OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System.
Apart from coordinating the Horizon 2020-funded project BiCIKL, scholarly publisher and technology provider Pensoft has been the engine behind what is likely to be the first production-stage semantic system to run on top of a reasonably-sized biodiversity knowledge graph.
OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System.
As of February 2023, OpenBiodiv contains 36,308 processed articles; 69,596 taxon treatments; 1,131 institutions; 460,475 taxon names; 87,876 sequences; 247,023 bibliographic references; 341,594 author names; and 2,770,357 article sections and subsections.
In fact, OpenBiodiv is a whole ecosystem comprising tools and services that enable biodiversity data to be extracted from the text of biodiversity articles published in data-minable XML format, as in the journals published by Pensoft (e.g. ZooKeys, PhytoKeys, MycoKeys, Biodiversity Data Journal), and other taxonomic treatments – available from Plazi and Plazi’s specialised extraction workflow – into Linked Open Data.
“I believe that OpenBiodiv is a good real-life example of how the outputs and efforts of a research project may and should outlive the duration of the project itself. Something that is – of course – central to our mission at BiCIKL.”
explains Prof Lyubomir Penev, BiCIKL’s Project Coordinator and founder and CEO of Pensoft.
“The basics of what was to become the OpenBiodiv database began to come together back in 2015 within the EU-funded BIG4 PhD project of Victor Senderov, later succeeded by another PhD project by Mariya Dimitrova within IGNITE. It was during those two projects that the backend Ontology-O, the first versions of RDF converters and the basic website functionalities were created,”
he adds.
At the time OpenBiodiv became one of the nine research infrastructures within BiCIKL tasked with the provision of virtual access to open FAIR data, tools and services, it had already evolved into a RDF-based biodiversity knowledge graph, equipped with a fully automated extraction and indexing workflow and user apps.
Currently, Pensoft is working at full speed on new user apps in OpenBiodiv, as the team is continuously bringing into play invaluable feedback and recommendation from end-users and partners at BiCIKL.
As a result, OpenBiodiv is already capable of answering open-ended queries based on the available data. To do this, OpenBiodiv discovers ‘hidden’ links between data classes, i.e. taxon names, taxon treatments, specimens, sequences, persons/authors and collections/institutions.
Thus, the system generates new knowledge about taxa, scientific articles and their subsections, the examined materials and their metadata, localities and sequences, amongst others. Additionally, it is able to return information with a relevant visual representation about any one or a combination of those major data classes within a certain scope and semantic context.
Users can explore the database by either typing in any term (even if misspelt!) in the search engine available from the OpenBiodiv homepage; or integrating an Application Programming Interface (API); as well as by using SPARQL queries.
On the OpenBiodiv website, there is also a list of predefined SPARQL queries, which is continuously being expanded.
“OpenBiodiv is an ambitious project of ours, and it’s surely one close to Pensoft’s heart, given our decades-long dedication to biodiversity science and knowledge sharing. Our previous fruitful partnerships with Plazi, BIG4 and IGNITE, as well as the current exciting and inspirational network of BiCIKL are wonderful examples of how far we can go with the right collaborators,”
While insect populations continue to decline, taxonomic expertise in Europe is at serious risk, confirms data obtained within the European Red List of Insect Taxonomists, a recent study commissioned by the European Union.
Expertise tends to be particularly poor in the countries with the richest biodiversity, while taxonomists are predominantly male and ageing
While insect populations continue to decline, taxonomic expertise in Europe is at serious risk, confirms data obtained within the European Red List of Insect Taxonomists, a recent study commissioned by the European Union.
Scientists who specialise in the identification and discovery of insect species – also known as insect taxonomists – are declining across Europe, highlights the newly released report by CETAF, International Union for Conservation of Nature (IUCN) and Pensoft. The authors of this report represent different perspectives within biodiversity science, including natural history and research institutions, nature conservation, academia and scientific publishing.
Despite the global significance of its taxonomic collections, Europe has been losing taxonomic expertise at such a rate that, at the moment nearly half (41.4%) of the insect orders are not covered by a sufficient number of scientists. If only EU countries are counted, the number looks only slightly more positive (34.5%). Even the four largest insect orders: beetles (Coleoptera), moths and butterflies (Lepidoptera), flies (Diptera) and wasps, bees, ants and sawflies (Hymenoptera) are only adequately ‘covered’ in a fraction of the countries.
To obtain details about the number, location and productivity of insect taxonomists, the team extracted information from thousands of peer-reviewed research articles published in the last decade, queried the most important scientific databases and reached out to over fifty natural science institutions and their networks. Furthermore, a dedicated campaign reached out to individual researchers through multiple communication channels. As a result, more than 1,500 taxonomists responded by filling in a self-declaration survey to provide information about their personal and academic profile, qualification and activities.
Then, the collected information was assessed against numerical criteria to classify the scientists into categories similar to those used by the IUCN Red List of Threatened SpeciesTM. In the European List of Insect Taxonomists, these range from Eroded Capacity (equivalent to Extinct) to Adequate Capacity (equivalent to Least Concern). The assessment was applied to the 29 insect orders (i.e. beetles, moths and butterflies etc.) to figure out which insect groups the society, conservation practitioners and decision-makers need not be concerned at this point.
Overview of the taxonomic capacity in European countries based upon the Red List Index (colour gradient goes from red (Eroded Capacity) to green (Adequate Capacity). Image by the European Red List of Taxonomists consortium.
