After attempting to create a biodiversity informatics Drupal group, and being unceremoniously rejected (fair play this bioinformatics group does mention biodiversity in it's mission statement), I am hijacking or contributing (whichever way you would like to look at it), to invite users to join the bioinformatics Drupal group to discuss the development of biodiversity tools in Drupal. I won't go so far as to change the mission statement, but group founders please feel free to embrace us if this takes off.
There are a growing number of Drupal based sites that are handling biodiversity data. The nature of funding in this field is such that developers are distributed across a wide number of institutions, more often than not as lone 'techies' with little support. I hope that in this group 'loners' and natural history computing departments alike will find a community of developers from which they can garner knowledge, share ideas, code and so on. I hope that we may, through a community based approach to development, take this field further, avoid the pitfalls of those before us, and start to combine our efforts to move away from the too often applicable adage of wheel reinventing.
To begin participation, a list of Drupal based sites handling biodiversity data follows, please feel free to edit, add, comment etc.
| Project | Description | Downloads |
|---|---|---|
| Bibliographic Knowledge Network (BKN) | A project to develop a suite of tools and services to encourage formation of virtual organizations in scientific communities of various types. | |
| BioGeobif | Data providers can add new Resources, download georeferenced records, and filter results through the BGB user interface. When queued, the records from Provider/Resources will be harvested, georeferenced through BioGeomancer, and formatted for return to users through password protected website. Any records with ambiguous results will be formatted such that a user can easily upload the files to the BioGeomancer website for hands-on evaluations. | |
| Bug Guide | An online community of naturalists who enjoy learning about and sharing our observations of insects, spiders, and other related creatures. | |
| CiteBank part of the Biodiversity Heritage Library. | Open access repository for biodiversity publications. | |
| Common Data Model (CDM) Data Portal provided by European Distributed Institute of Taxonomy (EDIT) | A set of four modules 'cdm_api', 'cdm_portal', 'cdm_taxontree' and 'cdm_mediauri' that enable Drupal to search, browse and display the biodiversity data hosted by a CDM (Common Data Model) driven data store. The resulting pages of this "DataPortal" partially mimic the layout of common taxonomic books. | CDM Data Portal |
| Internet Bird Collection | An on-line audiovisual library of the world's birds. | TaxiSelect |
| Islandora | Combines Drupal and Fedora open software application to create a digital asset management system. | Download |
| Indicia | An open source toolkit for building biological recording websites, with Drupal integration. | Downloads |
| iSpot provided by The Open University as part of the OPAL project, which is funded by the National Lottery through the Big Lottery Fund. | Wildlife observations, currently UK based. | |
| LepTree supported by the United States of America's National Science Foundation’s Assembling the Tree of Life program. | An international, community collaboration dedicated to advancing progress toward a phylogenetic tree for all Lepidoptera. | Source code |
| LifeDesks Sponsored by EOL | Dynamic Web environments for the online management and sharing of biodiversity research. | Modules |
| ORNIS funded by the National Science Foundation (NSF). | Provides access to natural history collections of birds and tools for data analysis and error-checking. | |
| Scratchpads (part of an EU Infrastructure proposal called VIBRANT) Sponsored by EDIT | A data publishing and social networking application that enables communities of biodiversity researchers to manage, share and publish taxonomic data online. | Modules |
| Science Collaboration Framework A project of the Initiative in Innovative Computing at Harvard University in collaboration with the Harvard Stem Cell Institute and Massachusetts General Hospital | Software toolkit to establish web-based virtual team organizations for researchers in biomedicine. | Modules Entrez Database Import |
| The Virtual Taxonomic Library (ViTaL) provided by European Distributed Institute of Taxonomy (EDIT) | To aid the discovery and accessibility of taxonomically relevant literature. | |
| Vital Signs | Environment and invasive species monitoring in Maine, USA | More info |
| Global Biodiversity Information Facility | GBIF is an international open data infrastructure, funded by governments. It allows anyone, anywhere to access data about all types of life on Earth, shared across national boundaries via the Internet. |
Non Drupal based biodiversity informatics content management systems:
| Project | Description | Downloads |
|---|---|---|
| Biofinity | A software framework that supports biodiversity and genomics research by relating data of participating labs with those of larger, public databases. | |
| Matrix (mx) | mx is a collaborative web-based content management system for evolutionary systematists, particularly those working on descriptive taxonomy. | Source code |
| India Biodiversity Portal | A unique repository of information on India's biodiversity. The Portal aims to provide open and free access to biodiversity information. | GitHub link |