Compliant with the GBIF Informatics Infrastructure / Architecture
Data consistency between NPT instances and GBIF
Open collaborative development and code maintenance
Modular
Extensible
Multilingual
Documented
Community driven
Configurable
Robust
Capability to efficiently track portal usage statistics
Intuitive and friendly end-user interface
Discoverable through search engines
Simple
Availability of API
Sustainability embedded at each stage of development
Interfaces and functionalities
Backend
SysAdmin level
Download components and updates
Install and configure components
Manager level
Choose Language
Customize look and feel
Name of the NPT instance
Show/hide metrics
Logo
Check data consistency
Portal configuration
Select and upload contextual data sources
GBIF index
Other data providers
Select and upload data types
Taxonomy
Species lists
Occurrence
Metadata
Data metrics
Institutions
Spatial data
Multimedia
Attributes
Experts
Annotations
Literature
Identification Aids
DNA
Manage portal features
User management
Permission control
User
Admin
Configure Harvesting Jobs schedules
FrontEnd
Discovery and access of biodiversity data
Taxonomic search
Possibility to search across all resources
Autocompletion
Advanced search (Filters)
Geospatial exploration (MapView)
Interactive Map
Select Data types
Select and apply Filters
Select Bounding box
Select Boundaries
Available geospatial data
Datasets
Draw a polygon
Visualization of results
Export in different formats
Search field
Flip to Treeview
Taxonomic exploration (TreeView)
Browse Tree
Display Results
Export in different formats
Search field
Web 2.0 user experience
User personalised channels to discover & access content
RSS feeds on user-defined content
MyGBIF
Sharing through Social networks
View and Export Search results
Usage metrics
Overview dashboard
Detailed stats
Network information
Network summary information
Network governance, structure and topology
Overview of data published
Data publishers profiles and statistics
Directories of institutions & experts
Feedback Button
Choose Language
Discovery and access of tools & services
APIs store (NPT compatible)
Data quality and annotation tools
Content contribution
Annotations to metadata?
Annotations to records?
Recommendations
Development
Framework
PHP/MySQL/Apache
APIs
Data flows - architecture
Access to data relevant for a Participant BIF but published by others
Webservices providing access to full DwC 1.4 elements
Maintained site for contributors
Software requirements
Use-case model Survey
Backend Users
Administrator
Topic
Security Officer
Topic
Data manager
Topic
Topic
Topic
Portal manager
Topic
Frontend Users
Visitor
Topic
Topic
Registered Visitor
Topic
Actors Survey
Primary Actors
Back office users
Administrators
Security Officers
Data managers
Portal managers
Frontend Users
Visitors
Registered visitors
Secondary Actors
GBIF registry
Data sources
GBIF webservices
IPT instances
Functional Requirements
Backend functionalities
Administator
Security officer
Data manager
Portal manager
Front end functionalities
Visitor
Registered Visitor
Non-Functional Requirements
Security Requirements
Capacity Requirements
Robustness Requirements
Interoperability Requirements
Operating Environment
Usability Requirements
Performance Requirements
Supportability Requirements
User Documentation Requirements
Design and implementation constraints
Interfaces
User interfaces
Pagination
Distribution map
Filter building interface
Hardware interfaces
Software interfaces
API
GBIF IPT
GBIF Webservices
GBIF Registry
Communications interface
Licencing agreements
Use Cases
Backend use cases
Administrator
Security officer
Data manager
Portal manager
Frontend use cases
Visitor
Registered Visitor
Business rules
Implementation
FAST WEBPRESENCE (NPT1)
Technologies
Drupal 7
Native modules
Core
Coder
Watchdog
Permissions
Internationalization
Custom Content Type
Scratchpads 1 modules
Left and Right
Backup
Feeds
Species Page
Apache/SoLR
Scratchpads 2 modules
DwC-A export
DwC-A import
Checklist export
NPT1 Custom modules
Occurrence records export
Audubon core format for multimedia files
GBIF Theming
Costum feeds
Sites maintenance
Aegir
Requirements
Functional
Backend functionalities
Administrator
UC-A1 - Manage modules
FR - A9 - View error logs
Security Officer
UC - S01 - Manage user accounts
FR - S06 - View audit logs
Data manager
FR - DM9 - Import multimedia
FR - DM11 - Edit multimedia metadata
FR - DM12 - Search multimedia resources by keyword
UC - DM9 - Backup portal data
UC - DM11 - Update taxonomic backbone
UC-DM12 - Install an extension
Portal manager
UC - PM1 - Configure visibility of data metrics
UC - PM3 - Customize NPT instance
Configure contact information
Manage languages
Manage news entries
Manage blog entries
Configure pages
Front-end functionalities
Visitor
UC - V1 - Send feedback to portal contact person
UC - V2 - View the distribution map
UC- V5 - Export distribution map as image
UC - V6 - Search portal using full text
UC - V8 - Export a checklist
UC - V9 - Choose language
FR - V38 - View data metrics
Non-functional
Security Requirements
SR1 - The system shall retain an audit log for all successful back end operations.
