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GBIF - NPT

By biodiversityaq

NPT Mindmap 23 september 2011.

Added: September 23, 2011 11:44:53

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GBIF - NPT

GBIF - NPT

A generic set of biodiversity informatics modules to deploy maintain and expand biodiversity data portals

1 History
1.1 Need identified Oct 2002
1.2 First release Dec 2002
1.3 Deployment of DiGIR network 2004
1.4 NPT as ranked priority Oct 2004
1.5 Draft requirements doc Oct 2005
1.6 Early prototype Apr 2006
1.7 Online survey 2009
1.8 NPT Advisory Group Dec 2009
1.9 NPT kickoff Nov 2010
1.10 NPT workshop Mar 2011
2 Objectives
2.1 Mobilize data
2.2 Deploy, maintain, extend Biodiversity portals
2.2.1 National
2.2.2 Thematic
2.2.3 Regional
2.3 Offer access to additional types of data
2.4 Leverage technical capacity within GBIF Community
3 Strategy
3.1 Capture Scope and Requirements
3.1.1 S&R document v0.1
3.1.1.1 discuss/report
3.1.1.1.1 S&R document v0.2
3.1.1.1.1.1 discuss/report
3.1.1.1.1.1.1 S&R document v0.3
3.1.1.1.1.1.1.1 discuss/report
3.1.1.1.1.1.1.1.1 S&R document V1.0
3.2 Develop communication channels
3.2.1 email, skype, telephone
3.2.2 NPT Google code page
3.2.3 NPT Blog
3.2.4 NPT Facebook Page
3.2.5 GBIF Community Site
3.2.6 Demo site
3.2.7 Mindmap site
3.2.8 Mockups site
3.2.9 NPT Workshops and meetings
3.2.10 Other workshops and meetings
3.3 Define Software Requirements
3.3.1 SRS document v0.1
3.3.1.1 discuss/report
3.3.1.1.1 SRS document v0.2
3.3.1.1.1.1 discuss/report
3.3.1.1.1.1.1 Reality-Check
3.3.1.1.1.1.1.1 S&R document V1.0
3.3.1.1.1.1.1.1.1 S&R document NPT1 V1.0
3.3.1.1.1.1.1.1.2 S&R document NPT2 V1.0
3.4 Identify Phased approach
3.4.1 Phase 1

NPT1 will deliver a simple web building toolkit to enable GBIF Participants to deploy an extensible web platform that serves as a portal to the GBIF network. Targetting GBIF Nodes who require a customized and hosted biodiversity data portal solution. The customization entails providing a editable national list of species based on GBIF occurrence data. This list provides the basis for retrieving customized national species distribution maps from the GBIF Data Portal to display within the NPT. The difference between NPT1 & NPT2 is based on the type of content exchange between the NPT and the GBIF Data Portal. NPT 1 focussed primarily on serving precomposed national data distribution maps similar to what the current GBIF Data Portal already provides at the global level.

3.4.2 Phase 2

NPT2 is based on the same underlying Drupal framework as NPT 1. NPT2 however also includes an advanced geospatial module capable of processing primary biodiversity data directly. This module supports the management and display of biodiversity data within the NPT itself. This supports more advanced geospatial capabilities such as filtering, integration with other geospatial layers on e.g. national protected areas.

