Crowdsourcing platform for Coimbra Herbarium

EXPLORATOR

The Herbarium of the University of Coimbra, Portugal, celebrated its 140th anniversary in 2020, but it is only since 2002 that the collection has been moving online to make sure that these priceless resources will be available to future generations. As the digitisation is a painstakingly slow process, the University has developed a platform to enable citizen scientists to contribute to the transcription of information to the database. The COI Catalogue, as it is known internationally, contains approximately 800,000 specimens, many of which are of great historical interest. The new crowdsourcing platform – EXPLORATOR – allows registered citizens to update the descriptive labels within the database workflow, with which it is fully integrated. The data validated by the platform is progressively added to the master database and therefore made available through the online catalogue. 

EXPLORATOR was developed by the Herbarium COI team within the framework of PORBIOTA, the Portuguese e-Infrastructure for information and research on biodiversity, which manages LifeWatch Portugal. It provides each user with an image and a form to be completed one field at a time. A help icon is available for each field to provide support at every stage of the process. When a value is submitted, the platform verifies whether different values have been submitted for that field and issues an alert for discrepancies.

This validation function allows less experienced citizen scientists working in EXPLORATOR to start with fields that are easily identified and helps them become familiar with the herbarium specimens and the type of information required. When a given number of responses are validated as correct, the user is given access to the next levels which unlock more complex fields.  The architecture therefore encourages learning and greater proficiency, as well as avoiding inadvertent errors.

User proficiency levels determine the assignation of confidence values to the data entered. Validation occurs when the sum of points for a value reaches 60. Answers from an expert user are worth 50 points and those from a basic user are only worth 10, so the same value would have to be submitted by six basic users to equal the work of one expert. As an additional safeguard, manual validation by an administrator is also possible. 

The EXPLORATOR platform currently accounts for 300 registered users and a total of 140,000 submissions, which relate to 36,000 validated fields. As only 12 percent of the catalogue materials have been processed so far, it is hoped that more citizen scientists will step forward and help speed up the work of the PORBIOTA e-infrastructure consortium in storing and managing biodiversity data that is essential for the national agenda for biodiversity research.

Metabarcoding and Metagenomics Conference

The 10th edition of the Trends in Biodiversity and Evolution Conference (TiBE2020), organised by the Research Centre in Biodiversity and Genetic Resources CIBIO- InBIO Associate Laboratory, at the University of Porto, Portugal, was conducted online from 9-11 December, with a focus on Metabarcoding and Metagenomics. 

The availability of ever more powerful DNA sequencing technologies has made possible exploration of the living world in ways that were beyond our imagination just ten years ago. Researchers at all levels came together to discuss the application of metabarcoding and metagenomics to foster new and more cost-efficient environmental assessment and monitoring programs in ecological and environmental research. 

Staged over three afternoons, the programme was divided into three sections: Molecular surveys of biodiversity and invasive species; Next generation biomonitoring of aquatic and terrestrial ecosystems; and Understanding species interactions in complex ecosystems. Keynote speakers from France, UK and USA as well as 24 other communications selected from received abstracts. The conference was attended by nearly 200 participants from 24 different countries, and representing over 60 research institutions.

TiBE2020 was also the closing event of the ERA Chair in Environmental Metagenomics – ENVMETAGEN, funded by the European Commission’s H2020 Framework Program, an initiative that enhanced the capacity of InBIO to tackle societal challenges related to the loss of biodiversity, degradation of ecosystem services and sustainable development, at regional, national and international levels.

CIBIO InBIO is part of LifeWatch Portugal. 

TiBE2020 Metabarcoding and Metagenomics

Trends in Biodiversity and Evolution

9-11 December 2020, online. The tenth edition of the Trends in Biodiversity and Evolution (TiBE) conference will be virtual this year and focus on Metabarcoding and Metagenomics. The meeting, held over three afternoons, will discuss exciting developments associated with the advent of ever more powerful DNA sequencing technologies, which are opening possibilities to explore the living world in ways that were unimaginable just a decade ago.

This annual Trends inn Biodiversity and Evolution event is organised by CIBIO-InBIO, the Research Centre in Biodiversity and Genetic Resources, connected through PORBIOTA with LifeWatch Portugal. It brings together senior researchers, post-graduate and graduate students working in the fields of biodiversity and evolutionary biology, to discuss cutting-edge findings in topics related to metabarcoding and metagenomic techniques, and their application in ecological and environmental research. The TiBE2020 conference is jointly organised by the CompBio and ApplEcol research groups. It will be hosted on an online platform that will facilitate networking opportunities and allow poster presentations. The programme, including both plenary and short presentations from selected abstracts, is divided into three sessions:

• Molecular surveys of biodiversity and invasive species

• Next generation biomonitoring of aquatic and terrestrial ecosystems

• Understanding species in interactions in complex ecosystems.

