Core 1 @ Stanford University BioPortal Lynn Murphy Archana
Vembakam
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Goal Software development process how we achieve our goal Demo
Topics GRANT BioPortal
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Goal - What are we trying to produce? Enterprise level,
production quality software Industrial-strength, mission critical,
robust, scalable Custom web application Functionality specific to
the ontology community User experience and interface design
tailored Not generic
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Software Development Process - How we achieve our goal Analysis
and Software Requirements Gathering
DesignDevelopmentTestingDeployment Oct 2005 Nov 2005 Dec 2005 Feb
2006 Jan 2006 Mar 2006 Project Start Effective Start Date for
Archana and Lynn
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Software Development Process: Analysis / Requirements Extracted
requirements from grant proposal Gathered functional requirements
from Berkeley regarding current OBO at Sourceforge Many
requirements general, high level - translation into specific tasks
necessary Developed functional requirements document which
identified users, user roles, and large list of functional
requirements for the project Requirements drive the design and
architecture of system early identification of requirements key
Must have, nice to have (rank) Changing requirements slows
development
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BioPortal Functionality Overview Ontology submission Submission
pipeline Validation - file type/completeness, syntax, content
Versioning Ontology metadata Categorize ontologies Associate
provenance & ontology editing info with particular ontology
classes Support a web-of-trust platform for rating ontology
quality
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File / Version Submission Basic Validation Further Validation
Background Processing File to Holding Bin User Notified By Email
OBO Librarian Review Convert file to LexGrid DB Schema Indexing
Using LexGrid Alignment - PROMPT User Interface Control back to UI
Success? DB Status Change Workflow Ontology Submission Format
Validation Success? DB Status Change Yes No Yes No Yes
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BioPortal Functionality Overview - Continued Ontology indexes
and services All ontology content in the BioPortal is parsed,
validated, and indexed URIs for all terms, even if none provided
Term alignment across ontologies Terminological services (LexGrid -
Mayo) Double metaphone, exact and partial search Web services for
users and applications Find ontology terms Map free-text to
ontologies
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BioPortal Functionality Overview - Continued Ontology
visualization Tree display Graph-based visualization Interactive
visualization (Jambalaya - UVic) Ontology navigation (UVic)
Personalized guidance (degree-of-interest modeling) Tools to let
users focus on ontology subsets pertinent to their context (e.g.,
data to be annotated) Pictorially-guided navigation of ontologies
Ontology subsets based on biological scale
(organ/tissue/cell/molecule) Ontology alignment and difference
Alignment - find related ontologies Difference - track changes in
versions of ontologies
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BioPortal Functionality Overview: Ontology Visualization
Dynamically-generated graph to display subsets of large
ontologies
Work by Nigam Shah BioPortal Functionality Overview: Ontology
Visualization Pictorial-guided ontology navigation
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Software Development Process: Phased Development Developed
project plan functionality developed in phases Phase 1 - build
framework / subsystem which will translate into a scalable, robust
application Unsexy before sexy Functionality Authorization /
Authentication sign in, sign out, user registration, password
assistance, account maintenance Ontologies tabular list, category
(tree) list, view (text), download New ontology submission file
upload and metadata capture, versioning Metadata view details,
update, download in XML Versions list, view details, update,
version submission
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Software Development Process: Design Investigated software
resources Protg, PROMPT, LexGrid Necessary to install, determine
features and examine code to determine if and how technologies
could be used Example: installed LexGrid, determined functionality
gaps, communicated requirements to Mayo Looking beyond Phase 1 to
future phases so other teams can begin needed work now Researched
technology stack (Java, JBoss, Java Server Faces, JMS, etc.)
Prototyped functionality authentication / authorization, serving
files through Apache / Tomcat, connection between user interface
and session beans, etc. Designed architecture
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Software Development Process: Design Considerations Disparate
user interface need for remote and local access Distributed
transactions Cache Aspect oriented programming (AOP) Background and
message driven processing Rapid development (POJO) SOAP
Authentication and Authorization
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JAAS Authorization & Authentication JBoss Application
Server JMS Messaging Java Mail Generic Subsystem Oracle Database
Soap Services External access WebDAV File access module Apache Web
Server User Interface JSF, JSP, Servlets, Applets, CSS, HTML
Message Driven Beans Session Beans Entity Beans PROMPT APIProtg
APILexGrid API Architecture
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Software Development Process: Development Yay! We finally get
to code! Spent time setting up development environment Subversion,
build scripts, etc. Began coding mid-January approximately 6 weeks
~70 Java files, 20+ screens already Writing production code not
one-off development
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Software Development Process: Testing & Deployment Testing
Need to develop unit tests so that new features can be incorporated
without introducing instability Crucial to be able to roll out
later phases Deployment Ongoing meetings with various Stanford IT
departments Cost benefit analysis as to where BioPortal should be
hosted Backup and failover strategy, power considerations, hardware
specifications, machine configurations
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Demo Demo is actual working code not one-off development
Design, color scheme, layout will change No navigational features
(tabs, etc.) Data hand-entered for purposes of testing and demo may
be inaccurate
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Summary Goal is production quality, enterprise level custom web
application Development processes in place to ensure quality,
robust, supportable software Functionality introduced in phases
base system and framework first Requirements drive architecture
Phase 1 rollout Approximate date June Gating factors Moving files,
their versions and associated metadata from current Sourceforge
site Availability of production environment Logo ???