3.5 Delineate High-Level Architecture (NPT1)
3.6 Identify Do-ers (NPT1)
3.7 Start Development of Phase 1
3.8 Delineate High-Level Architecture (NPT2)
3.9 Identify Do-ers (NPT2)
3.10 Start Development of Phase 2
4 Stakeholders
4.1 Communities
4.1.1 GBIF Participants
4.1.1.1 Country participants
4.1.1.1.1 Africa
4.1.1.1.1.1 Benin
4.1.1.1.1.2 Burkina Faso
4.1.1.1.1.3 Cameroon
4.1.1.1.1.4 Central African Republic
4.1.1.1.1.5 Equatorial Guinea
4.1.1.1.1.6 Ghana
4.1.1.1.1.7 Guinea
4.1.1.1.1.8 Kenya
4.1.1.1.1.9 Madagascar
4.1.1.1.1.10 Mauritania
4.1.1.1.1.11 Morrocco
4.1.1.1.1.12 Republic of Congo
4.1.1.1.1.13 South Africa
4.1.1.1.1.14 Tanzania
4.1.1.1.1.15 Togo
4.1.1.1.1.16 Uganda
4.1.1.1.2 Asia
4.1.1.1.2.1 India
4.1.1.1.2.2 Indonesia
4.1.1.1.2.3 Japan
4.1.1.1.2.4 Republic of Korea
4.1.1.1.2.5 Pakistan
4.1.1.1.2.6 Philippines
4.1.1.1.3 Europe
4.1.1.1.3.1 Andorra
4.1.1.1.3.2 Austria
4.1.1.1.3.3 Belgium
4.1.1.1.3.4 Bulgaria
4.1.1.1.3.5 Denmark
4.1.1.1.3.6 Estonia
4.1.1.1.3.7 Finland
4.1.1.1.3.8 France
4.1.1.1.3.9 Germany
4.1.1.1.3.10 Iceland
4.1.1.1.3.11 Ireland
4.1.1.1.3.12 Luxemburg
4.1.1.1.3.13 Netherlands
4.1.1.1.3.14 Norway
4.1.1.1.3.15 Poland
4.1.1.1.3.16 Portugal
4.1.1.1.3.17 Slovakia
4.1.1.1.3.18 Slovania
4.1.1.1.3.19 Spain
4.1.1.1.3.20 Sweden
4.1.1.1.3.21 Switzerland
4.1.1.1.3.22 United Kingdom
4.1.1.1.4 North America
4.1.1.1.4.1 Canada
4.1.1.1.4.2 United States
4.1.1.1.5 Oceania
4.1.1.1.5.1 Australia
4.1.1.1.5.2 New Zealand
4.1.1.1.6 Latin America
4.1.1.1.6.1 Argentina
4.1.1.1.6.2 Chile
4.1.1.1.6.3 Columbia
4.1.1.1.6.4 Costa Rica
4.1.1.1.6.5 Cuba
4.1.1.1.6.6 Mexico
4.1.1.1.6.7 NIcaragua
4.1.1.1.6.8 Peru
4.1.1.1.6.9 Uruguay
4.1.1.2 Associate participants
4.1.1.2.1 ACB
4.1.1.2.2 ARCOS
4.1.1.2.3 BGCI
4.1.1.2.4 BioNet-ANDINONET
4.1.1.2.5 BioNet-ASEANET
4.1.1.2.6 BioNet-EASIANET
4.1.1.2.7 BioNet-INTERNATIONAL
4.1.1.2.8 BioNet-SAFRINET
4.1.1.2.9 Bioversity International
4.1.1.2.10 CABI BioScience
4.1.1.2.11 CBOL
4.1.1.2.12 ICIMOD
4.1.1.2.13 ICIPE
4.1.1.2.14 ICLEI
4.1.1.2.15 ICZN
4.1.1.2.16 ILTER
4.1.1.2.17 ISIS
4.1.1.2.18 ITIS
4.1.1.2.19 MSEF
4.1.1.2.20 NatureServe
4.1.1.2.21 Nordgen
4.1.1.2.22 NSCA
4.1.1.2.23 CETAF
4.1.1.2.24 Chinese Taipei
4.1.1.2.25 CYTED
4.1.1.2.26 Discover Life
4.1.1.2.27 Diversitas
4.1.1.2.28 EEA
4.1.1.2.29 EoL
4.1.1.2.30 ETI Bioinformatics
4.1.1.2.31 EWT
4.1.1.2.32 Finding Species
4.1.1.2.33 OBIS
4.1.1.2.34 PBIF
4.1.1.2.35 SCAR
4.1.1.2.36 SINEPAD
4.1.1.2.37 SMEBD
4.1.1.2.38 Species2000
4.1.1.2.39 SPNHC
4.1.1.2.40 TDWG
4.1.1.2.41 UNEP-WCMC
4.1.1.2.42 WDCBE
4.1.1.2.43 FreshwaterLife
4.1.1.2.44 IABIN
4.1.1.2.45 iBOL
4.1.1.2.46 WFCC
4.1.1.2.47 Wildscreen
4.1.2 Exterior initiatives
4.2 NPT-AG
4.2.1 Anne Mette Nielsen
4.2.2 Bruno Danis
4.2.3 Burke Chih-Jen Ko
4.2.4 Cees Hof
4.2.5 David Remsen
4.2.6 Douglas Hyde
4.2.7 Francisco Pando
4.2.8 Guy Baillargeon
4.2.9 Katja Christensen
4.2.10 Maria Auxiliadora Mora
4.2.11 Mélianie Raymond
4.2.12 Mihail-Constantin Carausu
4.2.13 Nabil Youdjou
4.2.14 Nicolas Noé
4.2.15 Peter Desmet
4.2.16 Steve Wilkinson
4.2.17 Tim Robertson
4.2.18 Wouter Addink
4.3 NPT-TTF
4.3.1 André Heughebaert
4.3.2 Ben Donnelly
4.3.3 Bruno Danis
4.3.4 Burke Chih-Jen Ko
4.3.5 David Remsen
4.3.6 Ei Fujioka
4.3.7 Julien Cigar
4.3.8 Mihail-Constantin Carausu
4.3.9 Nabil Youdjou
4.3.10 Nicolas Noé
4.3.11 Peter Desmet
4.3.12 Simon Rycroft
4.3.13 Sylvain Renaudier
4.3.14 Tim Robertson
4.3.15 Vincent Smith
4.4 Testers
4.5 Developers
4.6 GBIF-Secretariat
5 Constraints
5.1 Time
5.2 Community feedback
5.3 (Fast) Ongoing developments
5.4 High Demand/Expectations
5.5 Developing on real Demands, not Assumptions!
5.6 Does a one size fits all approach work
6 Scoping
6.1 Users
6.1.1 Toolkit (back end) SysAdmin

Minimal competence level: Install and configure Apache webserver Install and maintain DB Answer issues from manager