Abstracts are invited either as 15-minute oral presentations, or as 2-minute poster videos. Please note that only registered participants will be accepted as presenting authors. Abstract submission deadline is 27 October, 2020. Click here to download the abstract submission template. 

United for #Biodiversity

The Natural History and Science Museum of the University of Porto (MHNC-UP), including its Botanical Garden and Hall of Biodiversity – Ciência Viva Center – is the first institution from Portugal to become an official member of the European Commission Global Coalition ‘United for #Biodiversity‘, a campaign calling for stronger mobilisation in raising awareness about the need to protect biodiversity.

As a member of LifeWatch Portugal, MHNC-UP has joined this global movement to call the attention of world leaders to the pressing need to take immediate and concerted action to protect nature by acting locally and worldwide, and is proud to be one with the 10 institutions (including the Oceanographic Institute of Monaco, Central Park Zoo and Biotopia Munich) and 16 international organisations that have already signed up to this global initiative. Around 500 institutions are expected to take part by the end of 2020.

Launched by EU Commissioner for Environment Virginijus Sinkevicius, the United for #Biodiverstiy coalition calls for strong mobilization of all national research centers, science and natural history museums, botanic gardens, zoos, parks, aquariums and others to make their voices heard about the crisis that nature is facing. At a time when science is warning that 1 million species are at risk of extinction within decades because of human activities, jeopardizing the very future of humanity, there is a critical need to unite all possible forces in the lead up to COP26. 

The Natural History and Science Museum of the University of Porto’s mission is to promote the advancement and dissemination of knowledge about evolution, diversity and the convergence between the natural and cultural worlds, Its displays seek to stimulate curiosity about both natural and cultural phenomena and contribute to their understanding, fostering a dialogue between the arts, science and technology.  

Ecology Day 2020 in Portugal

Ecology Day

Ecology Day was firstly established in 2016, to celebrate the 150th anniversary of the date when Ernst Haeckel coined the term “ecology”. The first event to mark this special date was held in Brussels at the European Parliament that same year, organised by the European Ecological Federation (EEF). From that year on, September 14 has been set as Ecology Day.

Inspired by this celebration in Brussels, the Portuguese Ecological Society (SPECO – Sociedade Portuguesa de Ecology), and the EEF have been promoting the concept since 2017, making the most of generous sponsorship from the UNESCO Portuguese Commission. This annual celebration of Ecology Day now occurs worldwide with the dual purposes of bringing ecology and ecologists closer to society, and  promoting and fostering scientific literacy.

In 2019, Ecology Day stepped up to an international scale, and in 2020 SPECO proposed to EEF the launch of an online platform in which all interested institutions, researchers, associations and others could independently register their activities. This enabled a prompt submission of activities and resources, which were immediately made available to browse. As shown in the map above, this year there were over 150 activities spread across the globe. With a majority of digital, online offerings, the mobilisation towards this date was impressive, especially given the current state of public health worldwide.

In Portugal, Ecology Day 2020 was a big success, with SPECO contributing to events in many municipalities which provided their inhabitants with enriching ecology-related cultural and educational activities. Science centres, museums, universities, LIFE projects, research and educational institutions and environmental protection associations came together to offer the public a wealth of initiatives, such as guided tours (in-person and virtually), exhibitions, debates, seminars, webinars, workshops, challenges, games, short story sessions for children, book presentations, educational videos, murals and illustrations, and scientific articles, among others. The impact of these initiatives will be the subject of an in-depth assessment, whose outcomes will be published as soon as possible.

Bearing in mind that the on-going endorsement of this date by UNESCO depends on the number of initiatives organised, SPECO has been keen to reinforce and promote the events,  and publicise the outcomes. To broaden and consolidate the celebration of this important date, and to highlight the relevance of ecology as an important arm of science, the Portuguese Ecological Society takes this opportunity to encourage all interested parties to start preparations for their contributions in 2021. 

Portuguese Pollinators

Polinizadores de Portugal"

PORBIOTA/LifeWatch Portgual together with a plethora of museums, academic institutions, NGOs, municipalities, schools and other partners in Portugal, is promoting the “Polinizadores de Portugal” initiative to foster public (individual) participation in the collection of distribution data of Portuguese pollinators. 

