City Nature Challenge (24-27 april 2020)

Observe nature from one ocean to the other The City Nature Challenge is an international initiative celebrating worldwide biodiversity. Cities in several countries have organize friendly challenges in order to see which community will harvest most observations of nature, find the most species or have the most participants to the City Nature Challenge. With the […]

Data cleaning, publication and re-use: a list of tools, materials and documentations

Cleaning, enrichment and publication of data is the everyday life of the Canadensys team, as well as the the curators, coordinators, technicians, volunteers, students, … that are working in collections to digitize and publish specimens, or collecting data on the field, or even trying to digitize datasets/papers published and historically important. The task can be […]

Importance of the work of volunteers in biodiversity

With the development of citizen sciences platforms and applications, like iNaturalist, eBird or the Herbonautes, the involvement of volunteers in the collect, digitalization and quality improvement of data is drastically increasing. The vast majority of occurrences published on GBIF are observations, mostly collected through citizen science applications and initiatives. In university and museum collections, volunteers […]

Strengthening the Living Atlases Community of Practice

The GBIF Secretariat has funded two half-time positions in the network to assist in developing a growing community of practice around ‘Living Atlases’. Vicente Ruiz Jurado of the Atlas of Living Spain will act as technical coordinator, with responsibility for supporting developers, improving technical documentation and building a shared roadmap. Marie Elise Lecoq of VertNet […]

How to prepare your data for publication, and what to do with open data [Montréal Workshop]

Where: Room B104/B106, Biodiversity Centre, Montréal Botanical Garden, Montréal When: 16-18 April 2019 Who: Carole Sinou (Canadensys), Anne Bruneau (Université de Montréal), other speakers to be announced Preparing a dataset in order to publish on an aggregator like Canadensys or GBIF can be quite fastidious, but data cleaning and standardisation are the key points to […]

How to prepare your data for publication, and what to do with open data [Vancouver Workshop]

Where: Michael Smith Labs (MSL), room 101, University of British Columbia When: 7-9 November 2018 Who: Carole Sinou (Canadensys), Jeannette Whitton and Wayne Maddisson (UBC), Deborah Paul (iDigBio) Preparing a dataset in order to publish on an aggregator like Canadensys or GBIF can be quite fastidious, but data cleaning and standardisation are the key points […]

How to prepare your data for publication, and what to do with open data [Wolfville Workshop]

Where: Acadia Room, K.C. Irving Environmental Science Centre, Acadia University, Wolfville, Nova Scotia When: 15-17 october 2018 Who: Carole Sinou (Canadensys), Alain Beliveau and Allison Walker (E.C. Smith Herbarium, Acadia University), Mary Kennedy (OBIS Canada) Preparing a dataset in order to publish on an aggregator like Canadensys or GBIF can be quite fastidious, but data […]

Mission Herbonautes – Immersion en Amérique du Nord

Note: the mission is only in French but it is quite straightforward to navigate in the platform You have some free time ahead and you would like to help with the digitization of the Marie-Victorin herbarium (Herbarium of the University of Montréal) ? The herbarium is working with the crowdsourcing platform Les Herbonautes, developed by […]

Tutorial n°4: how to only select occurrences with coordinates and/or images?

Before To limit the search to occurrences with geographic coordinates and/or images in the old Explorer, you would use the filters ‘Coordinates’ or ‘Images’ in the ‘Extra’ section. Choose the ‘Coordinates’ or ‘Image(s)’ filter Click on ‘Yes’ and then on ‘Add Filter’ Click on the ‘Search current filter’ button Wait for all the occurrences to […]

Tutorial n°3: How to search for a specific collection?

Before To search for a specific collection in the old Explorer, you would choose the filter ‘Dataset Name’ (or ‘Institution’, or ‘IPT resource’). For example, if I want to retrieve all the occurrences of the Québec’s herbarium (QUE), I will: Choose the ‘Dataset Name’ filter In thr drop-down menu, click on ‘Herbier du Québec (QUE)’ […]

Tutorial n°2: how to search for occurrences form a specific location?

Before Wether you are preparing your next field trip, your family vacation or you just want to now what have been collected around you house, searching for a specific location on the old Explorer is easy. Choose one of the ‘Location’ filter: ‘country’, ‘State/Province’, ‘Municipality’, ‘Locality’, depending on the level of precision you need. Note: […]

Tutorial n°1: How to have access to all the occurrences of a specific taxon?