SR2 - The system shall restrict access to all functionalities altering data to data managers (BR4)
SR3 - The system shall restrict access to user management to security officers (BR3)
SR4 - The system shall restrict access to module management and distribution map configuration to administrators (BR6)
SR5 - The system shall restrict access to portal manager for the following functionalities: manage blog posts, pages and news entries, customize NPT instance and choose languages available on the front end (BR5)
Robustness Requirements
RR2 - The system should perform reasonably under important workload (queries and data discovery)
RR3 - Any errors should be trapped and not seen by users
RR4 - If an error occurs while the system is updating the index, the system shall restore the index to the state it was in before the update to ensure index consistency
Interoperability Requirements
IR1 - The system shall allow importing checklist resources DwC-A files
IR8 - The system shall allow exporting occurrences records as images
IR10 - The system shall allow using the Audubon Core format for multimedia metadata
Operating Environment
OE1 - The system shall operate with the two latest major releases of the following Web browsers: Firefox, Opera, Chrome, Internet Explorer and Safari
OE2 - The system shall operate on a server running Linux, Windows server or Mac OS
Usability Requirements
UR3 - Maintenance in terms of user interface configuration, user rights management, and data source(s) customization should be done at the management level with visual tools
UR4 - The system shall allow a visitor to select the language used on the front end
Supportability Requirements
SupR1 - A clear and standard practice for the maintenance and documentation of code should be set in place, agreed and communicated as a best practice. Any features developed outside the core of the NPT should follow that practice.
User Documentation Requirements
UD2 - Three installation guides with step-by-step instructions shall be provided (one for each of the OS the system can operate on)
UD3 - A wiki, organized around the different types of users, on the NPT Google Code site, similar to that developed for the GBIF IPT project will be available
Design and implementation constraints
CO1 - The system should be implemented using open-source technologies
CO2 - The system shall be written in PHP
CO4 - The system should be built in a modular way, which ensures that component functionalities can be adjusted, added, improved, removed or exchanged without impacting the application as a whole. Approaching the system using development best practices such as MVC (Model-View-Controller) can allow this sort of modularity
CO5 - The NPT development and implementation should follow design principles that will enable future growth, both in terms of the addition of new functionality or through modification of existing functionality. In addition, NPT developers should provide the possibility to consume services and functions that are created elsewhere. Examples include reference taxonomic data sources, mapping functions or web map services (WMS).
CO6 - Sustainability embedded at each stage of development. The developers of the NPT should be mindful of the strategic implications of development choices to the long term sustainability of the NPT in a number of key areas: underlying hardware and software; development tools and frameworks; level of effort for system administrators and portal managers; level of interest and engagement of users, including researchers, data providers and other interested visitors.
