Search results

The Herbarium of Meise Botanic Garden is in the top 15 herbaria worldwide. The collection comprises some four million specimens, which are important for scientific research. Digitisation of specimens includes imaging, transcription of label information, linking data and making the results publicly accessible online. In addition to facilitating researchers' access to specimens, digitisation also brings new possibilities for analysis and discovery of new data, such as the vast amount of information on handwritten labels. In the DOE! project (Digitale Ontsluiting Erfgoedcollecties), funded by the Flemish Government, 1.2 million herbarium sheets from the African and Belgian collections were digitised. We have received additional funding to digitise a further 1.4 million specimens for the remaining vascular plants and macro-algae collections, by October 2021. These include the historic collections of Von Martius and Van Heurck. Carl Friedrich Philipp von Martius (1794–1868) was a pioneering explorer whose expeditions led to the discovery of many species. He amassed over 300,000 specimens, some of which were used to compile the first Flora of Brazil. Henri Van Heurck (1838–1909) also gathered herbarium specimens from all over the world, including a specimen originally from the collection of Linnaeus. Despite this being our second mass digitisation project, there are significant differences in our approach. This is partly due to lessons learned from the first project and partly to the nature of the collections themselves. The differences in the tendering process, specimen preparation, workflow and data capture will be explained. Making these specimens openly available online through www.botanicalcollections.be is valuable to scientific research as well as valorising of our collections. Currently, the site attracts 7000 users a year, which adds up to 15,000 sessions a year and the average session is more than 8 minutes. This means that people are actively using our website and these numbers can be expected to grow as we ...

When researchers and managers are asked to rank the issues that prevent adequate control of invasive species, lack of public awareness is at the top of the list (Dehnen‐Schmutz et al. 2018). It is therefore imperative to raise the general public's awareness of the potential risks of introducing alien species into the wild. Green Pioneers, a citizen science project funded by the Flemish Government, (Fig. 1) aims to address this issue in Belgium, across age groups. The project aims to Create awareness on invasive species, highlighting how invasions can be avoided and how to mitigate their impact. Improve communication between citizens and scientists on conservation and invasive plant species. Augment the quality and quantity of data on invasive species. The project is developing three kinds of activity, specifically to attract a broad demographic: - 'Young Pioneers', by developing tools for teachers in science, technology, engineering and mathemathics for school children from 12-15 years old. - 'Online Pioneers', through our online citizen science platform DoeDat.be, by helping with the transcription of label information on herbarium specimens, - and 'Visiteers', by inviting companies and working age people to help us in the collection and to inform them about invasive species. Finally, we will be organizing a BioBlitz in spring 2020 at Meise Botanic Garden where we will celebrate plants and all our Green Pioneers, while also spreading the message of invasive plant awareness. During our 48 hour BioBlitz, scientists, volunteers and citizens are workig together to survey the biodiversity of our Botanic Garden. Ultimately, Green Pioneers aim to encourage recording of alien species by amateur botanists and create a generation of responsible gardeners who understand the consequences of releasing invasive alien plants into the wild.

The Herbarium of Meise Botanic Garden is in the top 15 herbaria worldwide. The collection comprises some four million specimens, which are important for scientific research. Digitisation of specimens includes imaging, transcription of label information, linking data and making the results publicly accessible online. In addition to facilitating researchers' access to specimens, digitisation also brings new possibilities for analysis and discovery of new data, such as the vast amount of information on handwritten labels. In the DOE! project (Digitale Ontsluiting Erfgoedcollecties), funded by the Flemish Government, 1.2 million herbarium sheets from the African and Belgian collections were digitised. We have received additional funding to digitise a further 1.4 million specimens for the remaining vascular plants and macro-algae collections, by October 2021. These include the historic collections of Von Martius and Van Heurck. Carl Friedrich Philipp von Martius (1794–1868) was a pioneering explorer whose expeditions led to the discovery of many species. He amassed over 300,000 specimens, some of which were used to compile the first Flora of Brazil. Henri Van Heurck (1838–1909) also gathered herbarium specimens from all over the world, including a specimen originally from the collection of Linnaeus. Despite this being our second mass digitisation project, there are significant differences in our approach. This is partly due to lessons learned from the first project and partly to the nature of the collections themselves. The differences in the tendering process, specimen preparation, workflow and data capture will be explained. Making these specimens openly available online through www.botanicalcollections.be is valuable to scientific research as well as valorising of our collections. Currently, the site attracts 7000 users a year, which adds up to 15,000 sessions a year and the average session is more than 8 minutes. This means that people are actively using our website and these numbers can be expected to grow as we add more specimens and functionality.