Before You were able to do that easily in the old Explorer, by using the ‘Scientific Name’ filter. For example, if I need all the occurrences of Taraxacum officinale, I will: Choose the ‘Scientific Name’ filter Type the latin name of the taxon you are looking for Click on the ‘Search’ button View the video […]

New Canadensys Explorer: get to know it!

Our new Explorer, based on the Atlas of Living Australia framework, has been running for few weeks now. After month and month of hard work, this new platform is running and available! Some details has to be polished, but we are working on it! If you find some bugs or dead ends, please contact us. […]

Join the team! Canadensys is seeking a Biodiversity Informatics Manager.

You are curious, a nature lover and passionate about biodiversity informatics? Resourceful, autonomous and the head full of ideas? You know what GBIF, TDWG, DWC, SPNCH, and other acronyms means? This job will probably interest you (and you interest us)! The complete description of the position is available here. If you know someone that match […]

Developing Biodiversity Informatics in Haiti : towards a better knowledge of the biological richness of the country

The project, funded by a BID small grant, was organized in partnership with the Cayes Botanic Garden, Canadensys and GBIF. A workshop took place from the 20th to 23rd of September at the Cayes Botanical Garden, and participants from all over the country were presents, including representatives of the National Botanic Garden, the Ouanaminthe Botanic […]

Inaugural Digital Data in Biodiversity Research Conference

iDigBio and the University of Michigan has organized, on the 5th and 6th of May 2017, the inaugural conference on Digital Data in Biodiversity Research, in Ann Arbor, Michigan. This conference has brought together researchers from United States, Canada and all over the world, and was a great opportunity to discover new projects, tools or […]

Workshop: introduction to the publication of biodiversity data

In partnership with the ABQ, Canadensys offered two workshops in May, for the professionals and organizations interested in publishing their data on Canadensys and GBIF. This one day workshop has been divided in two parts. Association des Biologistes du Québec (ABQ) The Association des Biologistes du Québec (ABQ) is an association of more than 800 […]

Darwin Core Hour, Chapter 5: DwC Standards in Practice – Introduction to the GBIF IPT

Darwin Core Hour The Darwin Core Hour, a series of webinars organized by iDigBio, aims to answer general questions about Darwin Core standards and related topics. From their website : “Darwin Core has become a broadly-used standard for biodiversity data sharing since its inception as a standard by the organization Biodiversity Information Standards (TDWG) in […]

Réseau des Milieux Naturels Protégés : link occurrence data to protected areas

The Réseau des Milieux Naturels Protégés (RMN) is an organization in Québec promoting the protection and conservation of private natural areas, as well as the sensibilisation of citizens and landowners to the importance of the conservation of this natural areas for biodiversity in Québec. This network includes organizations and individuals across Québec and inventories more […]

Welcome to Jérémy, our new programmer

Hi, My name is Jérémy Goimard and I have just started as a computer programmer for biodiversity at Canadensys. My main task is to take care of the server and to develop web applications and open source tools for Canadensys and its community. I am also going to be in charge of the technical assistance […]

Getting students involved in biodiversity informatics

This is a guest post by Jana Vamosi, the Director of the University of Calgary Herbarium. The University of Calgary got involved in Canadensys this year (see also the IPT resource webpage), through a project designed for students to learn about species distribution modeling. We wanted students to understand all components of species distribution modeling, […]

Integrated Publishing Toolkit (IPT) v 2.3.2, DOI assignment, and Dataset Licensing

The Canadensys team recently updated our Integrated Publishing Toolkit (IPT), our data repository software developed by the Global Biodiversity Information Facility (GBIF) to version 2.3.2, the latest and greatest released version. We are proud to have participated in the development of this new version, especially in the assignment of DOIs to datasets. This was an […]

Biodiversity Informatics Programmer

The Biodiversity Centre of the Université de Montréal seeks a Biodiversity Informatics Programmer to develop and maintain web applications for the Canadensys network. Canadensys gathers biological collections data from Canadian universities, botanical gardens and museums in Canada. The network distributes this information via its own portal and through the Global Biodiversity Information Facility. The shared specimen […]

Biodiversity Informatics without borders: Uruguay, here we came

This is a guest post by Andrés Carvajales from the Uruguayan Ministry of Environment/Dirección Nacional de Medio Ambiente, one the main investigators of the GBIF Uruguay portal. 2015 has been an exciting year for biodiversity information management in Uruguay. Together with SiB Colombia, SiB Brazil and Canadensys, the Participant Node of GBIF in Uruguay has engaged in […]