On a country level, the results showed that Czechia, Germany and Russia demonstrate the most adequate coverage of insect groups. Meanwhile, Albania, Azerbaijan, Belarus, Luxembourg, Latvia, Ireland and Malta turned out to be the ones with insufficient number of taxonomists.
In most cases, the availability of experts seems to correlate to GDP, as wealthiest countries tend to invest more in their scientific institutions.
What is particularly worrying is that the lack of taxonomic expertise is more evident in the countries with the greatest species diversity. This trend may cause even more significant problems in the knowledge and conservation of these species, further aggravating the situation. Thus, the report provides further evidence about a global pattern where the countries richest in biodiversity are also the ones poorest in financial and human resources.
The research team also reminds that it is European natural history museums that host the largest scientific collections – including insects – brought from all over the globe. As such, Europe is responsible to the world for maintaining taxonomic knowledge and building adequate expert capacity.
Other concerning trends revealed in the new report are that the community of taxonomists is also ageing and – especially in the older groups – male-dominated (82%).
“One reason to have fewer young taxonomists could be due to limited opportunities for professional training (…), and the fact that not all professional taxonomists provide it, as a significant number of taxonomists are employed by museums and their opportunities for interaction with university students is probably not optimal. Gender bias is very likely caused by multiple factors, including fewer opportunities for women to be exposed to taxonomic research and gain an interest, unequal offer of career opportunities and hiring decisions. A fair-playing field for all genders will be crucial to address these shortcomings and close the gap.”
comments Ana Casino, CETAF’s Executive Director.
***
Entomologist examining a small insect under a microscope. Photo by anton_shoshin/stockadobe.com.
The European Red List of Taxonomists concludes with practical recommendations concerning strategic, science and societal priorities, addressed to specific decision-makers.
The authors give practical examples and potential solutions in support of their call to action.
For instance, in order to develop targeted and sustainable funding mechanisms to support taxonomy, they propose the launch of regular targeted Horizon Europe calls to study important insect groups for which taxonomic capacity has been identified to be at a particularly high risk of erosion.
To address specific gaps in expertise – such as the ones reported in the publication from Romania – a country known for its rich insect diversity, yet poor in taxonomic expertise – the consortium proposes the establishment of a natural history museum or entomological research institute that is well-fitted to serve as a taxonomic facility.
Amongst the scientific recommendations, the authors propose measures to ensure better recognition of taxonomic work at a multidisciplinary level. The scientific community, including disciplines that use taxonomic research, such as molecular biology, medicine and agriculture – need to embrace universal standards and rigorous conduct for the correct citation of scientific publications by insect taxonomists.
Societal engagement is another important call. “It is pivotal to widely raise awareness of the value and impact of taxonomy and the work of taxonomists. We must motivate young generations to join the scientific community” points Prof. Lyubomir Penev, Managing Director of Pensoft.
***
“Understanding taxonomy is a key to understanding the extinction risk of species. If we strategically target the gaps in expert capacity that this European Red List identifies, we can better protect biodiversity and support the well-being and livelihoods of our societies. With the climate crisis at hand, there is no time left to waste,”
added David Allen from the IUCN Red List team.
“As a dedicated supporter of the IUCN Red List, I am inspired by this call to strengthen the capacity, guided by evidence and proven scientific methods. However, Europe has much more scientific capacity than most biodiversity-rich regions of the world. So, what this report particularly highlights is the need for massively increasing investment in scientific discovery, and building taxonomic expertise, around the world,”
said Jon Paul Rodríguez, Chair of the IUCN Species Survival Commission.
***
Follow and join the conversation on Twitter using the #RedListTaxonomists hashtag.
All processes fit into a broad S-shaped envelope extending from the briefest to the most enduring biological events. For the first time, we have the first simple model that depicts the scope and scale of biology.
Arctic tern by Mark Stock, Schleswig-Holstein Wadden Sea National Park. License: CC BY-SA.
As biology is progressing into a digital age, it is creating new opportunities for discovery.
Increasingly, information from investigations into aspects of biology from ecology to molecular biology is available in a digital form. Older ‘legacy’ information is being digitized. Together, the digital information is accumulated in databases from which it can be harvested and examined with an increasing array of algorithmic and visualization tools.
From this trend has emerged a vision that, one day, we should be able to analyze any and all aspects of biology in this digital world.
However, before this can happen, there will need to be an infrastructure that gathers information from ALL sources, reshapes it as standardized data using universal metadata and ontologies, and made freely available for analysis.
That information also must make its way to trustworthy repositories to guarantee the permanent access to the data in a polished and fully suited for re-use state.
The first layer in the infrastructure is the one that gathers all old and new information, whether it be about the migrations of ocean mammals, the sequence of bases in ribosomal RNA, or the known locations of particular species of ciliated protozoa.
How many of these subdomains will be there?
To answer this, we need to have a sense of the scope and scale of biology.
With the Nature’s Envelope we have, for the first time, a simple model that depicts the scope and scale of biology. Presented as a rhetorical device by its author Dr David J. Patterson (University of Sydney, Australia), the Nature’s Envelope is described in a Forum Paper, published in the open-science journal Research Ideas and Outcomes(RIO).
