The Open Access Publisher Agenda Ÿ

+ The Open Access Publisher

Agenda Ÿ Oracle inter. Media Overview Ÿ Open Access for the Life Science Community Ÿ Bio. Med Central Business Model Ÿ Oracle Technologies used by Bio. Med Central

Oracle inter. Media Multimedia Databases Multi-Terabyte Performance

Agenda • The Media-enabled Oracle Platform Ÿ Benefits Ÿ Customer Experience g Ÿ Oracle Database 10 New Features Ÿ Proposed Enhancements

The Media-enabled Oracle Platform Ÿ Oracle Database 10 – – – g Storage, management, & retrieval of image, audio, video data Native format understanding, metadata extraction, methods for image processing Support for leading streaming media servers g Ÿ Oracle Application Server 10 – – – JSP, Servelet and PL/SQL application development support Media Adaptation Services for Wireless JDeveloper (BC 4 J) and Portal integration Ÿ Oracle Collaboration Suite – Metadata extraction for OCS Files

Benefits: Save labor, time and money Bio. Med Central: • Automated media processing, serving & integration New Mexico Department of Transportation: • A Single DBA designed, created, deployed, and maintains a 5 TB image management system Palazzo Braschi Museum - Rome: • Reduced image processing time by 90% to bulk load and process images as compared to client side tools. A US Central bank • On-line processing and rapid resolution of 26, 000 bad checks per day reduces handling and float costs.

Fast & Scalable Ÿ 1 TB image repository renders images in Web browser in less than 0. 4 second Ÿ Loads at device speeds Ÿ Multi-terabyte multimedia databases – – 5 TB database 140 million images Ÿ Scalable bulk load and process – – Parallel processes load 300, 000 images/hour Bulk process – tiff to gif conversion, scale to thumbnail * USB Paine Webber, Caixa Economica Federal, NM DOT

Secure and Manageable Ÿ Use all Oracle Database security features – authentication, auditing, encryption, access control, etc. Ÿ Banks and Commercial Web sites use it Ÿ One management environment for all data – Single DBA for 5 TB database – 3 TB financial database * A US Central Bank, Bio. Med Central, Cre 8 tiv - UK, Spa Microsystems – UK, NM DOT, Caixa Economica Federal

Oracle Simplifies Code Image Insert using Multimedia JSP Tag Library – An Example With JSP Tag Library: (14 point font) <ord: embed. Image conn. Cache = <% java. util. Vector other. Values. Vector = new java. util. Vector(); other. Values. Vector. add(fd. get. Parameter("desc")); other. Values. Vector. add(fd. get. Parameter("loc")); %> “ media. Parameters = "photo" other. Columns = "description, location" other. Values = "<%=other. Values. Vector%>" />

Without: (in 10 point font) <FORM ACTION="Photo. Album. Insert. jsp" METHOD="POST"stmt. set. String( 1, form. Data. get. Parameter( "description" ) ); ENCTYPE="MULTIPART/FORM-DATA"> rset = (Oracle. Result. Set)stmt. execute. Query(); Description: <INPUT TYPE="text" NAME="desc"><BR> rset. next(); Location: <INPUT TYPE="text" NAME="loc"><BR> Ord. Image photo = (Ord. Image)rset. get. Custom. Datum( 1, Photo: <INPUT TYPE ="file" NAME="photo"><BR> Ord. Image. get. Factory()); <INPUT TYPE ="submit" VALUE="submit"> rset. close(); </FORM> try stmt. close(); { // Load the photo into the database and set the // Parse multipart/form-data properties. form. Data. set. Servlet. Request( request ); form. Data. get. File. Parameter( "photo" ). load. Image( photo form. Data. parse. Form. Data(); ); // Update object in database // Insert new row into database stmt = (Oracle. Prepared. Statement)conn. prepare. Statement( "insert into spec_photos ( description, "update spec_photos set photo = ? where location, photo ) " + description = ? " ); " values ( ? , ORDSYS. ORDImage. init() )" ); stmt. set. Custom. Datum( 1, photo ); stmt. set. String( 1, form. Data. get. Parameter( "description" stmt. set. String( 2, form. Data. get. Parameter( ) ); "description" ) ); stmt. set. String( 2, form. Data. get. Parameter( "location" ) stmt. execute(); ); stmt. close(); stmt. execute. Update(); stmt. close(); // Commit changes // Fetch Ord. Image object from database conn. commit(); } stmt = finally { // Ensure JDBC connection is released any temp files are deleted. (Oracle. Prepared. Statement)conn. prepare. Statement( "select photo from spec_photos where description = ? album. release(); form. Data. release(); for update" ); } %>

g New Oracle 10 Multimedia Features Ÿ Standards Support – SQL/MM Still Image Ÿ New version of Java Advanced Imaging and additional image processing operators Ÿ Support for additional media formats – • • • Microsoft ASF, MPEG 2 & MPEG 4 Microsoft Windows Media Server Plugin Real Server Plugin for Helix Server XML DB integration