6.1.2 NPT (backend) Manager

Competence Web-based content management

6.1.3 Deployed portal (front-end) Users
6.1.3.1 data providers
6.1.3.2 scientists
6.1.3.3 general user
6.1.4 Primary Users
6.1.5 Secondary Users
6.2 General requirements
6.2.1 Free & Open source solutions
6.2.2 Multi-platform

at least Win and Linux (last one preferred)

6.2.3 Compliant with the GBIF Informatics Infrastructure / Architecture

Implies good communication between GBIFS and NPT stakeholders

6.2.4 Data consistency between NPT instances and GBIF
6.2.5 Open collaborative development and code maintenance
6.2.6 Modular
6.2.7 Extensible
6.2.8 Multilingual
6.2.9 Documented

Needed to get developers involved

6.2.10 Community driven
6.2.11 Configurable
6.2.12 Robust

Software, standards and documentation

6.2.13 Capability to efficiently track portal usage statistics
6.2.14 Intuitive and friendly end-user interface
6.2.15 Discoverable through search engines
6.2.16 Simple

to use and maintain

6.2.17 Availability of API

Defined as providing access to NPT functions for future development by partners. Code accessible from the outside, engaging key partners providing access to specific services or functionality. goes two ways: consuming services or publishing them.

6.2.18 Sustainability embedded at each stage of development

easy to maintain, host and maintain; fully adoption of a common framework

6.3 Interfaces and functionalities
6.3.1 Backend
6.3.1.1 SysAdmin level
6.3.1.1.1 Download components and updates

components include documentation on issue tracking (google code site)

6.3.1.1.2 Install and configure components
6.3.1.2 Manager level
6.3.1.2.1 Choose Language
6.3.1.2.2 Customize look and feel
6.3.1.2.2.1 Name of the NPT instance
6.3.1.2.2.2 Show/hide metrics

statistics data usage

6.3.1.2.2.3 Logo
6.3.1.2.3 Check data consistency

Consistency between local and global (GBIF) index

6.3.1.2.4 Portal configuration
6.3.1.2.4.1 Select and upload contextual data sources

Possibility to harvest data from GBIF OR/AND other data sources

6.3.1.2.4.1.1 GBIF index
6.3.1.2.4.1.2 Other data providers
6.3.1.2.4.2 Select and upload data types

Based on DwC.

6.3.1.2.4.2.1 Taxonomy

functionality should be there, even if there is no unique taxonomic provider

6.3.1.2.4.2.2 Species lists
6.3.1.2.4.2.3 Occurrence
6.3.1.2.4.2.4 Metadata
6.3.1.2.4.2.5 Data metrics
6.3.1.2.4.2.6 Institutions
6.3.1.2.4.2.7 Spatial data

countries boudaries, EEZ, blablabla

6.3.1.2.4.2.8 Multimedia
6.3.1.2.4.2.9 Attributes

"endemic", "benthic", "endangered"

6.3.1.2.4.2.10 Experts
6.3.1.2.4.2.11 Annotations
6.3.1.2.4.2.12 Literature
6.3.1.2.4.2.13 Identification Aids
6.3.1.2.4.2.14 DNA
6.3.1.2.4.3 Manage portal features

should be considered at the beginning of designed phase

6.3.1.2.5 User management
6.3.1.2.5.1 Permission control

possibility to delegate management work

6.3.1.2.5.1.1 User
6.3.1.2.5.1.2 Admin
6.3.1.2.6 Configure Harvesting Jobs schedules

The NPT manager is able to schedule the data harvesting jobs. He's big enough to do this manually.

6.3.2 FrontEnd
6.3.2.1 Discovery and access of biodiversity data
6.3.2.1.1 Taxonomic search

Google-type "intelligent" search: box in which anything can be searched from a single text field Output grouped by eg data types (to be refined) restrict to Taxonomy, DwC and GBIF-metadata profile fields Search all textual content

6.3.2.1.1.1 Possibility to search across all resources
6.3.2.1.1.2 Autocompletion

acts like an extra filter

6.3.2.1.2 Advanced search (Filters)

Fit for complex queries on taxonomy, DwC + GBIF metadata profile content transport GBIF functionalities re-advanced search

6.3.2.1.3 Geospatial exploration (MapView)

simple GIS interface to search and browse data include contextual autocomplete

6.3.2.1.3.1 Interactive Map
6.3.2.1.3.1.1 Select Data types

Occurrence, Checklists, Metadata

6.3.2.1.3.1.2 Select and apply Filters

List is not exhaustive

6.3.2.1.3.1.2.1 Select Bounding box
6.3.2.1.3.1.2.2 Select Boundaries

countries, blablbal

6.3.2.1.3.1.2.3 Available geospatial data

documented (metadata) spatialized data added to geoserver examples: environmental data, topography, ecoregions,...

