European Distributed Institute of Taxonomy (EDIT) | Vince Smith

European Distributed Institute of Taxonomy (EDIT) | Vince Smith

EDIT is an EU funded Network of Excellence program with the goal of reducing the fragmentation of biological taxonomic research and coordinating an effort to facilitate taxonomic research using the World Wide Web. Within EDIT there has been much discussion about this can be achieved and I want to explain what my NHM colleagues and I have been doing as part of this project.

Good to see somebody else has been looking into these kind of things and sees the benefit of using pre-rolled CMS’s for biodiversity data.

Scratchpad Modules | EDIT WP6

Scratchpad Modules | EDIT WP6 lists the modules used for the species scratchpads. Definitely worth reading!

Distrowar – ubuntu vs. suse vs. red hat vs. fedora vs. debian

Courtesy of Google Trends

You tell me which one is Ubuntu? My guess is they’re taking over – thank goodness. Bug No 1 does seem to be in trouble tho as the overall searches for linux seem to be dropping.

_________EDIT____________________

Scrub that last comment – microsoft searches are dropping as well.

Using open source software to design, develop, and deploy a collaborative Web site, Part 1: Introduction and overview

Using open source software to design, develop, and deploy a collaborative Web site provides a good overview as to the reasons why using an OS CMS to implement a web application (and why to use Drupal).

Open Directory – Science: Biology

The Open Directory seems to know what’s going on – there are more Biology pages relating to Flora and Fauna than any other discipline.

* Flora and Fauna (12,035)
* Agriculture@ (2,390)
* Anatomy@ (44)
* Bioarchaeology@ (5)
* Biochemistry and Molecular Biology (1,266)
* Biogeochemistry@ (66)
* Bioinformatics (532)
* Biomechanics (43)
* Biophysics (78)
* Biotechnology (326)
* Botany (724)
* Cell Biology (348)
* Cryobiology (170)
* Developmental Biology (86)
* Ecology (929)
* Evolution (167)
* Exobiology@ (32)
* Food Science@ (225)
* Genetics (937)
* Genomics@ (33)
* Histology (17)
* Immunology (254)
* Medicine@ (11,224)

NBII Digital Image Library – Grasses

NBII Digital Image Library – Grasses has a library of freely available public domain images of biodiversity – not many grasses by lots of trees.

Googlemap | drupal.org

Googlemap | drupal.org More mapping – add location to nodes (specimens?) and these will be plotted on a map page

Googlemap.module integrates with the locative data added to Drupal’s native RSS feeds by location.module. Nodes in the RSS feed are plotted on a administrator-configurable map.

This module uses Google’s official mapping API (http://www.google.com/apis/maps/).

Carto – opengis web mapping | drupal.org

Carto – opengis web mapping | drupal.org – can also include google maps within widgets.

The Carto module makes the mappingwidgets framework available to nodes in Drupal. This enables the browsing of maps (available from opengis compliant web mapping services) in drupal nodes.

General functionality:

* carto filter to include mapping widgets in any drupal node
* default block for an overview map (with zoom in functionality) or a simple legend
* custom blocks can be defined using the carto filter containing any type of mappingwidget; e.g. a custom overview/legend block or a button-block.
* node type for specifying opengis web mapping services; block and RSS feeds for recently added WMS’es; ogc getmap/getcapabilities request can be done through drupal.
* RSS feeds for recent maps (per user or overall)

Additional info:

Mapbuilder | drupal.org

Mapbuilder | drupal.org – could be used to produce customised distribution maps

The Mapbuilder module integrates the Community Mapbuilder web mapping client with Drupal.

It adds the Mapbuilder context and configuration as content types and can produce the corresponding xml output to be used as input to a Mapbuilder client.
A filter is added for showing Mapbuilder clients inline.

Further developments are being done on the 5.x version of this module. Differences in functionality between the releases:
* support for xml schema for mapbuilder context: ViewContext or OWSContext

Services | drupal.org

Services | drupal.org may be a dream come true – integrate with existing web services – the sky is the limit.

The services module package was created out of a need for a standardized solution of integrating external applications with Drupal, specifically Flash and Flex applications.

Note: XMLRPC server support is included in this package. To enable AMF support for Flash and Flex, you must download and install the AMFPHP server module in addition to this module.

**More information and documentation coming soon!
Features:

* service browser
* manage api keys
* services are defined in modules using the service api
* servers such as XMLRPC and AMFPHP are defined in modules using the server api

Service modules included:

* node service
* user service
* taxonomy service
* system service
* views service

Server modules included:

* xmlrpc server

Sql authentication | drupal.org

Sql authentication is potentially useful to connect to external databases and retrieve records. Could be useful for connecting to the monocot checklist and herbarium catalogue – I’d much rather connect to these using an API though.

SQL authentication is a module that uses the external authentication methods in Drupal to connect to any other database.

Whether that is a PHPbb MySQL database, or another drupal site in postgresql does not really matter. It is fully configurable and easy to use. Multiple hashing algorythms are supported too, configurable in the settings interface.

Its user-end system is similar to the drupalID, with one difference: your data will not go unencrypted over the big bad web.