Farewell to Christian Gendreau

The Canadensys team bids farewell to Christian Gendreau, the Lead Informatics Developer who has accepted a post at the Global Biodiversity Information Facility (GBIF) Secretariat in Copenhagen, DK. He has been a pillar for our network for the last four years and he will be sorely missed. He will be a superb new addition to […]

A New Simple Extension for Multimedia files

Canadensys Now Displays Content Using the New Simple Multimedia Extension Last spring, the Global Biodiversity Information Facility (GBIF) published a new Simple Multimedia extension to Darwin Core. Starting with images, the Canadensys IPT now offers an optional Simple Multimedia extension to display media (images) metadata associated with occurrence data and checklists. Instead of the « […]

The Erosion of Collections-Based Science: Alarming Trend or Coincidence?

The post below originally appeared on The Plant Press, October 28, 2014 and is gratefully reproduced here with permission from Vicki Funk and Gary Krupnick. From Plant Press, Vol. 17, No. 4, October 2014. A Curator’s PerspectiveBy Vicki A. Funk* Update: Editor’s Note – The phrase ‘A Curator’s Perspective’ was intended to convey that the […]

Workshop Proposal : Canadensys New Research Initiatives

UPDATED Friday, January 22, 2015 We have been funded by the Natural Sciences and Engineering Research Council and the Québec Centre for Biodiversity Science to host a 2-day workshop February 19 and 20, 2015. Workshop Proposal: Canadensys New Research Initiatives Could species occurrence or specimen data generated in the past or by other studies and […]

Have We Got the Names “Right”?

The Consortium of Northeastern Herbaria met at the Biodiversity Centre at the University of Montreal on Friday, June 13 and Saturday, June 14. Talks on Friday were split into two engaging sessions on outreach and updates on member activities. A workshop was held on Saturday entitled, “Nomenclature & Taxonomy in Collections: Have we got the […]

New Features and Data in the Explorer

Last week, we released a new version of the Canadensys Explorer that has a number of new capabilities. Many of these enhancements were implemented in collaboration with Dr. James Macklin, Research Scientist, Botany and Biodiversity Informatics at Agriculture and Agri-Food Canada. The Canadian Biodiversity Information Facility (CBIF) in partnership with Canadensys intends to use the […]

Enhancements to the VASCAN Checklist Builder

The Vascular Plants of Canada website received some updates to its checklist builder today, making it easier to use. Provinces and Territories on the map are now clickable, the main occurrence options were reworded, and treatment of Saint Pierre and Miquelon and Greenland is now more explicit. Saint Pierre and Miquelon & Greenland The Vascular […]

VASCAN’s Web Service 0.1

Today we released a web service for the database of Vascular Plants of Canada (VASCAN). We did this in response to several requests from users that are not well fulfilled via a web site or via custom downloads. This new capability was several weeks in the making because we took great care to develop a […]

Customizing the IPT v 2.0.5

In a much older post Peter Desmet, the first Biodiversity Informatics Manager for Canadensys, described how he adjusted the look & feel of our default installation of GBIF’s Integrated Publishing Toolkit (IPT), v. 2.0.3. With a few adjustments to some key files such as a stylesheet and a handful of templates, our IPT repository resembled […]

An indoor field trip: visiting Canada’s national spider collection

This is a guest post by Dr. Christopher Buddle that originally appeared on his blog, Arthropod Ecology. Last week I traveled up to Ottawa with two of my students – our goal was to visit the Arachnid collection at the Canadian National Collection of Insects (CNCI) (and Arachnids and Nematodes). The spider collection is housed […]

Canadensys explorer surpasses 1M records

We are pleased to announce that the Canadensys Explorer has surpassed one million occurrence records contributed by its partners. This milestone represents over a third of what we aim to help mobilize by end of 2013 and showcases the immense human effort at each partnering institution as well as the capacity of the Candensys technical […]

Leafcutter bee new to science with specimen data on Canadensys

Dr. Cory Sheffield, Research Scientist & Curator of Invertebrate Zoology at the Royal Saskatchewan Museum in Regina, SK had a paper published April 3, 2013 in the journal ZooKeys in which he named and described Megachile chomskyi. This new species of leafcutter bee is approximately 13mm long, has a relatively long tongue, white pubescence and […]