“Polinizadores de Portugal” (Pollinators of Portugal), is a citizen science project launched by CIBIO-InBIO and Parque Biológico de Gaia, and is based on the BioDiversity4All platform, the Portuguese node of the iNaturalist Network. The intention is to better understand the distribution of pollinating species, their rarity and the periods in which flowers are visited. Since January, over 18000 records of more than 1800 species of arthropods have already been submitted. 

The first public campaign took place in May, during the lockdown, when citizens were called on to use a camera or cell phone and register the pollinators that visit flowers at home and surrounding areas, while fully respecting the safety measures in place. Citizens inspected pots on their balconies and in the gardens and more than 5,500 records were gathered in a single month.

Moths and butterflies were the most recorded insects, followed by beetles, flies and the group that includes bees, wasps and ants. 

A new campaign will take place 12-20 September, celebrating Ecology Day on 14 September and International Microorganism Day on 17 September, to help focus attention on the intricate connections between organisms, nature and our daily lives. 

The data recovered comprises mostly information on insects and will be an important contribution to the knowledge and study of the entomofauna of Portugal. It will also constitute a precious tool to assist in the elaboration of the first Red List of Invertebrates in Portugal. Can you help us? We are counting on you too! Here are those links again: BioDiversity4All, and the Launch of the National Citizen Science Project.

Workshop: Online Bioinformatic Platforms to support Metabarcoding and Metagenomics research and Applications

The pan-European Workshop, held in Porto from 26 – 28 February, in the Research Centre in Biodiversity and Genetic Resources (CIBIO-InBIO) at the Vairão campus of the University of Porto, Portugal, boasted a very specific title: ‘Online Bioinformatic Platforms to Support Metabarcoding and Metagenomics Research and Applications’.

The workshop witnessed more than 30 participants from nine European countries (Belgium, Estonia, Germany, Greece, Italy, Norway, Portugal, Slovenia, Spain, Switzerland) with different expertise and backgrounds, ranging from metagenomics and metabarcoding, to ecology and ICT.

1) Checking existing distributed Bioinformatics e-Resources within the LifeWatch ERIC communities of practice,

2) Reaching a common understanding of users’ requirements and needs in Virtual Research Environments, and

3) Proposing an efficient and realistic and engaging mechanism from an ICT perspective, capable of federating those e-Resources within the LifeWatch ERIC VREs.

Examples of evidence-based research were provided by the European Open Science Cloud (EOSC), MIRRI (Microbial Research Resource Infrastructure), ELIXIR (which unites Europe’s leading life science organisations in managing and safeguarding the ever-growing volumes of data generated), other Research Infrastructures and Bioinformatics initiatives.

The outcome of the three days was a plan with well-identified next steps towards the co-construction of the bioinformatic platform.

North and West Africa vertebrate observation dataset

PORBIOTA dataset

PORBIOTA/LifeWatch Portugal has made available a new vertebrate observation and distribution dataset of North and West Africa, which is now accessible through the Global Biodiversity Information Facility and GBIF.PT. 

The dataset comprises information on fishes, amphibians, reptiles and mammals mostly from the deserts and arid regions of North and West Africa, especially from the Sahara and Sahel ecoregions, including Algeria, Burkina Faso, Chad, Egypt, Guinea-Bissau, Libya, Mali, Mauritania, Morocco, Niger, Senegal and Tunisia. It also includes a few scattered observations from Armenia, Greece, Iran, Malawi, Portugal, Spain, and Turkey. 

These data span a temporal scope of about 18 years (1999 to 2017), and were collected by the BIODESERTS Research Group of the Research Centre in Biodiversity and Genetic Resources-Research Network in Biodiversity and Evolutionary Biology (Associate Laboratory), University of Porto (CIBIO-InBIO), under the coordination of José Carlos Brito, who also has credit for the photograph.

Records were obtained mainly using random sampling procedures, by visual encounter surveys. The species’ identification was confirmed by molecular marker analyses and observations were published in scientific journals. It was possible to identify an overall 5 364 occurrence: 2 493 for Reptilia, 1 838 for Mammalia, 794 for Amphibia and 239 for Actinopterygii.  

For more information and data set please click here.