GrassBase Updated

The World Grass Species database has been updated with a number of very important changes. With this new name we hope to become a central resource for Agrostologists worldwide.

New Name

The database has been christened GrassBase following the trend of a number of other web projects.

New Descriptions

Just over 150 new descriptions have been incorporated into the database, including their associated nomenclature (which can be found in the updated synonymy database). This brings our total number of species with descriptions to 10,982. If you feel we are missing any data please don’t hesitate to inform us. If you have an earlier version of the nomenclature database please download it again as the links will be out of date.

New Search Page

We have finally updated our search page and it is now much faster. In addition you can add GrassBase to your personal Google Homepage to quickly search our data.

Generic Descriptions

We have successfully generated descriptions for all grass genera from our species descriptions using Delta’s built in abilities to summarise individual taxon descriptions.

New Links

Each description page (species and genera) has been enhanced with the provisions of links that will search a number of different internet resources, including searching for specimens on Kew’s Herbarium Catalogue and electronic Plant Information Centre or ePIC. Many of the specimens within the Herbarium Catalogue are type specimens and have been scanned at high resolution which will help with your identification process. Additional links are also provided to GBIF (the Global Biodiversity Information Facility) , w3 TROPICOS and Google. These links will help to streamline your data gathering process, giving you more time to focus on what’s important to you.

Ubuntu Studio – Let your Creativity Fly

OOh – this’ll get those creative juices flowing!
Ubuntu Studio – Let your Creativity Fly
Coming this April…

Ubuntu Studio. A multimedia creation derivative of Ubuntu.

Ubuntu Studio is aimed at the linux audio, video and graphic enthusiast as well as professional.

Upload previews | drupal.org

Upload previews | drupal.org

Adds image preview thumbnails to the file attachment section on node editing pages. That way, users can see what image they are dealing with instead of guessing it from the file name. To prevent ultra wide tables, a file is now spread over two lines with the first displaying the image and the filename and the second one containing the checkboxes for deletion and listing, as well as the file size information.

XML Sitemap (formerly Google Sitemap) | drupal.org

XML Sitemap (formerly Google Sitemap) will enable google to see GrassBase’s contents.

The XML Sitemap module creates a XML sitemap in accordance with the Sitemaps.org specification.

The module maintains a short change history for nodes in order to better approximate the change frequency. It calculates the relative priority of each node based on node type, number of comments, and promotion. It can optionally submit your sitemap to Google (support for other search engines will be added once they support the ping interface) whenever it is changed and can log when your sitemap is downloaded by a search engine.

This module was originally written as a part of the Google Summer of Code program.

Pathauto | drupal.org

Pathauto will generate nice clean urls that help with site navigation. The Category module has a category_pathauto module that becomes available when pathauto is installed, which will enable sensible link creation.

The pathauto module automatically generates path aliases for various kinds of content (nodes, categories, users) when no explicit alias is provided by the user.

Discussion group: Stay up to date on Pathauto Development and provide insight by subscribing to the Paths Group on Groups.Drupal

Version Compatability Note: You must use the version of Pathauto that corresponds to your Drupal installation (e.g. 4.6, 4.7, etc.) Pathauto currently has three branches that are being maintained to varying degrees.

* Pathauto for 4.6 will get “bug fixes” if it’s a really critical bug.
* Pathauto for 4.7 still gets bug fixes.
* Pathauto 5.x is mostly updated for Drupal5.0. You can follow and assist with 5.0 updating in the Issue Queue. The 5.x version is also the home to any feature development or changes in functionality, so it may break your site.

Markdown with SmartyPants | drupal.org

Markdown with SmartyPants will be useful to write easy to format page text. Insert links with [[square brackets]]

The Markdown with SmartyPants module allows you to enter content using Markdown, a simple, plain text syntax that is filtered into valid XHTML, and will automatically convert plain ASCII characters to their proper Unicode entities in context (“curly quotes,” et al.) using SmartyPants.

Existing import / export modules in Drupal contrib

Jeremy Epstein has developed an Import/Export API for drupal. In doing so he has also documented JExisting import / export modules in Drupal contrib

Import / Export API | drupal.org

Import / Export API | drupal.org
Very useful for importing/exporting species description. Still in beta mode, but will hopefully work.

The import / export API allows for the definition of data entities within Drupal. The definition system lets data entities be related to each other, and it includes a number of different field types. It also supports a system of import (parsing) and export (rendering) engines, for formats such as XML and CSV. Data entities are able to be exported from, and imported into, a Drupal site, for purposes such as backup, offline editing, data migration, and data transfer between Drupal databases.

This module is currently in beta mode, and testers are welcome. Documents such as specs, schedules, and status updates can be found on the wiki.

This is one of the Google Summer of Code 2006 Drupal projects.

OAI-PMH Module | drupal.org

OAI-PMH Module could be useful for providing access to species description nodes.

This module provides an Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH), interface to the Bibliography Module.

Currently it only exposes metadata from the biblio module; however if there was demand I believe that it could be made configurable to expose other node types as well.

This module was inspired by and I have used some code from http://physnet.uni-oldenburg.de/oai/ writen by Heinrich Stamerjohanns.