6.3.2.1.3.1.2.4 Datasets
6.3.2.1.3.1.2.5 Draw a polygon
6.3.2.1.3.1.3 Visualization of results
6.3.2.1.3.2 Export in different formats

same as GBIF portal: selected no limitation in size

6.3.2.1.3.3 Search field
6.3.2.1.3.4 Flip to Treeview

see GBIF protected areas widget

6.3.2.1.4 Taxonomic exploration (TreeView)

Possibility to explore all hierarchized resources

6.3.2.1.4.1 Browse Tree
6.3.2.1.4.2 Display Results
6.3.2.1.4.3 Export in different formats

same as GBIF portal: selected no limitation in size

6.3.2.1.4.4 Search field
6.3.2.1.5 Web 2.0 user experience
6.3.2.1.5.1 User personalised channels to discover & access content
6.3.2.1.5.1.1 RSS feeds on user-defined content
6.3.2.1.5.1.2 MyGBIF

personal space to store recent searches and customized content, eg using pre-defined queries. also keeps the user informed on news in his area of interest. thematic portal inside a portal

6.3.2.1.5.1.3 Sharing through Social networks
6.3.2.1.6 View and Export Search results

same as GBIF portal: selected no limitation in size

6.3.2.2 Usage metrics
6.3.2.2.1 Overview dashboard
6.3.2.2.1.1 Detailed stats

Access to raw data

6.3.2.3 Network information
6.3.2.3.1 Network summary information

Dashboard page

6.3.2.3.1.1 Network governance, structure and topology
6.3.2.3.1.2 Overview of data published
6.3.2.3.2 Data publishers profiles and statistics
6.3.2.3.3 Directories of institutions & experts
6.3.2.4 Feedback Button

Mails to NPT manager. he decides how to deal with request.

6.3.2.5 Choose Language

The end user is able to toggle between the different languages in wich the NPT webportal is made available.

6.3.2.6 Discovery and access of tools & services
6.3.2.6.1 APIs store (NPT compatible)
6.3.2.6.2 Data quality and annotation tools

This is a role for the IPT: data should be cleaned before it gets in the global index

6.3.2.7 Content contribution
6.3.2.7.1 Annotations to metadata?
6.3.2.7.2 Annotations to records?
6.4 Recommendations
6.5 Development
6.5.1 Framework
6.5.1.1 PHP/MySQL/Apache
6.5.2 APIs
6.5.3 Data flows - architecture
6.5.3.1 Access to data relevant for a Participant BIF but published by others
6.5.3.1.1 Webservices providing access to full DwC 1.4 elements
6.5.4 Maintained site for contributors
7 Software requirements
7.1 Use-case model Survey
7.1.1 Backend Users
7.1.1.1 Administrator
7.1.1.1.1 Topic
7.1.1.2 Security Officer
7.1.1.2.1 Topic
7.1.1.3 Data manager
7.1.1.3.1 Topic
7.1.1.3.2 Topic
7.1.1.3.3 Topic
7.1.1.4 Portal manager
7.1.1.4.1 Topic
7.1.2 Frontend Users
7.1.2.1 Visitor
7.1.2.1.1 Topic
7.1.2.1.2 Topic
7.1.2.2 Registered Visitor
7.1.2.2.1 Topic
7.2 Actors Survey
7.2.1 Primary Actors
7.2.1.1 Back office users
7.2.1.1.1 Administrators
7.2.1.1.2 Security Officers
7.2.1.1.3 Data managers
7.2.1.1.4 Portal managers
7.2.1.2 Frontend Users
7.2.1.2.1 Visitors
7.2.1.2.2 Registered visitors
7.2.2 Secondary Actors
7.2.2.1 GBIF registry
7.2.2.2 Data sources
7.2.2.2.1 GBIF webservices
7.2.2.2.2 IPT instances
7.3 Functional Requirements
7.3.1 Backend functionalities
7.3.1.1 Administator
7.3.1.2 Security officer
7.3.1.3 Data manager
7.3.1.4 Portal manager
7.3.2 Front end functionalities
7.3.2.1 Visitor
7.3.2.2 Registered Visitor
7.4 Non-Functional Requirements
7.4.1 Security Requirements
7.4.2 Capacity Requirements
7.4.3 Robustness Requirements
7.4.4 Interoperability Requirements
7.4.5 Operating Environment
7.4.6 Usability Requirements
7.4.7 Performance Requirements
7.4.8 Supportability Requirements
7.4.9 User Documentation Requirements
7.4.10 Design and implementation constraints
7.5 Interfaces
7.5.1 User interfaces
7.5.1.1 Pagination
7.5.1.2 Distribution map
7.5.1.3 Filter building interface
7.5.2 Hardware interfaces
7.5.3 Software interfaces
7.5.3.1 API
7.5.3.2 GBIF IPT
7.5.3.3 GBIF Webservices
7.5.3.4 GBIF Registry
7.5.3.5 Communications interface
7.5.4 Licencing agreements
7.6 Use Cases
7.6.1 Backend use cases
7.6.1.1 Administrator
7.6.1.2 Security officer
7.6.1.3 Data manager
7.6.1.4 Portal manager
7.6.2 Frontend use cases
7.6.2.1 Visitor
7.6.2.2 Registered Visitor
7.7 Business rules
8 Implementation
8.1 FAST WEBPRESENCE (NPT1)
8.1.1 Technologies
8.1.1.1 Drupal 7
8.1.1.1.1 Native modules
8.1.1.1.1.1 Core
8.1.1.1.1.2 Coder
8.1.1.1.1.3 Watchdog
8.1.1.1.1.4 Permissions
8.1.1.1.1.5 Internationalization
8.1.1.1.1.6 Custom Content Type
8.1.1.1.2 Scratchpads 1 modules
8.1.1.1.2.1 Left and Right
8.1.1.1.2.2 Backup
8.1.1.1.2.3 Feeds
8.1.1.1.2.4 Species Page
8.1.1.1.2.5 Apache/SoLR
8.1.1.1.3 Scratchpads 2 modules
8.1.1.1.3.1 DwC-A export
8.1.1.1.3.2 DwC-A import
8.1.1.1.3.3 Checklist export
8.1.1.1.4 NPT1 Custom modules
8.1.1.1.4.1 Occurrence records export
8.1.1.1.4.2 Audubon core format for multimedia files
8.1.1.1.4.3 GBIF Theming
8.1.1.1.4.4 Costum feeds
8.1.1.1.5 Sites maintenance
8.1.1.1.5.1 Aegir