2nd Dahlem-Type Workshop

2nd Dahlem-Type Workshop

The LifeWatch ERIC Internal Joint Initiative was launched in October 2019 to design and construct a Virtual Research Environment capable of processing and modelling available data on one of the planet’s most burning biodiversity issues, the proliferation of Non-indigenous and Invasive Species (NIS), in order to help mitigate their impacts. 

Development of a new Virtual Research Environment (VRE) is essential to further integrate the tools and services available in the LifeWatch ERIC web portal. The process will allow stakeholders greater ability to develop their research activities within the e-Science Infrastructure, whilst also clearly demonstrating the added value that LifeWatch ERIC’s advanced technologies can bring not only to the biodiversity and ecosystem scientific community, but to policymaking and human wellbeing around the globe. 

The conceptual paper and workflow-timeline developed at the 1st Dahlem-type workshop in Seville, Spain, 14-18 October, formed the basis of this 2nd Dahlem-type Workshop, organised in Rome, Italy, from 2-6 December, this time coordinated by the LifeWatch ERIC CTO, Juan Miguel González-Aranda. This 2nd Dahlem-type workshop delivered the first prototype of the new LifeWatch ERIC Non-indigenous and Invasive Species Virtual Research Environment. The collaborative construction and deployment approach and the intense interaction between ICT and NIS experts made it possible to achieve definition of the requirements and needs of the scientific community and of the main architecture layers (application, e-Services composition, e-infrastructure integration, and resources) that underpin the VRE. 

1st Dahlem-type Workshop

LifeWatch ERIC just launched an Internal Joint Initiative (IJI) focusing on the topic of Non-indigenous and Invasive Species (NIS) with the aim of developing new dedicated Virtual Research Environments. The IJI kicked off with the organisation of the LifeWatch ERIC 1st Dahlem-type Workshop: Current and future challenges of NIS in Europe, which took place from 14th to 18th October, in the Casa de la Ciencia, and the V. De Madariaga Foundation, in Seville, Spain. 

The choice of the Dahlem-type1 workshop stems from the desire of the infrastructure to use the most participative interdisciplinary approach in the search for new perspectives to drive the international research agenda on NIS and to involve relevant communities in the development of validation cases. For this reason, experts from different domains – from scientists working in the field of NIS, to ICT specialists and bio-informaticians – gathered in Seville to select the most promising research and management questions, identify the resources and tools available and specify those to be developed.

As a first step, participants identified and clustered the main issues related to NIS and discussed two macro topics, 1) risks and impacts of NIS, and 2) long-term responses of both the NIS and the native communities after invasion. Participants agreed on the development of a general framework to describe and estimate both risks and impacts of NIS (Topic one) and responses from the perspective of both NIS and native communities (Topic two) in the context of climate change. Several validation cases were proposed for each topic to apply this new framework.

On topic one, the suggested validation cases focus on the EU-scale assessment of ecosystem and habitat-type vulnerability to NIS in the context of climate change, including an assessment of sink source dynamics for specific, model, ecosystem types such as harbour ecosystems. On topic two, the chosen validation cases are based on the availability of long-term data series on a number of relevant invaders: (1) Caulerpa taxifolia and racemose; (2) Callinectes sapidus & other Crustaceans; (3) freshwater fishes at a global scale; (4) Mnemiopsis; (5) Rugulopteryx; (6) Ailanthus invasion and response monitoring with satellite images; (7) Metagenomics for invasive species; and (8) early detection of NIS with the metagenomic approach. An additional validation case was also proposed for later collaboration dealing with the risk for human health of NIS as vectors of pathogens.

The  LifeWatch ERIC ICT team’s contribution was to highlight those data resources and services required for the development of the validation cases and to suggest the implementation of an innovative approach, LifeBlock, a LifeWatch ERIC service that for the first time ever applies blockchain technology to biodiversity science. 

As an immediate result of this collaboration, scientists and ICT experts jointly outlined a conceptual paper and designed a workflow that will serve as an organised timeline along which different e-tools have to be developed to help address relevant issues related to NIS for scientists, managers, decision-makers and society.

The next Dahlem-type workshop will take place in Rome from 2nd to 6th December 2019, this time driven and coordinated by the ICT community, to produce a second technical paper and pave the way towards developing the required Virtual Research Environments.

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1 A Dahlem-type Workshop is defined as a quest for knowledge through an interdisciplinary communication process aimed at expanding the boundaries of current knowledge, addressing high-priority problems, identifying gaps in knowledge, posing questions aimed at directing future inquiries, and suggesting innovative approaches for solutions.