This is achieved by compiling information about the processes conducted by all living organisms. The processes occur at all levels of organization, from sub-molecular transactions, such as those that underpin nervous impulses, to those within and among plants, animals, fungi, protists and prokaryotes. Further, they are also the actions and reactions of individuals and communities; but also the sum of the interactions that make up an ecosystem; and finally, the consequences of the biosphere as a whole system.
Nature’s Envelope, in green, includes all processes carried out by, involving, or the result of the activities of any and all organisms. The axes depict the duration of events and the sizes of participants using a log10 scale. Image by David J. Patterson. License: CC BY.
In the Nature’s Envelope, information on sizes of participants and durations of processes from all levels of organization are plotted on a grid. The grid uses a logarithmic (base 10) scale, which has about 21 orders of magnitude of size and 35 orders of magnitude of time. Information on processes ranging from the subatomic, through molecular, cellular, tissue, organismic, species, communities to ecosystems is assigned to the appropriate decadal blocks.
Examples include movements from the stepping motion of molecules like kinesin that move forward 8 nanometres in about 10 milliseconds; or the migrations of Arctic terns which follow routes of 30,000 km or more from Europe to Antarctica over 3 to 4 months.
The extremes of life processes are determined by the smallest and largest entities to participate, and the briefest and most enduring processes.
The briefest event to be included is the transfer of energy from a photon to a photosynthetic pigment as the photon passes through a chlorophyll molecule several nanometres in width at a speed of 300,000 km per second. That transaction is conducted in about 10-17 seconds. As it involves the smallest subatomic particles, it defines the lower left corner of the grid.
The most enduring is the process of evolution that has been progressing for almost 4 billion years. The influence of the latter has created the biosphere (the largest living object) and affects the gas content of the atmosphere. This process established the upper right extreme of the grid.
All biological processes fit into a broad S-shaped envelope that includes about half of the decadal blocks in the grid. The envelope drawn round the initial examples is Nature’s Envelope.
“Nature’s envelope will be a useful addition to many discussions, whether they deal with the infrastructure that will manage the digital age of biology, or provide the context for education on the diversity and range of processes that living systems engage in.
The version of Nature’s Envelopepublished in the RIO journal is seen as a first version, to be refined and enhanced through community participation,”
comments Patterson.
***
Original source:
Patterson DJ (2022) The scope and scale of the life sciences (‘Nature’s envelope’). Research Ideas and Outcomes 8: e96132. https://doi.org/10.3897/rio.8.e96132
In 2018, NHM London’s digitisation team started a project to digitise non-type herbarium material from the legume family. A recent data paper in the Biodiversity Data Journal reports on the outcomes.
You can find the original blog post by the Natural History Museum of London, reposted here with minor edits.
Legumes are a group of plants that include soybeans, peas, chickpeas, peanuts and lentils. They are a significant source of protein, fibre, carbohydrates, and minerals in our diet and some, like the cowpea, are resistant to droughts.
The project’s outcomes were published in a data paper in the Biodiversity Data Journal. Within the project, the digitisation team aimed to collectively digitise non-type herbarium material from the legume family. This includes rosewood trees (Dalbergia), padauk trees (Pterocarpus) and the Phaseolinae subtribe that contains many of the beans cultivated for human and animal food.
Guinea, Ethiopia, Sudan, Kenya, Uganda, Tanzania, Mozambique, Malawi and Madagascar
Asian
Bangladesh, Myanmar, Nepal, New Guinea and India
Southern and Central American
Guatemala, Honduras, El Salvador, Nicaragua, Bolivia, Argentina and Brazil
ODA-listed Countries
The legume groups: Dalbergia, Pterocarpus and Phaseolinae,were chosen for digitisation to support the development of dry beans as a sustainable and resilient crop, and to aid conservation and sustainable use of rosewood and padauk trees. Some of these beans, especially cow pea and pigeon pea, are sustainable and resilient crops, as they can be grown in poor-quality soils and are drought stress resistant. This makes them particularly suitable for agricultural production where the growing of other crops would be difficult.
Digitally discoverable herbarium specimens can provide important information about the distribution of individual species, as well as highlighting which species occur naturally together.
While there have been collaborative efforts between herbaria in the past, these have tended to prioritise digitisation of type specimens: the example specimens for which a species is named.
Types are important to identification, but being individual specimens, they don’t offer insights into species distribution over time. By focusing on the non-types across the world and over the last 200 years, we have released a brand-new resource to the global scientific community.
Searching for beans
This collection was digitised by creating an inventory record for each specimen, attaching images of each herbarium sheet, and then transcribing more data and georeferencing the specimens, providing an accurate locality in space and time for their collection.
We originally had four months and three members of staff to digitise over 11,000 specimens. The Covid-19 lockdown was ironically rather lucky for this project as it enabled us to have more time to transcribe and georeference all of the records.
say the researchers behind the digitisation project.
Map showing breakdown of records by country.
“We were able to assign country-level data to 10,857 out of the total number of 11,222 records. We were also able to transcribe the collectors’ names from the majority of our specimen labels (10,879 out of 11,222). Only 770 out of the 2,226 individuals identified during this project collected their specimens in ODA listed countries. The highest contributors were: Richard Beddome (130 specimens), Charles Clarke (110), Hans Schlieben (98) and Nathaniel Wallich (79). The breakdown of records by ODA country can be seen in the chart below. “
Map showing breakdown of records by country and pie chart showing distribution by ODA listed countries.