Proposed Enhancements Ÿ Parse TIFF headers for user-specified attributes Ÿ Metadata mgt. , e. g. microarrays, gels, mass spec. Ÿ Characterize a region of interest for an image Ÿ Plug-in 3 rd party algorithms & utilities Ÿ Manage media metadata in XML DB Ÿ Describe user-defined file formats Ÿ Keep a history of changes to images Ÿ Handle 3 -D images (time/volume) Ÿ DICOM Support

Session id: 40363 Multimedia Database Improves the Bottom Line Matthew Cockerill Technical Director Bio. Med Central

Bio. Med Central and Oracle Ÿ Bio. Med Central is an Open Access publisher of biomedical research Ÿ Oracle database technology used to deliver a cost-effective online publishing solution Ÿ Goals – – Make the publishing process more efficient through online tools and automation Increase accessibility of research by removing subscription barriers

Oracle technology used by Bio. Med Central Ÿ Bio. Med Central’s database – – – 70 gigabytes of data (and growing rapidly) Lots of traditional relational data (e. g. 250, 000 registered users) Also serves as a repository for images, movies, PDFs and other rich media Ÿ Key technologies used – – – Real Application Clusters Data Guard Oracle Text – – XML DB Oracle inter. Media

What is wrong with traditional science publishing? Ÿ Subscription-only access to scientific research is a legacy of the economics of print Ÿ Scientists do all the hard work – – performing the research writing up the article acting as peer reviewers acting as journal editors Ÿ Traditional publishers take ownership of the copyright and sell limited access back to the scientific community Ÿ In the age of the web that makes no sense for science Ÿ Open Access publishers make research freely accessible and redistributable by scientists

Benefits of Open Access Ÿ Research instantly accessible to the entire scientific community Ÿ Digital permanence (many copies) Ÿ A route off the subscriptions treadmill – Subscriptions to traditional journals have increased at 10 -15% per annum Ÿ Data mining Ÿ Grid computing

Tony Blair “[The] national e-science grid … intends to make access to computing power, scientific data repositories and experimental facilities as easy as the web makes access to information. ” - Tony Blair, May 2002

The Open Access movement Ÿ Public Library of Science – – New not-for-profit publisher formed by a group of scientists Has received $9 m from Gordon and Betty Moore Foundation to start new Open Access journals Ÿ Soros Foundation – Has provided $3 m to support Open Access publishing in developing and transitional countries Ÿ Sabo bill – – Congressman Martin Sabo recently introduced the Public Access to Science Act in Congress If passed it would ensure that all US federally funded research would be published with Open Access

Bio. Med Central architecture Ÿ Oracle 9 i Database 9 i – – Stores relational data (e. g. user registration info) Also acts as repository for files associated with Ÿ submitted manuscripts Ÿ published articles Ÿ Web server farm – – – Runs many different journal websites, all driven by the same Oracle database Extensive use of Java and XSLT Media content streamed from the database using servlets

Key Oracle Technologies used by Bio. Med Central Ÿ Real Application Clusters Ÿ Data Guard Ÿ Oracle Text Ÿ XML DB Ÿ Oracle inter. Media

Importance of high availability Ÿ Science is a global enterprise, so Bio. Med Central’s websites are busy 24 hours a day Ÿ Scientists entrust their research and reputation to us - they must have confidence that their research will be available Ÿ Major institutional customers demand high reliability Ÿ Bio. Med Central delivers high availability using a combination of RAC and Data Guard

Real Application Clusters Ÿ Bio. Med Central was one of the first organizations in the UK to deploy 9 i RAC Ÿ Main database runs on a pair of dual CPU Sun Fire V 480 servers Ÿ Delivers high availability in the event of single node failure Ÿ Oracle upgrades/patches do currently require downtime however (for now!)