When researchers and managers are asked to rank the issues that prevent adequate control of invasive species, lack of public awareness is at the top of the list (Dehnen‐Schmutz et al. 2018). It is therefore imperative to raise the general public's awareness of the potential risks of introducing alien species into the wild. Green Pioneers, a citizen science project funded by the Flemish Government, (Fig. 1) aims to address this issue in Belgium, across age groups. The project aims to Create awareness on invasive species, highlighting how invasions can be avoided and how to mitigate their impact. Improve communication between citizens and scientists on conservation and invasive plant species. Augment the quality and quantity of data on invasive species. The project is developing three kinds of activity, specifically to attract a broad demographic: - 'Young Pioneers', by developing tools for teachers in science, technology, engineering and mathemathics for school children from 12-15 years old. - 'Online Pioneers', through our online citizen science platform DoeDat.be, by helping with the transcription of label information on herbarium specimens, - and 'Visiteers', by inviting companies and working age people to help us in the collection and to inform them about invasive species. Finally, we will be organizing a BioBlitz in spring 2020 at Meise Botanic Garden where we will celebrate plants and all our Green Pioneers, while also spreading the message of invasive plant awareness. During our 48 hour BioBlitz, scientists, volunteers and citizens are workig together to survey the biodiversity of our Botanic Garden. Ultimately, Green Pioneers aim to encourage recording of alien species by amateur botanists and create a generation of responsible gardeners who understand the consequences of releasing invasive alien plants into the wild.

The botanicalcollections.be website (http://www.botanicalcollections.be) is the culmination of the three year Digitale Ontsluiting Erfgoedcollecties (DOE!) project. Over this period we have digitally imaged 1.2 million African and Belgian herbarium specimens and much of their label data. All these data are freely available on our new virtual herbarium www.botanicalcollections.be. For this we have to thank a generous grant from the Flemish Government. The site was officially launched on the 23rd March, 2018, at the Fourth Annual Meeting of Plant Ecology and Evolution held at Bouchout Castle in Meise Botanic Garden (https://sites.google.com/plantentuinmeise.be/ampee4/). Before developing the website we conducted a user requirements analysis (Vissers et al. 2017. These requirements formed the basis for development from initial design to the finished product. Lots of features were incorporated to make the site as user-friendly and usable as possible; persistent URIs, zoomable and downloadable images and access to data. Each specimen can be annotated and is available in a machine readable format. The goal of the botanicalcollections.be website is not only to make digitized specimens from the Botanic Garden available, but also to centralize and display the herbarium specimens from other Belgian herbaria. A cooperation agreement will make collaboration easy and transparent. The benefits to herbaria of participating in this virtual herbarium include greater publicity, the ability to show how their specimens contribute to overall knowledge, and a mechanism for identifying where to focus future collecting efforts, all of which help validate their worth to institutional administrators. In addition, such cooperation helps build professional relationships who, because of disparate interests and obligations, might not normally connect with each other.

There are many ways to capture data from herbarium specimen labels. Here we compare the results of in-house verses out-sourced data transcription with the aim of evaluating the pros and cons of each approach and guiding future projects that want to do the same. In 2014 Meise Botanic Garden (BR) embarked on a mass digitization project. We digitally imaged of some 1.2 million herbarium specimens from our African and Belgian Herbaria. The minimal data for a third of these images was transcribed in-house, while the remainder was out-sourced to a commercial company. The minimal data comprised the fields: specimen's herbarium location, barcode, filing name, family, collector, collector number, country code and phytoregion (for the Democratic Republic of Congo, Rwanda & Burundi). The out-sourced data capture consisted of three types: additional label information for central African specimens having minimal data; complete data for the remaining African specimens; and, species filing name information for African and Belgian specimens without minimal data. As part of the preparation for out-sourcing, a strict protocol had to be established as to the criteria for acceptable data quality levels. Also, the creation of several lookup tables for data entry was necessary to improve data quality. During the start-up phase all the data were checked, feedback given, compromises made and the protocol amended. After this phase, an agreed upon subsample was quality controlled. If the error score exceeded the agreed level, the batch was returned for retyping. The data had three quality control checks during the process, by the data capturers, the contractor's project managers and ourselves. Data quality was analysed and compared in-house versus out-sourced modes of data capture. The error rate by our staff versus the external company was comparable. The types of error that occurred were often linked to the specific field in question. These errors include problems of interpretation, legibility, foreign languages, typographic errors, etc. A significant amount of data cleaning and post-capture processing was required prior to import into our database, despite the data being of good quality according to protocol (error < 1%). By improving the workflow and field definitions a notable improvement could be made in the "data cleaning" phase. The initial motivation for capturing some data in-house was financial. However, after analysis, this may not have been the most cost effective approach. Many lessons have been learned from this first mass digitisation project that will implemented in similar projects in the future.

