1. Interface for Glyco Vault Functionality and requirements. Initial proposal. Maciej Janik

2. Glyco Vault Serves as a storage for files with experiment results, item descriptions, ontologies, etc. Data is heterogenous. Amount of data will be massively increasing. Hierarchical storage (as file system) is not enough – users need to add annotations. Users should be able to find interesting data (relatively) easy.

3. Interface functionality (basic) What we expect from Glyco Vault? Insert file to GV Get file from GV Delete specific file from GV Annotate with metadata Get file annotations Find file(s)

4. Sample file properties in GV Basic ID (unique) Name Date created User (owner) File type (InForma) Modification record … Specific (extended) Machine used for experiment Associated workflow Names of used samples Version number Other linked files …

5. File description (metadata) We cannot limit properties to currently known – schema must be flexible to accommodate future changes. File ID: GV-123 Name: ABC.txt Version: 9 Created: 2007-02-13 Owner: Will Machine: PCR Tissue: Parrot …

6. Ontological File System for GV File GV-123 ABC.txt 9 2007-02-13Will PCR Parrot Version Machine ID Creation date Owner Name Tissue Binaries Ontology with File-centric view. File is connected to its properties and other Files

7. Protocol data in GlycoVault Prepare samples Final result Statistical Analysis Get raw data Run PCR machine Description of samples Well assignment Person preparing Date/time of experiment PCR configuration Machine description (use of resource) Raw results (binaries) Raw results (values with annotation) Intermediate analytic data Final values of fluorescence Assigned to specific genes

8. Ontologies for annotation UserDefined attributes ProPreO ProtocolSchema GlycO and others … CoreFileOnt Core descriptions for all stored files (id, name, user, date …) Descriptions of used protocols and produced data Processes Data provenance Machines, etc. Data-specific ontologies Attributes and relations defined by users (not captured by other ontologies)

9. Insert and annotate file Insert simple file with its type FileID insert(Object aBinaries, InForma aType) Manage annotations boolean annotate(FileID aFile, Annotation aMetadata) boolean removeAnnotation(FileID aFile, Annotation aMetadata) Annotations Relation  Resource (object) Relation  Literal (value) Use of PropreO ontolgy (in some part) Add standard, independent file metadata

10. Get file and its annotations Get raw data file from GV Object getFile(FileID aFile) return binaries associated with file stored in Glyco Vault Get file descriptions Annotation[] describe(FileID aFile) return all direct annotations of a file to display for user Get file in specific format using InForma transformation should be external to GV

11. Search for files Find file by annotations In simple form, describe constraints directly associated with file FileID[] find(AnnotationConstraint[] aConstraints) Annotation constraint includes relation, value object and/or filter on value SPARQL queries with constraints in file ontology for complex cases GUI query builder/wizard with file metadata

12. Search for files Search is essential part of system and most complicated one. Efficient (DB/KB performance) Easy for users (GUI, Web) Browsing methods should be also added for easer navigation Idea: Faceted type browsing for files, eg. http://e-culture.multimedian.nl/demo/facet http://e-culture.multimedian.nl/demo/facet Use of Leon’s tool for browsing files and their descriptions

13. Interface (initial proposal) FileID insert(Object aBinaries, InForma aType) boolean annotate(FileID aFile, Annotation aMetadata) boolean removeAnnotation(FileID aFile, Annotation aMetadata) Object getFile(FileID aFile) Annotation[] describe(FileID aFile) FileID[] find(AnnotationConstraint[] aConstraints) boolean delete(FileID aFile) Type: Annotation Type: AnnotationConstraint

14. File ontology access Access to file ontology is needed to construct proper annotation Use of defined resources, eg. PCR Machine Creation of resources Specific instances Classes and hierarchies Listing available types and/or formats for annotations Possible access: Choice from pre-populated list Result of ‘can query’ Suggest as you type (Lucene index) List of classes with attributes and individuals (LSDIS library)

15. Administrators File system uses ontology, so administrators must be able to modify existing ontology to handle new types of annotations Maybe creation of some classes and instances can be pushed to specific users? During development easiest is to use direct ontology access Direct insert/delete of triples Use of SPARQL Later  some GUI interface would be required

16. GlycoVault on Oracle and Jena SQL Oracle platform API Jena Data (ont) Data (bin) JDBC read only full JDBC (administrator) SPARQL Ont Management experiment tables D2R server

17. GlycoVault – hybrid access Access via JDBC and SPARQL Ontologies will have a pointer to SQL data, can be a query, how to get real values (?) Data will be duplicated between SQL tables and ontology. What should be granularity of ontology data? JDBC access is read only for consistency purposes Modification allowed only for administrators