Workflow
Do-ers
Scratchpads Team
NPT Developer
GBIF-S
Hosting
Developement phase: NHM
Production phase: GBIF-S
TASKS
Determine the GBIF APi specifications for NPTV1
Validation, coding, testing and integration of modules
Setup a mockup site with theming
Development of NPT setup and editing workflow
Testing phase, including a small group of testers
Scratchpads NPT Profile definition
Implementation of the NPT
Testing phase with standard testing procedure
Overall Architecture
NPT1 High-level Architecture
NPT1+SOPHISTICATED GEOSPATIAL TOOLS (NPT2)
Technologies
Scenario 1
Drupal 7
Native modules
Core
Coder
Watchdog
Permissions
Internationalization
Custom Content Type
Scratchpads 1 modules
Left and Right
Backup
Feeds
Species Page
Apache/SoLR
Scratchpads 2 modules
DwC-A import
Checklist export
NPT1 Custom modules
Occurrence records export
Audubon core format for multimedia files
GBIF Theming
Costum feeds
NPT2 Custom modules
DwC-A export
EML profiling
Data sources configuration
Occurrence Data view
Filters building
Sites maintenance
Aegir
GeoSpatial component
Search Interface
OpenLayers
EXTJS
Javascript
PHP
Mapping Engine
Geoserver
Mapping configuration
Additional Spatial layer
Geo Database
PostGres
PostGIS
Scenario 2
Drupal 7
Native modules
Core
Coder
Watchdog
Permissions
Internationalization
Custom Content Type
Scratchpads 1 modules
Left and Right
Backup
Feeds
Species Page
Apache/SoLR
Scratchpads 2 modules
DwC-A import
Checklist export
NPT1 Custom modules
Occurrence records export
Audubon core format for multimedia files
GBIF Theming
Costum feeds
NPT2 Custom modules
DwC-A export
EML profiling
Data sources configuration
Occurrence Data view
Filters building
Mapping Kit
Map client
OpenLayers map client
Flash map client
Java map client
Map assist
Map context
WMS
Map layer
Map to pdf
Geodata
Mapserver
Sites maintenance
Aegir
Do-ers
Scratchpads Team
MGEL Team
NPT Developer
GBIF-S
Requirements
NPT1
Functional
Backend functionalities
Administrator
UC-A1 - Manage modules
FR - A9 - View error logs
Security Officer
UC - S01 - Manage user accounts
FR - S06 - View audit logs
Data manager
FR - DM9 - Import multimedia
FR - DM11 - Edit multimedia metadata
FR - DM12 - Search multimedia resources by keyword
UC - DM9 - Backup portal data
UC - DM11 - Update taxonomic backbone
UC-DM12 - Install an extension
Portal manager
UC - PM1 - Configure visibility of data metrics
UC - PM3 - Customize NPT instance
Configure contact information
Manage languages
Manage news entries
Manage blog entries
Configure pages
Front-end functionalities
Visitor
UC - V1 - Send feedback to portal contact person
UC - V2 - View the distribution map
UC- V5 - Export distribution map as image
UC - V6 - Search portal using full text
UC - V8 - Export a checklist
UC - V9 - Choose language
FR - V38 - View data metrics
Non-functional
Security Requirements
SR1 - The system shall retain an audit log for all successful back end operations.
SR2 - The system shall restrict access to all functionalities altering data to data managers (BR4)
SR3 - The system shall restrict access to user management to security officers (BR3)
SR4 - The system shall restrict access to module management and distribution map configuration to administrators (BR6)
SR5 - The system shall restrict access to portal manager for the following functionalities: manage blog posts, pages and news entries, customize NPT instance and choose languages available on the front end (BR5)
Robustness Requirements
RR2 - The system should perform reasonably under important workload (queries and data discovery)
RR3 - Any errors should be trapped and not seen by users
RR4 - If an error occurs while the system is updating the index, the system shall restore the index to the state it was in before the update to ensure index consistency
Interoperability Requirements
IR1 - The system shall allow importing checklist resources DwC-A files
IR8 - The system shall allow exporting occurrences records as images
IR10 - The system shall allow using the Audubon Core format for multimedia metadata
Operating Environment
OE1 - The system shall operate with the two latest major releases of the following Web browsers: Firefox, Opera, Chrome, Internet Explorer and Safari
OE2 - The system shall operate on a server running Linux, Windows server or Mac OS
Usability Requirements
UR3 - Maintenance in terms of user interface configuration, user rights management, and data source(s) customization should be done at the management level with visual tools
UR4 - The system shall allow a visitor to select the language used on the front end
Supportability Requirements
SupR1 - A clear and standard practice for the maintenance and documentation of code should be set in place, agreed and communicated as a best practice. Any features developed outside the core of the NPT should follow that practice.
User Documentation Requirements
UD2 - Three installation guides with step-by-step instructions shall be provided (one for each of the OS the system can operate on)
UD3 - A wiki, organized around the different types of users, on the NPT Google Code site, similar to that developed for the GBIF IPT project will be available
Design and implementation constraints
CO1 - The system should be implemented using open-source technologies
CO2 - The system shall be written in PHP
CO4 - The system should be built in a modular way, which ensures that component functionalities can be adjusted, added, improved, removed or exchanged without impacting the application as a whole. Approaching the system using development best practices such as MVC (Model-View-Controller) can allow this sort of modularity
CO5 - The NPT development and implementation should follow design principles that will enable future growth, both in terms of the addition of new functionality or through modification of existing functionality. In addition, NPT developers should provide the possibility to consume services and functions that are created elsewhere. Examples include reference taxonomic data sources, mapping functions or web map services (WMS).