Launch of Tools and Services

We’re pleased to launch a new Tools section on our data portal. This first instance contains web forms and programming interfaces that convert geographic coordinates in degrees/minutes/seconds to decimal degrees and to atomize dates into numerical representations of day, month, and year. We welcome any feedback you may have on the speed, accuracy, and presentation […]

Open Data

The Canadensys development team participated in the International Open Data Day 2013 organized by QuébecOuvert on February 23, 2013. This event took place in Montréal, Québec to correspond with the International Open Data Day hackathon. We produced a large text file download of all the occurrence data shared by our participating organizations to help make […]

Link Love: DOIs for Darwin Core Archives

Canadensys now assigns digital object identifiers (DOIs) to the Darwin Core Archives (DwC-A) it hosts and serves via its Integrated Publishing Toolkit (IPT) repository of checklist and occurrence data. For example, the DOI for the Royal Ontario Museum’s Green Plant Herbarium (TRT) is doi:10.5886/g7j6gct1 and that for the University of Montréal Biodiversity Centre’s Marie-Victorin Herbarium […]

Delightful Explorations

The Canadensys Explorer is reaching 1M collection records. As this landmark nears, we realize that its dynamic map is becoming less usable. The recognition of patterns and the ability to zoom in to specific collection localities are becoming challenging tasks. With the help of Vizzuality, we are investigating dynamic clustering methods that are triggered when […]

New Canadensys explorer features: stats view & occurrence pages

We are happy to announce two new features for the Canadensys explorer: stats view & occurrence pages. Stats view In addition to map and table view, you can now display basic statistics about your query in stats view. Just click the button at the top and the explorer will crunch the numbers for you. The […]

How (not) to design a checklist

This guest post by David Baxter originally appeared on the One2Many blog. Last week the Royal Ontario Museum (ROM) and some other local organizations coordinated a Bioblitz in Rouge Park, an urban wilderness park in Toronto. In a sentence, a bioblitz is an event where expert biologists, naturalists, and volunteers all come together in an […]

Launch of the Canadensys explorer

This post is also available in French. We are very pleased to announce the beta version of the Canadensys explorer. The tool allows you to explore, filter, visualize and download all the specimen records published through the Canadensys network. The explorer currently aggregates nine published collections, comprising over half a million specimen records, with many […]

Why we should publish our data under Creative Commons Zero (CC0)

With the first datasets getting published and more coming soon, the issue comes up under what license we – the Canadensys community and the individual collections – will publish our data. Dealing with the legal stuff can be tedious, which is why we have looked into this issue with the Canadensys Steering Committee & Science […]

New terms in Darwin Core

For the first time since its ratification in October 2009, Darwin Core has been revised! But don’t panic: it’s probably not going to affect your data publication. Darwin Core is a community standard, so anyone can submit ideas, suggestions or corrections via the Darwin Core issue tracker (guidelines to do so can be found here). […]

VASCAN portal and database are now open source

The Database of Vascular Plants of Canada (VASCAN) web portal and its database are now open source. The code is hosted on our Google Code site and can be used by anyone to create their own checklist portal. By doing so, we hope that the time and effort that went into developing VASCAN can benefit […]

Updating a customized IPT

This is a follow-up of the post Customizing the IPT. As mentioned at the very end of my post about customizing the IPT, I face a problem when I want to install a new version of the GBIF Integrated Publishing Toolkit: installing it will overwrite all my customized files! Luckily Tim Robertson gave me a […]

How many species?

This guest post by Terry Wheeler originally appeared on the Lyman Entomological Museum blog. One of the fundamental rules of running a business is that you have to keep track of your inventory. If you don’t know what’s in the warehouse, or who works for you, you’re not going to get very far as a […]

VASCAN functionalities

This post is also available in French. Our Database of a vascular plants of Canada (VASCAN) is a bit over a year old now (launched on October 22, 2010) and the response has been great so far! The site is averaging 1,850 visits / 20,500 page views a month from over a 100 countries, and […]

Counting all specimens at the Marie-Victorin Herbarium

Last summer, 36 volunteers inventoried all of the 22,000+ vascular plant specimen folders of our Marie-Victorin Herbarium (MT), in preparation of its move to the Université de Montréal Biodiversity Centre. I gave a talk about the process, results and potential two weeks ago at the TDWG 2011 Annual Conference in New Orleans: You can read […]