Aegir is a set of Drupal modules that helps you maintain your Drupal sites.

8.1.2 Requirements
8.1.2.1 Functional
8.1.2.1.1 Backend functionalities
8.1.2.1.1.1 Administrator
8.1.2.1.1.1.1 UC-A1 - Manage modules
8.1.2.1.1.1.2 FR - A9 - View error logs
8.1.2.1.1.2 Security Officer
8.1.2.1.1.2.1 UC - S01 - Manage user accounts
8.1.2.1.1.2.2 FR - S06 - View audit logs
8.1.2.1.1.3 Data manager
8.1.2.1.1.3.1 FR - DM9 - Import multimedia
8.1.2.1.1.3.2 FR - DM11 - Edit multimedia metadata
8.1.2.1.1.3.3 FR - DM12 - Search multimedia resources by keyword
8.1.2.1.1.3.4 UC - DM9 - Backup portal data
8.1.2.1.1.3.5 UC - DM11 - Update taxonomic backbone
8.1.2.1.1.3.6 UC-DM12 - Install an extension
8.1.2.1.1.4 Portal manager
8.1.2.1.1.4.1 UC - PM1 - Configure visibility of data metrics
8.1.2.1.1.4.2 UC - PM3 - Customize NPT instance
8.1.2.1.1.4.3 Configure contact information
8.1.2.1.1.4.4 Manage languages
8.1.2.1.1.4.5 Manage news entries
8.1.2.1.1.4.6 Manage blog entries
8.1.2.1.1.4.7 Configure pages
8.1.2.1.2 Front-end functionalities
8.1.2.1.2.1 Visitor
8.1.2.1.2.1.1 UC - V1 - Send feedback to portal contact person
8.1.2.1.2.1.2 UC - V2 - View the distribution map
8.1.2.1.2.1.3 UC- V5 - Export distribution map as image
8.1.2.1.2.1.4 UC - V6 - Search portal using full text
8.1.2.1.2.1.5 UC - V8 - Export a checklist
8.1.2.1.2.1.6 UC - V9 - Choose language
8.1.2.1.2.1.7 FR - V38 - View data metrics
8.1.2.2 Non-functional
8.1.2.2.1 Security Requirements
8.1.2.2.1.1 SR1 - The system shall retain an audit log for all successful back end operations.
8.1.2.2.1.2 SR2 - The system shall restrict access to all functionalities altering data to data managers (BR4)
8.1.2.2.1.3 SR3 - The system shall restrict access to user management to security officers (BR3)
8.1.2.2.1.4 SR4 - The system shall restrict access to module management and distribution map configuration to administrators (BR6)
8.1.2.2.1.5 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)
8.1.2.2.2 Robustness Requirements
8.1.2.2.2.1 RR2 - The system should perform reasonably under important workload (queries and data discovery)
8.1.2.2.2.2 RR3 - Any errors should be trapped and not seen by users
8.1.2.2.2.3 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
8.1.2.2.3 Interoperability Requirements
8.1.2.2.3.1 IR1 - The system shall allow importing checklist resources DwC-A files
8.1.2.2.3.2 IR8 - The system shall allow exporting occurrences records as images
8.1.2.2.3.3 IR10 - The system shall allow using the Audubon Core format for multimedia metadata
8.1.2.2.4 Operating Environment
8.1.2.2.4.1 OE1 - The system shall operate with the two latest major releases of the following Web browsers: Firefox, Opera, Chrome, Internet Explorer and Safari
8.1.2.2.4.2 OE2 - The system shall operate on a server running Linux, Windows server or Mac OS
8.1.2.2.5 Usability Requirements
8.1.2.2.5.1 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
8.1.2.2.5.2 UR4 - The system shall allow a visitor to select the language used on the front end
8.1.2.2.6 Supportability Requirements
8.1.2.2.6.1 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.
8.1.2.2.7 User Documentation Requirements
8.1.2.2.7.1 UD2 - Three installation guides with step-by-step instructions shall be provided (one for each of the OS the system can operate on)
8.1.2.2.7.2 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
8.1.2.2.8 Design and implementation constraints
8.1.2.2.8.1 CO1 - The system should be implemented using open-source technologies
8.1.2.2.8.2 CO2 - The system shall be written in PHP
8.1.2.2.8.3 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
8.1.2.2.8.4 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).
8.1.2.2.8.5 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.
8.1.3 Workflow
8.1.4 Do-ers
8.1.4.1 Scratchpads Team
8.1.4.2 NPT Developer
8.1.4.3 GBIF-S
8.1.5 Hosting
8.1.5.1 Developement phase: NHM
8.1.5.2 Production phase: GBIF-S
8.1.6 TASKS
8.1.6.1 Determine the GBIF APi specifications for NPTV1
8.1.6.2 Validation, coding, testing and integration of modules
8.1.6.3 Setup a mockup site with theming
8.1.6.4 Development of NPT setup and editing workflow
8.1.6.5 Testing phase, including a small group of testers
8.1.6.6 Scratchpads NPT Profile definition