From our data, we can see the peak decade of collection was the 1930s, with almost half (4,583 specimens or 49,43%) collected between 1900 and 1950 (Fig. 10).
This peak can be attributed to three of our most prolific collectors: Arthur Kerr, John Gossweiler and Georges Le Testu, all of whom were most active in the 1930s. The oldest specimen (BM013713473) was collected by Mark Catesby (1683-1749) in the Bahamas in 1726.
they explain.
An interesting, but perhaps unsurprising, finding is that our collection is strongly male-dominated.
There are only two women (Caroline Whitefoord and Ynes Mexia) in the list of our top 50 plant collectors and they are not close to the most prolific collectors.
We identified more women in the rest of our records, but their contribution is on average less than 25 specimens per person in the dataset consisting of more than 10,000 specimens. In contrast, the top five male collectors contributed 10% of our collection.
they continued
Releasing Rosewoods
Both the Pterocarpus and Dalbergia genera include species that are used as expensive good quality timber that is prone to illegal logging. Many species such as Pterocarpus tinctorius are also listed on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. By releasing this new resource of information on all these plants from three of the biggest herbaria in the world, we can share this datа with the people who are taking care of biodiversity in these countries. The data can be used to identify hotspots, where the tree is naturally growing and protect these areas. These data would also allow much closer attention to be paid to areas that could be targets for illegal logging activity.
Pterocarpus tinctorius is a species of padauk tree that is listed as endangered on the IUCN Red List.
Cowpea (Vigna unguiculata) is a food and animal feed crop grown in the semi-arid tropics.
The ODA-listed countries are economically impoverished and disproportionately prone to be disadvantaged with the changing climate whether from flood or drought or increase in temperature.
Using data to identify good, nutritious plant species that can be grown in such conditions can therefore benefit local communities, potentially reducing dependence on imports, aid and on less resilient crops.
the team adds in conclusion.
***
This dataset is now openly available on the Museum’s Data Portal and a data paper about this work has been released in the Biodiversity Data Journal.
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Stay in touch with the Digitisation team by following us on Instagram and Twitter.
Don’t forget to also follow the Biodiversity Data Journal on Twitter and Facebook.
The FAIR Data Place – the key and final product of the partnership – is meant to provide scientists with all types of biodiversity data “at their fingertips”
The Horizon 2020 – funded project BiCIKL has reached its halfway stage and the partners gathered in Plovdiv (Bulgaria) from the 22nd to the 25th of October for the Second General Assembly, organised by Pensoft.
The BiCIKL project will launch a new European community of key research infrastructures, researchers, citizen scientists and other stakeholders in the biodiversity and life sciences based on open science practices through access to data, tools and services.
BiCIKL’s goal is to create a centralised place to connect all key biodiversity data by interlinking 15 research infrastructures and their databases. The 3-year European Commission-supported initiative kicked off in 2021 and involves 14 key natural history institutions from 10 European countries.
BiCIKL is keeping pace as expected with 16 out of the 48 final deliverables already submitted, another 9 currently in progress/under review and due in a few days. Meanwhile, 21 out of the 48 milestones have been successfully achieved.
Prof. Lyubomir Penev (BiCIKL’s project coordinator Prof. Lyubomir Penev and CEO and founder of Pensoft) opens the 2nd General Assembly of BiCIKL in Plovdiv, Bulgaria.
The hybrid format of the meeting enabled a wider range of participants, which resulted in robust discussions on the next steps of the project, such as the implementation of additional technical features of the FAIR Data Place (FAIR being an abbreviation for Findable, Accessible, Interoperable and Reusable).
This FAIR Data Place online platform – the key and final product of the partnership and the BiCIKL initiative – is meant to provide scientists with all types of biodiversity data “at their fingertips”.
This data includes biodiversity information, such as detailed images, DNA, physiology and past studies concerning a specific species and its ‘relatives’, to name a few. Currently, the issue is that all those types of biodiversity data have so far been scattered across various databases, which in turn have been missing meaningful and efficient interconnectedness.
Additionally, the FAIR Data Place, developed within the BiCIKL project, is to give researchers access to plenty of training modules to guide them through the different services.
Halfway through the duration of BiCIKL, the project is at a turning point, where crucial discussions between the partners are playing a central role in the refinement of the FAIR Data Place design. Most importantly, they are tasked with ensuring that their technologies work efficiently with each other, in order to seamlessly exchange, update and share the biodiversity data every one of them is collecting and taking care of.
By Year 3 of the BiCIKL project, the partners agree, when those infrastructures and databases become efficiently interconnected to each other, scientists studying the Earth’s biodiversity across the world will be in a much better position to build on existing research and improve the way and the pace at which nature is being explored and understood. At the end of the day, knowledge is the stepping stone for the preservation of biodiversity and humankind itself.
The Biodiversity Knowledge Hub is no longer existing on paper only! We are opening the 2nd day of the #BiCIKL_H2020 General Assembly looking at the prototype of the BKH created by the @LifeWatchERIC team. It's so exciting to see projects taking shape! 🤩 #Plovdivpic.twitter.com/RidzwBpxZx
“Needless to say, it’s an honour and a pleasure to be the coordinator of such an amazing team spanning as many as 14 partnering natural history and biodiversity research institutions from across Europe, but also involving many global long-year collaborators and their infrastructures, such as Wikidata, GBIF, TDWG, Catalogue of Life to name a few,”
said BiCIKL’s project coordinator Prof. Lyubomir Penev, CEO and founder of Pensoft.