The botanicalcollections.be website (http://www.botanicalcollections.be) is the culmination of the three year Digitale Ontsluiting Erfgoedcollecties (DOE!) project. Over this period we have digitally imaged 1.2 million African and Belgian herbarium specimens and much of their label data. All these data are freely available on our new virtual herbarium www.botanicalcollections.be. For this we have to thank a generous grant from the Flemish Government. The site was officially launched on the 23rd March, 2018, at the Fourth Annual Meeting of Plant Ecology and Evolution held at Bouchout Castle in Meise Botanic Garden (https://sites.google.com/plantentuinmeise.be/ampee4/). Before developing the website we conducted a user requirements analysis (Vissers et al. 2017. These requirements formed the basis for development from initial design to the finished product. Lots of features were incorporated to make the site as user-friendly and usable as possible; persistent URIs, zoomable and downloadable images and access to data. Each specimen can be annotated and is available in a machine readable format. The goal of the botanicalcollections.be website is not only to make digitized specimens from the Botanic Garden available, but also to centralize and display the herbarium specimens from other Belgian herbaria. A cooperation agreement will make collaboration easy and transparent. The benefits to herbaria of participating in this virtual herbarium include greater publicity, the ability to show how their specimens contribute to overall knowledge, and a mechanism for identifying where to focus future collecting efforts, all of which help validate their worth to institutional administrators. In addition, such cooperation helps build professional relationships who, because of disparate interests and obligations, might not normally connect with each other.

There are many ways to capture data from herbarium specimen labels. Here we compare the results of in-house verses out-sourced data transcription with the aim of evaluating the pros and cons of each approach and guiding future projects that want to do the same. In 2014 Meise Botanic Garden (BR) embarked on a mass digitization project. We digitally imaged of some 1.2 million herbarium specimens from our African and Belgian Herbaria. The minimal data for a third of these images was transcribed in-house, while the remainder was out-sourced to a commercial company. The minimal data comprised the fields: specimen's herbarium location, barcode, filing name, family, collector, collector number, country code and phytoregion (for the Democratic Republic of Congo, Rwanda & Burundi). The out-sourced data capture consisted of three types: additional label information for central African specimens having minimal data; complete data for the remaining African specimens; and, species filing name information for African and Belgian specimens without minimal data. As part of the preparation for out-sourcing, a strict protocol had to be established as to the criteria for acceptable data quality levels. Also, the creation of several lookup tables for data entry was necessary to improve data quality. During the start-up phase all the data were checked, feedback given, compromises made and the protocol amended. After this phase, an agreed upon subsample was quality controlled. If the error score exceeded the agreed level, the batch was returned for retyping. The data had three quality control checks during the process, by the data capturers, the contractor's project managers and ourselves. Data quality was analysed and compared in-house versus out-sourced modes of data capture. The error rate by our staff versus the external company was comparable. The types of error that occurred were often linked to the specific field in question. These errors include problems of interpretation, legibility, foreign languages, typographic ...

Herbarium specimens hold a wealth of data about plants; where they come from, where they were collected and by whom. Once digitized, these data can be searched, mapped and compared. However, the information on specimens is often handwritten and even the best software systems cannot read it. This is where we get real value from citizen involvement. Digitizing these data is only possible with the aid of human intelligence. DoeDat is a multilingual open-source platform for transcription, based upon the DigiVol program of the Australian Museum and Atlas of Living Australia. DoeDat is a product of our digitization project Digital Access to Cultural Heritage Collections (DOE!), funded by the Flemish Government. DoeDat is about creating data and also, 'Doe Dat' means 'do that' in Dutch. DoeDat will help us digitize our collections, and will also give the public the chance to take an active part in the process. We aim to build a community of enthusiastic online volunteers who will help us liberate botanical data from specimen labels and documents. We launched the platform on Science Day and within two months, more than one hundred volunteers had transcribed more than 4,000 specimens. Join in at www.DoeDat.be