technical instructions to deploy the content and parameters of the NPT instances

8.1.6.7 Implementation of the NPT

setup on the production server, including Aegir setup

8.1.6.8 Testing phase with standard testing procedure
8.1.7 Overall Architecture
8.1.7.1 NPT1 High-level Architecture
8.2 NPT1+SOPHISTICATED GEOSPATIAL TOOLS (NPT2)
8.2.1 Technologies
8.2.1.1 Scenario 1
8.2.1.1.1 Drupal 7
8.2.1.1.1.1 Native modules
8.2.1.1.1.1.1 Core
8.2.1.1.1.1.2 Coder
8.2.1.1.1.1.3 Watchdog
8.2.1.1.1.1.4 Permissions
8.2.1.1.1.1.5 Internationalization
8.2.1.1.1.1.6 Custom Content Type
8.2.1.1.1.2 Scratchpads 1 modules
8.2.1.1.1.2.1 Left and Right
8.2.1.1.1.2.2 Backup
8.2.1.1.1.2.3 Feeds
8.2.1.1.1.2.4 Species Page
8.2.1.1.1.2.5 Apache/SoLR
8.2.1.1.1.3 Scratchpads 2 modules
8.2.1.1.1.3.1 DwC-A import
8.2.1.1.1.3.2 Checklist export
8.2.1.1.1.4 NPT1 Custom modules
8.2.1.1.1.4.1 Occurrence records export
8.2.1.1.1.4.2 Audubon core format for multimedia files
8.2.1.1.1.4.3 GBIF Theming
8.2.1.1.1.4.4 Costum feeds
8.2.1.1.1.5 NPT2 Custom modules
8.2.1.1.1.5.1 DwC-A export
8.2.1.1.1.5.2 EML profiling
8.2.1.1.1.5.3 Data sources configuration
8.2.1.1.1.5.4 Occurrence Data view
8.2.1.1.1.5.5 Filters building
8.2.1.1.1.6 Sites maintenance
8.2.1.1.1.6.1 Aegir

Aegir is a set of Drupal modules that helps you maintain your Drupal sites.

8.2.1.1.2 GeoSpatial component
8.2.1.1.2.1 Search Interface
8.2.1.1.2.1.1 OpenLayers
8.2.1.1.2.1.2 EXTJS
8.2.1.1.2.1.3 Javascript
8.2.1.1.2.1.4 PHP
8.2.1.1.2.2 Mapping Engine
8.2.1.1.2.2.1 Geoserver
8.2.1.1.2.2.1.1 Mapping configuration
8.2.1.1.2.2.1.2 Additional Spatial layer
8.2.1.1.2.3 Geo Database
8.2.1.1.2.3.1 PostGres
8.2.1.1.2.3.2 PostGIS
8.2.1.2 Scenario 2
8.2.1.2.1 Drupal 7
8.2.1.2.1.1 Native modules
8.2.1.2.1.1.1 Core
8.2.1.2.1.1.2 Coder
8.2.1.2.1.1.3 Watchdog
8.2.1.2.1.1.4 Permissions
8.2.1.2.1.1.5 Internationalization
8.2.1.2.1.1.6 Custom Content Type
8.2.1.2.1.2 Scratchpads 1 modules
8.2.1.2.1.2.1 Left and Right
8.2.1.2.1.2.2 Backup
8.2.1.2.1.2.3 Feeds
8.2.1.2.1.2.4 Species Page
8.2.1.2.1.2.5 Apache/SoLR
8.2.1.2.1.3 Scratchpads 2 modules
8.2.1.2.1.3.1 DwC-A import
8.2.1.2.1.3.2 Checklist export
8.2.1.2.1.4 NPT1 Custom modules
8.2.1.2.1.4.1 Occurrence records export
8.2.1.2.1.4.2 Audubon core format for multimedia files
8.2.1.2.1.4.3 GBIF Theming
8.2.1.2.1.4.4 Costum feeds
8.2.1.2.1.5 NPT2 Custom modules
8.2.1.2.1.5.1 DwC-A export
8.2.1.2.1.5.2 EML profiling
8.2.1.2.1.5.3 Data sources configuration
8.2.1.2.1.5.4 Occurrence Data view
8.2.1.2.1.5.5 Filters building
8.2.1.2.1.6 Mapping Kit
8.2.1.2.1.6.1 Map client
8.2.1.2.1.6.2 OpenLayers map client
8.2.1.2.1.6.3 Flash map client
8.2.1.2.1.6.4 Java map client
8.2.1.2.1.6.5 Map assist
8.2.1.2.1.6.6 Map context
8.2.1.2.1.6.7 WMS
8.2.1.2.1.6.8 Map layer
8.2.1.2.1.6.9 Map to pdf
8.2.1.2.1.6.10 Geodata
8.2.1.2.1.6.11 Mapserver
8.2.1.2.1.7 Sites maintenance
8.2.1.2.1.7.1 Aegir

Aegir is a set of Drupal modules that helps you maintain your Drupal sites.