“I see our meeting in Plovdiv as a practical demonstration of our eagerness and commitment to tackle the long-standing and technically complex challenge of breaking down the silos in the biodiversity data domain. It is time to start building freeways between all biodiversity data, across (digital) space, time and data types. After the last three days that we spent together in inspirational and productive discussions, I am as confident as ever that we are close to providing scientists with much more straightforward routes to not only generate more biodiversity data, but also build on the already existing knowledge to form new hypotheses and information ready to use by decision- and policy-makers. One cannot stress enough how important the role of biodiversity data is in preserving life on Earth. These data are indeed the groundwork for all that we know about the natural world”
Prof. Lyubomir Penev added.
Christos Arvanitidis (CEO of LifeWatch ERIC) at the 2nd General Assembly of the BiCIKL project.
“The point is: do we want an integrated structure or do we prefer federated structures? What are the pros and cons of the two options? It’s essential to keep the community united and allied because we can’t afford any information loss and the stakeholders should feel at home with the Project and the Biodiversity Knowledge Hub.”
Joe Miller, Executive Secretary and Director at GBIF, commented:
“We are a brand new community, and we are in the middle of the growth process. We would like to already have answers, but it’s good to have this kind of robust discussion to build on a good basis. We must find the best solution to have linkages between infrastructures and be able to maintain them in the future because the Biodiversity Knowledge Hub is the location to gather the community around best practices, data and guidelines on how to use the BiCIKL services… In order to engage even more partners to fill the eventual gaps in our knowledge.”
Joana Pauperio (biodiversity curator at EMBL-EBI) atthe 2nd General Assembly of the BiCIKL project.
“BiCIKL is leading data infrastructure communities through some exciting and important developments”
said Dr Guy Cochrane, Team Leader for Data Coordination and Archiving and Head of the European Nucleotide Archive at EMBL’s European Bioinformatics Institute (EMBL-EBI).
“In an era of biodiversity change and loss, leveraging scientific data fully will allow the world to catalogue what we have now, to track and understand how things are changing and to build the tools that we will use to conserve or remediate. The challenge is that the data come from many streams – molecular biology, taxonomy, natural history collections, biodiversity observation – that need to be connected and intersected to allow scientists and others to ask real questions about the data. In its first year, BiCIKL has made some key advances to rise to this challenge,”
“As a partner, we, at the Biodiversity Information Standards – TDWG, are very enthusiastic that our standards are implemented in BiCIKL and serve to link biodiversity data. We know that joining forces and working together is crucial to building efficient infrastructures and sharing knowledge.”
The project will go on with the first Round Table of experts in December and the publications of the projects who participated in the Open Call and will be founded at the beginning of the next year.
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Learn more about BiCIKL on the project’s website at: bicikl-project.eu
The uncertainty about a person’s identity hampers research, hinders the discovery of expertise, and obstructs the ability to give attribution or credit for work performed.
Worldwide, natural history institutions house billions of physical objects in their collections, they create and maintain data about these items, and they share their data with aggregators such as the Global Biodiversity Information Facility (GBIF), the Integrated Digitized Biocollections (iDigBio), the Atlas of Living Australia (ALA), Genbank and the European Nucleotide Archive (ENA).
Even though these data often include the names of the people who collected or identified each object, such statements may be ambiguous, as the names frequently lack any globally unique, machine-readable concept of their shared identity.
Despite the data being available online, barriers exist to effectively use the information about who collects or provides the expertise to identify the collection objects. People have similar names, change their name over the course of their lifetime (e.g. through marriage), or there may be variability introduced through the label transcription process itself (e.g. local look-up lists).
As a result, researchers and collections staff often spend a lot of time deducing who is the person or people behind unknown collector strings while collating or tidying natural history data. The uncertainty about a person’s identity hampers research, hinders the discovery of expertise, and obstructs the ability to give attribution or credit for work performed.
Disambiguation activities: the act of churning strings into verifiable things using all available evidence – need not be done in isolation. In addition to presenting a workflow on how to disambiguate people in collections, we also make the case that working in collaboration with colleagues and the general public presents new opportunities and introduces new efficiencies. There is tacit knowledge everywhere.
More often than not, data about people involved in biodiversity research are scattered across different digital platforms. However, with linking information sources to each other by using person identifiers, we can better trace the connections in these networks, so that we can weave a more interoperable narrative about every actor.
That said, inconsistent naming conventions or lack of adequate accreditation often frustrate the realization of this vision. This sliver of natural history could be churned to gold with modest improvements in long-term funding for human resources, adjustments to digital infrastructure, space for the physical objects themselves alongside their associated documents, and sufficient training on how to disambiguate people’s names.
“He aha te mea nui o te ao. He tāngata, he tāngata, he tāngata.”
“What is the most important thing in the world? It is people, it is people, it is people.”
(Māori proverb)
The process of properly disambiguating those who have contributed to natural history collections takes time.
The disambiguation process involves the extra challenge of trying to deduce “who is who” for legacy data, compared to undertaking this activity for people alive today. Retrospective disambiguation can require considerable detective work, especially for scarcely known people or if the community has a different naming convention. Provided the results of this effort are well-communicated and openly shared, mercifully, it need only be done once.
At the core of our research is the question of how to solve the issue of assigning proper credit.
