interface and define data items XSLT transformations generate web pages and produce a valid PDB file from the XML data. Easily modifiable for other deposition scenarios by changing the XML schema. Web-services (SOAP) compatible. AutoDep 4.0 (Architecture)

10 http://www.ebi.ac.uk/msd AutoDep 4.0 (Architecture) XSLT Data XML PDB File

11 http://www.ebi.ac.uk/msd AutoDep 4.0 (Architecture) Interface XMLAutodep XML Schema

12 http://www.ebi.ac.uk/msd AutoDep 4.0 Interface Architecture Harvesting Annotation/Value added data

13 http://www.ebi.ac.uk/msd AutoDep 4.0 (Harvesting) Many modern crystallography programs write out harvest files. Other programs write out PDB-style headers with refinement information. Autodep 4.0 parses file headers for Refmac, CNS, SHELX and X-PLOR and fills up relevant sections on the deposition form. Can also parse Refmac, Scala, Truncate and CNS harvest files and fill in information regarding refinement etc.

14 http://www.ebi.ac.uk/msd AutoDep 4.0 (Harvesting) Harvest File Upload

15 http://www.ebi.ac.uk/msd AutoDep 4.0 Interface Architecture Harvesting Annotation/Value added data

16 http://www.ebi.ac.uk/msd AutoDep 4.0 (Validation) Built-in structure validation Validation Reports generated include standard geometry and stereochemistry checks in addition to format.

17 http://www.ebi.ac.uk/msd Various items of data are returned to the depositor following annotation by the Curation Team. This information is only accessible to the depositor in their password-protected deposition session. AutoDep 4.0 (Annotation)

18 http://www.ebi.ac.uk/msd AutoDep 4.0 (Annotation)

19 http://www.ebi.ac.uk/msd Details of a heterogen new to the PDB AutoDep 4.0 (Annotation)

20 http://www.ebi.ac.uk/msd AutoDep 4.0 (Annotation)

21 http://www.ebi.ac.uk/msd AutoDep 4.0 (Annotation)

22 http://www.ebi.ac.uk/msd Future development plans Additional Annotation Reports (by end of the year) –Structure Similarity using MSDFold. –Small Motif identification using MSDMotif. –Ligand-binding site analysis using MSDSite. AutoDep Functionality –Accepting pdb_extract harvest files –Integration with CCPN. AutoDep 4.0 (Annotation)

23 http://www.ebi.ac.uk/msd Available free under license (GPL) for academic and industry use. Easy to install and useful for in-house archiving before deposition to the PDB via the MSD interface. In-house deposition produces a tar archive which can be uploaded to the public interface to complete deposition in minutes. Includes Tomcat, Java for intranet use, plus structure validation software. Produces formatted PDB file for in-house use. AutoDep 4.0

24 http://www.ebi.ac.uk/msd How to make it work together Include AutoDep as part of CCP4 distribution. –in-house data archival system –One step data deposition –Structure validation software –Could intergrate PISA, MSDfold CCP4 exports XML –One step data deposition using a link in ccp4i CCP4 and AutoDep 4.0

25 http://www.ebi.ac.uk/msd Flexible and Extensible (Java/XML technology) Provides an in-house structure archiving and validation system. Can be adapted to a SOAP service for SG pipelines with minimal effort. Mechanisms in place to return useful information via the AutoDep interface. Conclusions

26 http://www.ebi.ac.uk/msd AutoDep 4.0 request cycle

27 http://www.ebi.ac.uk/msd Funding

28 http://www.ebi.ac.uk/msd Annotation Team

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