8.2.2 Do-ers
8.2.2.1 Scratchpads Team
8.2.2.2 MGEL Team
8.2.2.3 NPT Developer
8.2.2.4 GBIF-S
8.2.3 Requirements
8.2.3.1 NPT1
8.2.3.1.1 Functional
8.2.3.1.1.1 Backend functionalities
8.2.3.1.1.1.1 Administrator
8.2.3.1.1.1.1.1 UC-A1 - Manage modules
8.2.3.1.1.1.1.2 FR - A9 - View error logs
8.2.3.1.1.1.2 Security Officer
8.2.3.1.1.1.2.1 UC - S01 - Manage user accounts
8.2.3.1.1.1.2.2 FR - S06 - View audit logs
8.2.3.1.1.1.3 Data manager
8.2.3.1.1.1.3.1 FR - DM9 - Import multimedia
8.2.3.1.1.1.3.2 FR - DM11 - Edit multimedia metadata
8.2.3.1.1.1.3.3 FR - DM12 - Search multimedia resources by keyword
8.2.3.1.1.1.3.4 UC - DM9 - Backup portal data
8.2.3.1.1.1.3.5 UC - DM11 - Update taxonomic backbone
8.2.3.1.1.1.3.6 UC-DM12 - Install an extension
8.2.3.1.1.1.4 Portal manager
8.2.3.1.1.1.4.1 UC - PM1 - Configure visibility of data metrics
8.2.3.1.1.1.4.2 UC - PM3 - Customize NPT instance
8.2.3.1.1.1.4.3 Configure contact information
8.2.3.1.1.1.4.4 Manage languages
8.2.3.1.1.1.4.5 Manage news entries
8.2.3.1.1.1.4.6 Manage blog entries
8.2.3.1.1.1.4.7 Configure pages
8.2.3.1.1.2 Front-end functionalities
8.2.3.1.1.2.1 Visitor
8.2.3.1.1.2.1.1 UC - V1 - Send feedback to portal contact person
8.2.3.1.1.2.1.2 UC - V2 - View the distribution map
8.2.3.1.1.2.1.3 UC- V5 - Export distribution map as image
8.2.3.1.1.2.1.4 UC - V6 - Search portal using full text
8.2.3.1.1.2.1.5 UC - V8 - Export a checklist
8.2.3.1.1.2.1.6 UC - V9 - Choose language
8.2.3.1.1.2.1.7 FR - V38 - View data metrics
8.2.3.1.2 Non-functional
8.2.3.1.2.1 Security Requirements
8.2.3.1.2.1.1 SR1 - The system shall retain an audit log for all successful back end operations.
8.2.3.1.2.1.2 SR2 - The system shall restrict access to all functionalities altering data to data managers (BR4)
8.2.3.1.2.1.3 SR3 - The system shall restrict access to user management to security officers (BR3)
8.2.3.1.2.1.4 SR4 - The system shall restrict access to module management and distribution map configuration to administrators (BR6)
8.2.3.1.2.1.5 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)
8.2.3.1.2.2 Robustness Requirements
8.2.3.1.2.2.1 RR2 - The system should perform reasonably under important workload (queries and data discovery)
8.2.3.1.2.2.2 RR3 - Any errors should be trapped and not seen by users
8.2.3.1.2.2.3 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
8.2.3.1.2.3 Interoperability Requirements
8.2.3.1.2.3.1 IR1 - The system shall allow importing checklist resources DwC-A files
8.2.3.1.2.3.2 IR8 - The system shall allow exporting occurrences records as images
8.2.3.1.2.3.3 IR10 - The system shall allow using the Audubon Core format for multimedia metadata
8.2.3.1.2.4 Operating Environment
8.2.3.1.2.4.1 OE1 - The system shall operate with the two latest major releases of the following Web browsers: Firefox, Opera, Chrome, Internet Explorer and Safari
8.2.3.1.2.4.2 OE2 - The system shall operate on a server running Linux, Windows server or Mac OS
8.2.3.1.2.5 Usability Requirements
8.2.3.1.2.5.1 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
8.2.3.1.2.5.2 UR4 - The system shall allow a visitor to select the language used on the front end
8.2.3.1.2.6 Supportability Requirements
8.2.3.1.2.6.1 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.
8.2.3.1.2.7 User Documentation Requirements
8.2.3.1.2.7.1 UD2 - Three installation guides with step-by-step instructions shall be provided (one for each of the OS the system can operate on)
8.2.3.1.2.7.2 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
8.2.3.1.2.8 Design and implementation constraints
8.2.3.1.2.8.1 CO1 - The system should be implemented using open-source technologies
8.2.3.1.2.8.2 CO2 - The system shall be written in PHP
8.2.3.1.2.8.3 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
8.2.3.1.2.8.4 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).
8.2.3.1.2.8.5 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.
8.2.3.2 NPT2
8.2.3.2.1 Functional
8.2.3.2.1.1 Backend functionalities
8.2.3.2.1.1.1 Administrator
8.2.3.2.1.1.1.1 UC-A1 - Manage modules