Informing policy on invasive species requires rapid mobilization of biodiversity data from many sources and converting these raw data into simple metrics and reliable information. Yet the data are collected by a wide variety of actors, both professional and amateur, and they are often divided by political and language barriers. Belgium is typical in that sense, we struggle with the fragmented data sources and restrictions on data mobility, while trying to answer the policy needs at both national and local levels. In 2017 we launched the TrIAS project that aims to resolve some of these problems. We envisage a future where data are rapidly mobilized, the spread of exotic species is regularly monitored, future risks are evaluated and potential impacts assessed [1]. In many ways we have similar aims to GFBio, though we may have found different solutions to the same problems. TrIAS is building workflows that openly publish species information and primary biodiversity data, then harvest those and other data, to create indicators, predictive models and policy support documentation. TrIAS is a consortium of 12 Belgian institutions together with another 9 stakeholder organizations. We aim to address terrestrial, freshwater and marine environments. The organizations involved include those involved in citizen science, pure and applied research, and wildlife management. TrIAS is an open science project; all the software are shared under an MIT Licence; all the data are shared under a CC0 licence waiver and all the documentation is shared under Creative Commons licenses. The hope is that this approach will contribute to the post-project sustainability, because the data and software can all be reused as a whole or in part, either in Belgium, or anywhere else it is needed. Such reuse need not be confined to alien species monitoring, but there is also a need for repeatability and rapid mobilization in other fields, such as red-listing of conservation worthy species. KEYWORDS: invasive species, rapid data publication, sustainability, biodiversity monitoring, cost-effective, Global Biodiversity Information Facility, R tools, controlled vocabularies, policy relevant REFERENCES: 1. Vanderhoeven, S., Adriaens, T., Desmet, P., Strubbe, D., Backeljau, T., Barbier, Y., Brosens, D., Cigar, J., Coupremanne, M., De Troch, R., Eggermont, H., Heughebaert, A., Hostens, K., Huybrechts, P., Jacquemart, A., Lens, L., Monty, A., Paquet, J., Prévot, C., Robertson, T., Termonia, P., Van De Kerchove, R., Van Hoey, G., Van Schaeybroeck, B., Vercayie, D., Verleye, T., Welby, S., Groom, Q. 2017. Tracking Invasive Alien Species (TrIAS): Building a data-driven framework to inform policy. Research Ideas and Outcomes. 3, e13414. https://doi.org/10.3897/rio.3.e13414

Herbarium specimens hold a wealth of data about plants; where they come from, where they were collected and by whom. Once digitized, these data can be searched, mapped and compared. However, the information on specimens is often handwritten and even the best software systems cannot read it. This is where we get real value from citizen involvement. Digitizing these data is only possible with the aid of human intelligence. DoeDat is a multilingual open-source platform for transcription, based upon the DigiVol program of the Australian Museum and Atlas of Living Australia. DoeDat is a product of our digitization project Digital Access to Cultural Heritage Collections (DOE!), funded by the Flemish Government. DoeDat is about creating data and also, 'Doe Dat' means 'do that' in Dutch. DoeDat will help us digitize our collections, and will also give the public the chance to take an active part in the process. We aim to build a community of enthusiastic online volunteers who will help us liberate botanical data from specimen labels and documents. We launched the platform on Science Day and within two months, more than one hundred volunteers had transcribed more than 4,000 specimens. Join in at www.DoeDat.be

Mass digitization is a large undertaking for a collection. It is disruptive of routine and can challenge long-held practises. Having been through the procedure and survived, we feel we have a lot of experience to share with other institutions who are considering taking on this challenge. The changes that digitization has made to our institution are positive and the digitization a success, but that is not to say that we would not have done some things differently, were we to repeat the exercise. In 2015 Meise Botanic Garden received a grant from the Flemish Government to upgrade its digitization infrastructure and mass digitize 1.2 million specimens from its African and Belgian Herbaria. The new infrastructure improved our workflow significantly, enabling us to digitize specimens five to ten times faster while also improving their quality. The mass digitization part of the project was split into two parts, imaging and transcription. The contract was awarded and out-sourced to Picturae, who started imaging in May 2016 using a conveyor belt installation. Prior to starting, a significant amount of preparation was required at the herbarium. Within one year, 1.2 million specimens were imaged. The images were captured as TIFF files and stored in triplicate at The Flemish Institute for Archiving (VIAA), while smaller derived JPEG 2000 and JPEG files were generated for day-to-day use. The second part of the project was label transcription. A third of the specimens were transcribed in-house for capturing minimal data (barcode, filing name, collector, collector number & country of origin). This was partly done to reduce costs, but also allowed us to compare in-house to out-sourced transcription. Some 500,000 specimens were transcribed, either completely or partially, by Alembo (subcontracted by Picturae).The remaining 200.000 specimens from our Belgian Herbarium are being transcribed using crowdsourcing. The latter is being realized through the citizen science platform DoeDat (www.doedat.be) that was launched in ...

