# Presentation: 610440

## Scientific Annotation MiddlewareSoftware infrastructure to support rich scientific records and the processes that produce them

- Jens SchwidderTara D. Gibson
- Computer Science Research GroupComputer Science and Mathematics Division
- James D. Myers
- National Center for Supercomputing Applications

**Notes:**
Title slide; What other names?

## Scientific Annotation Middleware (SAM) objectives

**Develop a lightweight, flexible middleware to support the creation and use of metadata and annotations**
**Support sharing of annotations among scientific applications, portals, problem-solving environments, and electronic notebooks**
**Improve the completeness, accuracy, and availability of the scientific record**
**Support mapping between the annotation schemas of different scientific domains, thus enabling collaboration **

## Middleware approach

**Various client and storage interfaces provide transparent integration of legacy applications as well as new applications using new, more powerful semantics**

## Characteristics

- Features

**Middleware design capable of integrating into multiple service architectures**
**“****Schema-less” store that accepts arbitrary content and metadata**
**Dynamic metadata/data translations to support evolving standards and lightweight integration**
**Layered design to allow basic and advanced clients and interactions between them**
**Meta–data translation/extraction**
**Semantic services**
**Distributed Authoring and Versioning (DAV)**
**Notebook services and user interfaces**
**Event notification using Java Messaging Service (JMS)**
**Prototype implementation of Java Content Repository (JCR)(JSR 170)****-based SAM layer that allows adding SAM capabilities to JCRs**

## Benefits of the SAM system

**Rich, accessible, integrated scientific records**
**Support for system-science cyber environments and collaboration across disciplines**
**Increased automation of metadata capture and data/metadata translation**
**Integrated electronic notebook, semantic relationship (e.g., provenance) tracking, and third-party annotation services**
**Open source, standards-based scientific content management services**
**Flexible authentication and authorization support**

## SAM-based electronic notebooks

**Take advantage of advanced SAM features, such as data translation**
**Provide hierarchical chapters/pages/notes **
**Provide add/view/search notes**
**Provide multiple client interfaces**
**Internationalized Electronic Laboratory Notebook (ELN) client**
**HTML-based Web interfaces**
**Enable applications to provide notebook functionality using SAM notebook API/components**
**Can serve as record with electronic signatures**
**Allow scientists to share notes in distributed teams**
**Allow email notifications **

## Community interactions

**Data Format Description Language (DFDL) standardization within the Global Grid Forum**
**JCR (JSR 170) standardization within the Java Community Process **
**Battelle records managers**
**DOE2000 electronic notebook (Enote and ELN) communities**
**PNNL Computational Science and Mathematics Division**
**Semantic data grid to store, generate, and query provenance information**

- Collaboratory for Multiscale Chemical Science (CMCS)—using SAM to support a portal-based community knowledge grid

- SAM-based internationalizedgrid-capable notebook

- Automated experiment records, user annotations,and customized instrument logs

- MAEviz—“Consequence-based Risk ManagementCyberenvironment”—using SAM to support shared data and provenance

**Notes:**
Community interaction and efforts. 

## CMCS use of SAM

**Powers CMCS knowledge management**
**Provides a node plus metadata/relationship view of underlying data sources**
**Supports put/get/search/access control of arbitrary data/metadata**
**Enables configurable metadata extraction from binary/ASCII/XML files**
**Enables semantic/graph queries**
**	****More information on CMCS at ****http://cmcs.org**

**Fortran**
**application**

**‘****Local disk’**

- Data grid

**DAV**

**DAV+**

**JMS**

**ELN**

**CMCS**

**Notes:**
Slide about CMCS using SAM as example.

## SAM 2.1.4 release

**DFDL, Web service, and XSLT-based metadata extraction and data translation capabilities**
**Improved semantic search capabilities using an extension of DAV searching and location and Lucene indexing **
**JDBC databases, file systems as data/metadata stores**
**Simple Web-based SAM and notebook administration**
**Internationalized ELN client (accepts UNICODE for Chinese/Japanese character sets)**
**Optional fully Web-based version of the ELN client**
**JAAS-based single-sign-on capabilities**
**Notarization server and proxy implementation**
**Command-line client and client API library**
**Jakarta Slide 2.1 code base**
**Requirements: Java 1.4 (or higher) and Tomcat 5.x**

## Spallation Neutron Source (SNS) Notebooks

**The electronic notebook software for the SNS is being developed based on the research done in the SAM project.**
**Support for different types of notebooks:**
**Instrument notebooks**
**Record events and annotations regarding an instrument.**
**Structure fixed; entries can’t be edited, but can be annotated.**
**Proposal notebooks**
**Contain research annotations for a proposal and its experiments.**
**Structure and editing policies under control of proposal PI.**
**Layered access control for SNS users and groups:**
**Personal notebooks. **
**Shared proposal and instrument notebooks.**
**Web-based user interfaces using AJAX.**
**Support for Wiki-formatting to support easy input of structured text.**
**JCR-based storage system.**

## More information about SAM

**Project information at****http://www.scidac.org/SAM**
**SAM source code hosted at ****http://sourceforge.net/projects/sam**
**BSD/Apache-style open source license**

**Notes:**
Where can I get more information? Which organizations and people were involved?

## Contact

- Jens Schwidder
- Computer Science and Mathematics DivisionComputer Science Research Group(865) 576-7928schwidderj@ornl.gov

-    Schwidder_SAM_SC07