8.2.3.2.1.1.1.2 FR - A9 - View error logs
8.2.3.2.1.1.2 Security Officer
8.2.3.2.1.1.2.1 UC - S01 - Manage user accounts
8.2.3.2.1.1.2.2 FR - S06 - View audit logs
8.2.3.2.1.1.3 Data manager
8.2.3.2.1.1.3.1 FR - DM9 - Import multimedia
8.2.3.2.1.1.3.2 FR - DM11 - Edit multimedia metadata
8.2.3.2.1.1.3.3 FR - DM12 - Search multimedia resources by keyword
8.2.3.2.1.1.3.4 UC - DM9 - Backup portal data
8.2.3.2.1.1.3.5 UC - DM11 - Update taxonomic backbone
8.2.3.2.1.1.3.6 UC-DM12 - Install an extension
8.2.3.2.1.1.4 Portal manager
8.2.3.2.1.1.4.1 UC - PM1 - Configure visibility of data metrics
8.2.3.2.1.1.4.2 UC - PM3 - Customize NPT instance
8.2.3.2.1.1.4.3 Configure contact information
8.2.3.2.1.1.4.4 Manage languages
8.2.3.2.1.1.4.5 Manage news entries
8.2.3.2.1.1.4.6 Manage blog entries
8.2.3.2.1.1.4.7 Configure pages
8.2.3.2.1.2 Front-end functionalities
8.2.3.2.1.2.1 Visitor
8.2.3.2.1.2.1.1 UC - V1 - Send feedback to portal contact person
8.2.3.2.1.2.1.2 UC - V2 - View the distribution map
8.2.3.2.1.2.1.3 UC- V5 - Export distribution map as image
8.2.3.2.1.2.1.4 UC - V6 - Search portal using full text
8.2.3.2.1.2.1.5 UC - V8 - Export a checklist
8.2.3.2.1.2.1.6 UC - V9 - Choose language
8.2.3.2.1.2.1.7 FR - V38 - View data metrics
8.2.3.2.1.2.2 Registered Visitor
8.2.3.2.2 Non-functional
8.2.3.2.2.1 Security Requirements
8.2.3.2.2.1.1 SR1 - The system shall retain an audit log for all successful back end operations.
8.2.3.2.2.1.2 SR2 - The system shall restrict access to all functionalities altering data to data managers (BR4)
8.2.3.2.2.1.3 SR3 - The system shall restrict access to user management to security officers (BR3)
8.2.3.2.2.1.4 SR4 - The system shall restrict access to module management and distribution map configuration to administrators (BR6)
8.2.3.2.2.1.5 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)
8.2.3.2.2.2 Robustness Requirements
8.2.3.2.2.2.1 RR2 - The system should perform reasonably under important workload (queries and data discovery)
8.2.3.2.2.2.2 RR3 - Any errors should be trapped and not seen by users
8.2.3.2.2.2.3 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
8.2.3.2.2.3 Interoperability Requirements
8.2.3.2.2.3.1 IR1 - The system shall allow importing checklist resources DwC-A files
8.2.3.2.2.3.2 IR8 - The system shall allow exporting occurrences records as images
8.2.3.2.2.3.3 IR10 - The system shall allow using the Audubon Core format for multimedia metadata
8.2.3.2.2.4 Operating Environment
8.2.3.2.2.4.1 OE1 - The system shall operate with the two latest major releases of the following Web browsers: Firefox, Opera, Chrome, Internet Explorer and Safari
8.2.3.2.2.4.2 OE2 - The system shall operate on a server running Linux, Windows server or Mac OS
8.2.3.2.2.5 Usability Requirements
8.2.3.2.2.5.1 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
8.2.3.2.2.5.2 UR4 - The system shall allow a visitor to select the language used on the front end
8.2.3.2.2.6 Supportability Requirements
8.2.3.2.2.6.1 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.
8.2.3.2.2.7 User Documentation Requirements
8.2.3.2.2.7.1 UD2 - Three installation guides with step-by-step instructions shall be provided (one for each of the OS the system can operate on)
8.2.3.2.2.7.2 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
8.2.3.2.2.8 Design and implementation constraints
8.2.3.2.2.8.1 CO1 - The system should be implemented using open-source technologies
8.2.3.2.2.8.2 CO2 - The system shall be written in PHP
8.2.3.2.2.8.3 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
8.2.3.2.2.8.4 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).
8.2.3.2.2.8.5 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.
8.2.4 Hosting
8.2.5 TASKS
8.2.6 Overall Architecture
8.2.6.1 NPT2 High-level Architecture, scenario 1
8.2.6.2 NPT2 High-level Architecture, scenario 2
8.3 NPT2+LONG-TERM VISION
8.3.1 Technology Scouting Platform
8.3.1.1 GBIF Community Site
8.3.1.2 GBIF ORC
8.3.1.3 NPT Modules
8.3.1.3.1 Drupal
8.3.1.3.2 OpenGeo
8.3.2 Capacity Building