CO6 - Sustainability embedded at each stage of development. The developers of the NPT should be mindful of the strategic implications of development choices to the long term sustainability of the NPT in a number of key areas: underlying hardware and software; development tools and frameworks; level of effort for system administrators and portal managers; level of interest and engagement of users, including researchers, data providers and other interested visitors.
NPT2
Functional
Backend functionalities
Administrator
UC-A1 - Manage modules
FR - A9 - View error logs
Security Officer
UC - S01 - Manage user accounts
FR - S06 - View audit logs
Data manager
FR - DM9 - Import multimedia
FR - DM11 - Edit multimedia metadata
FR - DM12 - Search multimedia resources by keyword
UC - DM9 - Backup portal data
UC - DM11 - Update taxonomic backbone
UC-DM12 - Install an extension
Portal manager
UC - PM1 - Configure visibility of data metrics
UC - PM3 - Customize NPT instance
Configure contact information
Manage languages
Manage news entries
Manage blog entries
Configure pages
Front-end functionalities
Visitor
UC - V1 - Send feedback to portal contact person
UC - V2 - View the distribution map
UC- V5 - Export distribution map as image
UC - V6 - Search portal using full text
UC - V8 - Export a checklist
UC - V9 - Choose language
FR - V38 - View data metrics
Registered Visitor
Non-functional
Security Requirements
SR1 - The system shall retain an audit log for all successful back end operations.
SR2 - The system shall restrict access to all functionalities altering data to data managers (BR4)
SR3 - The system shall restrict access to user management to security officers (BR3)
SR4 - The system shall restrict access to module management and distribution map configuration to administrators (BR6)
SR5 - The system shall restrict access to portal manager for the following functionalities: manage blog posts, pages and news entries, customize NPT instance and choose languages available on the front end (BR5)
Robustness Requirements
RR2 - The system should perform reasonably under important workload (queries and data discovery)
RR3 - Any errors should be trapped and not seen by users
RR4 - If an error occurs while the system is updating the index, the system shall restore the index to the state it was in before the update to ensure index consistency
Interoperability Requirements
IR1 - The system shall allow importing checklist resources DwC-A files
IR8 - The system shall allow exporting occurrences records as images
IR10 - The system shall allow using the Audubon Core format for multimedia metadata
Operating Environment
OE1 - The system shall operate with the two latest major releases of the following Web browsers: Firefox, Opera, Chrome, Internet Explorer and Safari
OE2 - The system shall operate on a server running Linux, Windows server or Mac OS
Usability Requirements
UR3 - Maintenance in terms of user interface configuration, user rights management, and data source(s) customization should be done at the management level with visual tools
UR4 - The system shall allow a visitor to select the language used on the front end
Supportability Requirements
SupR1 - A clear and standard practice for the maintenance and documentation of code should be set in place, agreed and communicated as a best practice. Any features developed outside the core of the NPT should follow that practice.
User Documentation Requirements
UD2 - Three installation guides with step-by-step instructions shall be provided (one for each of the OS the system can operate on)
UD3 - A wiki, organized around the different types of users, on the NPT Google Code site, similar to that developed for the GBIF IPT project will be available
Design and implementation constraints
CO1 - The system should be implemented using open-source technologies
CO2 - The system shall be written in PHP
CO4 - The system should be built in a modular way, which ensures that component functionalities can be adjusted, added, improved, removed or exchanged without impacting the application as a whole. Approaching the system using development best practices such as MVC (Model-View-Controller) can allow this sort of modularity
CO5 - The NPT development and implementation should follow design principles that will enable future growth, both in terms of the addition of new functionality or through modification of existing functionality. In addition, NPT developers should provide the possibility to consume services and functions that are created elsewhere. Examples include reference taxonomic data sources, mapping functions or web map services (WMS).
CO6 - Sustainability embedded at each stage of development. The developers of the NPT should be mindful of the strategic implications of development choices to the long term sustainability of the NPT in a number of key areas: underlying hardware and software; development tools and frameworks; level of effort for system administrators and portal managers; level of interest and engagement of users, including researchers, data providers and other interested visitors.