In our recent Methods paper, we discuss several methods for this, as well as available routes for making records available online that include not only the names of people expressed as text, but additionally twinned with their unique, resolvable identifiers.
Disambiguation is a cycle. Enrichment of the data feeds off itself leading to further disambiguation. As more names are disambiguated and more biographical data are accumulated, it becomes easier to disambiguate more names.
First and foremost, we should maintain our own public biographical data by making full use of ORCID. In addition to preserving our own scientific legacy and that of the institutions that employ us, we have a responsibility to avoid generating unnecessary disambiguation work for others.
For legacy data, where the people connected to the collections are deceased, Wikidata can be used to openly document rich bibliographic and demographic data, each statement with one or more verifiable references. Wikidata can also act as a bridge to link other sources of authority such as VIAF or ORCID identifiers. It has many tools and services to bulk import, export, and to query information, making it well-suited as a universal democratiser of information about people often walled-off in collection management systems (CMS).
A network of the top twenty most used identifiers for biologists on Wikidata.
Once unique identifiers for people are integrated in collection management systems, these may be shared with the global collections and research community using the new Darwin Core terms, recordedByID or identifiedByID along with the well-known, yet text-based terms, recordedBy or identifiedBy.
Approximately 120 datasets published through GBIF now make use of these identifier-based terms, which are additionally resolved in Bionomia every few weeks alongside co-curated attributions newly made there. This roundtrip of data – emerging as ambiguous strings of text from the source, affixed with resolvable identifiers elsewhere, absorbed into the source as new digital annotations, and then re-emerging with these fresh, identifier-based enhancements – is an exciting approach to co-manage collections data.
Round tripping. In Bionomia, people identifiers from Wikidata and ORCID are used to enrich data published via GBIF, thus linking natural history specimens to the world’s collectors.
Disambiguation work is particularly important in recognising contributors who have been historically marginalized. For example, gender bias in specimen data can be seen in the case of Wilmatte Porter Cockerell, a prolific collector of botanical, entomological and fossil specimens. Cockerell’s collections are often attributed to her husband as he was also a prolific collector and the two frequently collected together.
On some labels, her identity is further obscured as she is simply recorded as “& wife” (see example on GBIF). Since Wilmatte Cockerell was her husband’s second wife, it can take some effort to confirm if a specimen can be attributed to her and not her husband’s first wife, who was also involved in collecting specimens. By ensuring that Cockerell is disambiguated and her contributions are appropriately attributed, the impact of her work becomes more visible enabling her work to be properly and fairly credited.
Thus, disambiguation work helps to not only give credit where credit is due, thereby making data about people and their biodiversity collections more findable, but it also creates an inclusive and representative narrative of the landscape of people involved with scientific knowledge creation, identification, and preservation.
A future – once thought to be a dream – where the complete scientific output of a person is connected as Linked Open Data (LOD) is now.
Both the tools and infrastructure are at our disposal and the demand is palpable. All institutions can contribute to this movement by sharing data that include unique identifiers for the people in their collections. We recommend that institutions develop a strategy, perhaps starting with employees and curatorial staff, people of local significance, or those who have been marginalized, and to additionally capitalize on existing disambiguation activities elsewhere. This will have local utility and will make a significant, long-term impact.
The more we participate in these activities, the greater chance we will uncover positive feedback loops, which will act to lighten the workload for all involved, including our future selves!
The disambiguation of people in collections is an ongoing process, but it becomes easier with practice. We also encourage collections staff to consider modifying their existing workflows and policies to include identifiers for people at the outset, when new data are generated or when new specimens are acquired.
There is more work required at the global level to define, update, and ratify standards and best practices to help accelerate data exchange or roundtrips of this information; there is room for all contributions. Thankfully, there is a diverse, welcoming, energetic, and international community involved in these activities.
We see a bright future for you, our collections, and our research products – well within reach – when the identities of people play a pivotal role in the construction of a knowledge graph of life.
Groom Q, Bräuchler C, Cubey RWN, Dillen M, Huybrechts P, Kearney N, Klazenga N, Leachman S, Paul DL, Rogers H, Santos J, Shorthouse DP, Vaughan A, von Mering S, Haston EM (2022) The disambiguation of people names in biological collections. Biodiversity Data Journal 10: e86089. https://doi.org/10.3897/BDJ.10.e86089
Left: Cuong Pham, Jimmy Crigler, and Joshua Torres working on a community science platform in an exhibit at the Field Museum (photo by Melanie Pivarski, Roosevelt University). Right: The microscopic leaves of a liverwort, a primitive plant that helps scientists track climate change (photo by Lauren Johnson, Field Museum).
Ask any scientist — for every “Eureka!” moment, there’s a lot of less-than-glamorous work behind the scenes. Making discoveries about everything from a new species of dinosaur to insights about climate change entails some slogging through seemingly endless data and measurements that can be mind-numbing in large doses.
Community science shares the burden with volunteers who help out, for even just a few minutes, on collecting data and putting it into a format that scientists can use. But the question remains how useful these data actually are for scientists.
A new study, authored by a combination of high school students, undergrads and grad students, and professional scientists showed that when museum-goers did a community science activity in an exhibit, the data they produced were largely accurate, supporting the argument that community science is a viable way to tackle big research projects.