Mass digitization is a large undertaking for a collection. It is disruptive of routine and can challenge long-held practises. Having been through the procedure and survived, we feel we have a lot of experience to share with other institutions who are considering taking on this challenge. The changes that digitization has made to our institution are positive and the digitization a success, but that is not to say that we would not have done some things differently, were we to repeat the exercise. In 2015 Meise Botanic Garden received a grant from the Flemish Government to upgrade its digitization infrastructure and mass digitize 1.2 million specimens from its African and Belgian Herbaria. The new infrastructure improved our workflow significantly, enabling us to digitize specimens five to ten times faster while also improving their quality. The mass digitization part of the project was split into two parts, imaging and transcription. The contract was awarded and out-sourced to Picturae, who started imaging in May 2016 using a conveyor belt installation. Prior to starting, a significant amount of preparation was required at the herbarium. Within one year, 1.2 million specimens were imaged. The images were captured as TIFF files and stored in triplicate at The Flemish Institute for Archiving (VIAA), while smaller derived JPEG 2000 and JPEG files were generated for day-to-day use. The second part of the project was label transcription. A third of the specimens were transcribed in-house for capturing minimal data (barcode, filing name, collector, collector number & country of origin). This was partly done to reduce costs, but also allowed us to compare in-house to out-sourced transcription. Some 500,000 specimens were transcribed, either completely or partially, by Alembo (subcontracted by Picturae).The remaining 200.000 specimens from our Belgian Herbarium are being transcribed using crowdsourcing. The latter is being realized through the citizen science platform DoeDat (www.doedat.be) that was launched in November 2017. Many lessons have been learnt with respect to implementing mass digitization, both practically and sociologically. Many of the problems encountered during the project could have been avoided by changing the workflow. The addition of extra control points during the process could have reduced problems encountered later in the data capture process. Solving these problems at a later stage was time consuming. Trying to "save money" can result in a disruptive workflow, which may lead to a number of costly errors. Mass digitization has fundamentally changed the workflow in our collections and the way in which our herbarium is managed. All images for the African and Belgian collections may be now found on our new virtual herbarium www.botanicalcollections.be.

Citizen science is an approach of public participation in scientific research which has gained significant momentum in recent years. This is particularly evident in biology and environmental sciences where input from citizen scientists has greatly increased the number of publicly available observation data. However, there are still challenges in effective networking, data sharing and securing data quality. EU BON project has analyzed the citizen science landscape in Europe with regards to biodiversity research and proposes several policy recommendations. One of the recommendations is a Pan-European citizen science gateway for biodiversity data with dedicated tools for data collection and management. The prototypes of the gateway components are part of the EU BON biodiversity portal and described in current report.

The paper investigates how to implement open access to data in collection institutions and in the DiSSCo research infrastructure. Large-scale digitisation projects generate lots of images, but data transcription often remains backlogged for years. The paper discusses minimum information standards (MIDS) for digital specimens, and tentatively defines 4 hierarchical MIDS levels. Even partially available data can be useful for some purposes and it is recommended that data and media be made openly accessible after minimal delay. The paper then discusses the FAIR concepts and obstacles and restrictions to making data openly accessible. Legal restrictions for making data openly available are discussed from the perspective "as open as possible, as closed as (legally) necessary". Specific legislation applying to DiSSCo data are listed and guidelines on how to deal with each are made. The information architecture of DiSSCo is briefly described from the perspective of facilitating open access to data, and the essential features of DiSSCo and GBIF are compared against each other, noting that both have their distinctive roles but need close cooperation. Data policies and data management plans (DMP) of six ICEDIG collection institutions are reviewed. Typically, only one or the other exists, depending on how digitisation and related data management is organised. Data policies are found at institution level whereas DMPs seem to belong to project level. The paper comes to the following conclusions: 1) Digital Specimen Objects (DSO) must be findable and accessible already at the lowest (MIDS-0) level. Data should be deposited in a trusted public research data repository. 2) As far as possible, projects must enable third parties to access, mine, exploit, reproduce and dis­seminate this data by using a copyright waiver such as CC0 or an open access licence such as CC-BY. 3) Exceptions to openness policy must be stated clearly and strictly limited to reasons of national security, legal or regulatory compliance, sensitivity of ...