Data Guard Ÿ Bio. Med Central uses Data Guard to maintain a standby database Ÿ Standby database kept up to date by automated application of log files Ÿ Standby database can be used for reporting (in readonly mode) Ÿ If a prolonged outage of live db occurs (planned or unplanned), standby database can be activated Ÿ Data Guard makes it easy to roll back to the live configuration after planned outages

RAC/Data Guard configuration logfiles RAC Cluster Standby DB (Data Guard) Web server farm Reporting Main hosting location Standby location

RAC/Data Guard configuration RAC Cluster Standby DB (Data Guard) Web server farm Reporting Main hosting location Standby location

Key Oracle Technologies used by Bio. Med Central Ÿ Real Application Clusters Ÿ Data Guard Ÿ Oracle Text Ÿ XML DB Ÿ Oracle inter. Media

Use of Oracle Text Ÿ High performance full text article search Key benefits – – – Ease of maintenance (incremental online indexing) Structured searching of XML XPath support Unicode aware (smart base-character indexing) Filter procedures can be used to transform XML to be indexed

Structured search

XPath search Ÿ Prior to Oracle 9 i Database Release 2, relatively basic field restrictions based on XML tags were possible Ÿ Complex nesting of tags, or specific attribute values were difficult or impossible to search for Ÿ Oracle 9 i Database Release 2 support for Xpath field restrictions takes XML searching to another level Ÿ Now possible to search for all XML articles that contain a certain path (HASPATH), or that match a certain text expression at that path (INPATH)

XPath example Ÿ Article metadata identifying a series of related articles <meta> <classifications> <classification type="BMC" subtype="review_series_title" id="ar-cell">Cell-cell interactions in synovitis</classification> </classifications> </meta> Ÿ SQL syntax to retrieve all articles in that review series SELECT ARX_ID FROM ARX WHERE CONTAINS (ARX_FULL, 'HASPATH (//classification[@type="BMC“ AND @subtype="review_series_title" AND @id="ar-cell"])')>0;

Smart handling of Unicode

Key Oracle Technologies used by Bio. Med Central Ÿ Real Application Clusters Ÿ Data Guard Ÿ Oracle Text Ÿ XML DB Ÿ Oracle inter. Media

XML DB Ÿ Oracle support for XML standards in the database allows Bio. Med Central to manage article XML data within database Ÿ Examples of use – – Re-validate article XML against DTD after any update Application of XSLT transformations within database (e. g. as a pre-indexing filter)

Article XML (pre-transform) <bibl> <title> Genetic variability in MCF-7 sublines</title> <aug> <au id="A 1"> <snm>Nugoli</snm> <fnm>Melanie</fnm> <mi>JK</mi> <email>nugoli@valdorel. fnclcc. fr</email> </au> <au id="A 2"> <snm>Chuchana</snm> <fnm>Paul</fnm> <email>chuchana@valdorel. fnclcc. fr</email> </aug> <source>BMC Medical Research Methodology</source> … </bibl>

Article XML (post-transform) <bibl> <title> Genetic variability in MCF-7 sublines</title> <aug> <au id="A 1"> <snm>Nugoli</snm> <fnm>Melanie</fnm> <mi>JK</mi> <bnm>Nugoli_MJK</bnm> <email>nugoli@valdorel. fnclcc. fr</email> </au> <au id="A 2"> <snm>Chuchana</snm> <fnm>Paul</fnm> <bnm>Chuchana_P</bnm> <email>chuchana@valdorel. fnclcc. fr</email> </aug> <sourcefull>BMC Medical Research Methodology</ sourcefull> <sourceabbr>BMC Med Res Methodol</sourceabbr> </source> … </bibl>

Key Oracle Technologies used by Bio. Med Central Ÿ Real Application Clusters Ÿ Data Guard Ÿ Oracle Text Ÿ XML DB Ÿ Oracle inter. Media

inter. Media: Oracle as a media repository Ÿ Manuscript submission and workflow involves a complex interplay of files and metadata Ÿ Storing files directly in the database as BLOBs makes their management and manipulation much simpler Ÿ inter. Media provides a powerful set of tools to work with images in the database – – Extracting image metadata Scaling/cropping/format conversion

Full text article

Figure streamed from db

PDF streamed from database

Processing submitted files

Using inter. Media to manipulate images

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