“It was surprising how all age groups from young children, families, youth, and adults were able to generate high-quality taxonomic data sets, making observations and preparing measurements, and at the same time empowering community scientists through authentic contributions to science,”
“This study demonstrates the wonderful scientific outcomes that occur when an entire community comes together,”
says Melanie Pivarski, an associate professor of mathematics at Roosevelt University (USA) and the study’s lead author.
“We were able to combine a small piece of the Field Museum’s vast collections, their scientific knowledge and exhibit creation expertise, the observational skills of biology interns at Northeastern Illinois University (USA), led by our collaborator Tom Campbell, and our Roosevelt University student’s data science expertise. The creation of this set of high-quality data was a true community effort!”
The study focuses on an activity in an exhibition at the Field Museum, in which visitors could partake in a community science project. In the community science activity, museumgoers used a large digital touchscreen to measure the microscopic leaves photographs of plants called liverworts.
These tiny plants, the size of an eyelash, are sensitive to climate change, and they can act like a canary in a coal mine to let scientists know about how climate change is affecting a region. It’s helpful for scientists to know what kinds of liverworts are present in an area, but since the plants are so tiny, it’s hard to tell them apart. The sizes of their leaves (or rather, lobes — these are some of the most ancient land plants on Earth, and they evolved before true leaves had formed) can hint at their species. But it would take ages for any one scientist to measure all the leaves of the specimens in the Field’s collection. Enter the community scientists.
“Drawing a fine line to measure the lobe of a liverwort for a few hours can be mentally strenuous, so it’s great to have community scientists take a few minutes out of their day using fresh eyes to help measure a plant leaf. A few community scientists who’ve helped with classifying acknowledged how exciting it is knowing they are playing a helping hand in scientific discovery,”
says Heaven Wade, a research assistant at the Field Museum who began working on the MicroPlants project as an undergraduate intern.
Community scientists using the digital platform measured thousands of microscopic liverwort leaves over the course of two years.
“At the beginning, we needed to find a way to sort the high quality measurements out from the rest. We didn’t know if there would be kids drawing pictures on the touchscreen instead of measuring leaves or if they’d be able to follow the tutorial as well as the adults did. We also needed to be able to automate a method to determine the accuracy of these higher quality measurements,”
says Pivarski.
To answer these questions, Pivarski worked with her students at Roosevelt University to analyze the data. They compared measurements taken by the community scientists with measurements done by experts on a couple “test” lobes; based on that proof of concept, they went on to analyze the thousands of other leaf measurements. The results were surprising.
“We were amazed at how wonderfully children did at this task; it was counter to our initial expectations. The majority of measurements were high quality. This allowed my students to create an automated process that produced an accurate set of MicroPlant measurements from the larger dataset,”
says Pivarski.
The researchers say that the study supports the argument that community science is valuable not just as a teaching tool to get people interested in science, but as a valid means of data collection.
“Biological collections are uniquely poised to inform the stewardship of life on Earth in a time of cataclysmic biodiversity loss, yet efforts to fully leverage collections are impeded by a lack of trained taxonomists. Crowd-sourced data collection projects like these have the potential to greatly accelerate biodiversity discovery and documentation from digital images of scientific specimens,”
says von Konrat.
Research article:
Pivarski M, von Konrat M, Campbell T, Qazi-Lampert AT, Trouille L, Wade H, Davis A, Aburahmeh S, Aguilar J, Alb C, Alferes K, Barker E, Bitikofer K, Boulware KJ, Bruton C, Cao S, Corona Jr. A, Christian C, Demiri K, Evans D, Evans NM, Flavin C, Gillis J, Gogol V, Heublein E, Huang E, Hutchinson J, Jackson C, Jackson OR, Johnson L, Kirihara M, Kivarkis H, Kowalczyk A, Labontu A, Levi B, Lyu I, Martin-Eberhardt S, Mata G, Martinec JL, McDonald B, Mira M, Nguyen M, Nguyen P, Nolimal S, Reese V, Ritchie W, Rodriguez J, Rodriguez Y, Shuler J, Silvestre J, Simpson G, Somarriba G, Ssozi R, Suwa T, Syring C, Thirthamattur N, Thompson K, Vaughn C, Viramontes MR, Wong CS, Wszolek L (2022) People-Powered Research and Experiential Learning: Unravelling Hidden Biodiversity. Research Ideas and Outcomes 8: e83853. https://doi.org/10.3897/rio.8.e83853
“…the most realistic and tangible way out of the looming biodiversity crisis is to put a price tag on species and thereby a cost to actions that compromise them.”
So far, science has described more than 2 million species, and millions more await discovery. While species have value in themselves, many also deliver important ecosystem services to humanity, such as insects that pollinate our crops.
Meanwhile, as we lack a standardized system to quantify the value of different species, it is too easy to jump to the conclusion that they are practically worthless. As a result, humanity has been quick to justify actions that diminish populations and even imperil biodiversity at large.
In a study, published in the scholarly open-science journal Research Ideas and Outcomes, a team of Estonian and Swedish scientists propose to formalize the value of all species through a conceptual species ‘stock market’ (SSM). Much like the regular stock market, the SSM is to act as a unified basis for instantaneous valuation of all items in its holdings.
However, other aspects of the SSM would be starkly different from the regular stock market. Ownership, transactions, and trading will take new forms. Indeed, species have no owners, and ‘trade’ would not be about transfer of ownership rights among shareholders. Instead, the concept of ‘selling’ would comprise processes that erase species from some specific area – such as war, deforestation, or pollution.
“The SSM would be able to put a price tag on such transactions, and the price could be thought of as an invoice that the seller needs to settle in some way that benefits global biodiversity,”
explains the study’s lead author Prof. Urmas Kõljalg (University of Tartu, Estonia).
Conversely, taking some action that benefits biodiversity – as estimated through individuals of species – would be akin to buying on the species stock market. Buying, too, has a price tag on it, but this price should probably be thought of in goodwill terms. Here, ‘money’ represents an investment towards increased biodiversity.
“By rooting such actions in a unified valuation system it is hoped that goodwill actions will become increasingly difficult to dodge and dismiss,”
adds Kõljalg.
Interestingly, the SSM revolves around the notion of digital species. These are representations of described and undescribed species concluded to exist based on DNA sequences and elaborated by including all we know about their habitat, ecology, distribution, interactions with other species, and functional traits.
For the SSM to function as described, those DNA sequences and metadata need to be sourced from global scientific and societal resources, including natural history collections, sequence databases, and life science data portals. Digital species might be managed further by incorporating data records of non-sequenced individuals, notably observations, older material in collections, and data from publications.
The study proposes that the SSM is orchestrated by the international associations of taxonomists and economists.
“Non-trivial complications are foreseen when implementing the SSM in practice, but we argue that the most realistic and tangible way out of the looming biodiversity crisis is to put a price tag on species and thereby a cost to actions that compromise them,”
says Kõljalg.
“No human being will make direct monetary profit out of the SSM, and yet it’s all Earth’s inhabitants – including humans – that could benefit from its pointers.”
Original source
Kõljalg U, Nilsson RH, Jansson AT, Zirk A, Abarenkov K (2022) A price tag on species. Research Ideas and Outcomes 8: e86741. https://doi.org/10.3897/rio.8.e86741
The purpose of this call is to solicit, select and implement four to six biodiversity data-related scientific projects that will make use of the added value services developed by the leading Research Infrastructures that make the BiCIKL project.
The BiCIKL project invites submissions of Expression of Interest (EoI) to the First BiCIKL Open Call for projects. The purpose of this call is to solicit, select and implement four to six biodiversity data-related scientific projects that will make use of the added value services developed by the leading Research Infrastructures that make the BiCIKL project.
By opening this call, BiCIKL aims to better understand how it could support scientific questions that arise from across the biodiversity world in the future, while addressing specific scientific or technical biodiversity data challenges presented by the applicants.
We need and want to assess real-world problems and make the best possible use of our data and technical capabilities. This will greatly assist in defining the long-term development goals of the participating Research Infrastructures and improve the way they can technically and operationally work together to deliver greater scientific value.
explain the project partners.
The BiCIKL project – a Horizon 2020-funded project involving 14 European institutions, representing major global players in biodiversity research and natural history, and coordinated by Pensoft – establishes a European starting community of key research infrastructures, researchers, citizen scientists and other biodiversity and life sciences stakeholders based on open science practices through access to data, tools and services.
New Research Idea, published in RIO Journal presents a promising machine-learning ecosystem to unite experts around the world and make up for lacking taxonomic expertise.
In their Research Idea, published in Research Ideas and Outcomes (RIO Journal), Swiss-Dutch research team present a promising machine-learning ecosystem to unite experts around the world and make up for lacking expert staff
Guest blog post by Luc Willemse, Senior collection manager at Naturalis Biodiversity Centre (Leiden, Netherlands)
Imagine the workday of a curator in a national natural history museum. Having spent several decades learning about a specific subgroup of grasshoppers, that person is now busy working on the identification and organisation of the holdings of the institution. To do this, the curator needs to study in detail a huge number of undescribed grasshoppers collected from all sorts of habitats around the world.
The problem here, however, is that a curator at a smaller natural history institution – is usually responsible for all insects kept at the museum, ranging from butterflies to beetles, flies and so on. In total, we know of around 1 million described insect species worldwide. Meanwhile, another 3,000 are being added each year, while many more are redescribed, as a result of further study and new discoveries. Becoming a specialist for grasshoppers was already a laborious activity that took decades, how about knowing all insects of the world? That’s simply impossible.
Then, how could we expect from one person to sort and update all collections at a museum: an activity that is the cornerstone of biodiversity research? A part of the solution, hiring and training additional staff, is costly and time-consuming, especially when we know that experts on certain species groups are already scarce on a global scale.
We believe that automated image recognition holds the key to reliable and sustainable practises at natural history institutions.
Today, image recognition tools integrated in mobile apps are already being used even by citizen scientists to identify plants and animals in the field. Based on an image taken by a smartphone, those tools identify specimens on the fly and estimate the accuracy of their results. What’s more is the fact that those identifications have proven to be almost as accurate as those done by humans. This gives us hope that we could help curators at museums worldwide take better and more timely care of the collections they are responsible for.
However, specimen identification for the use of natural history institutions is still much more complex than the tools used in the field. After all, the information they store and should be able to provide is meant to serve as a knowledge hub for educational and reference purposes for present and future generations of researchers around the globe.
This is why we propose a sustainable system where images, knowledge, trained recognition models and tools are exchanged between institutes, and where an international collaboration between museums from all sizes is crucial. The aim is to have a system that will benefit the entire community of natural history collections in providing further access to their invaluable collections.
We propose four elements to this system:
A central library of already trained image recognition models (algorithms) needs to be created. It will be openly accessible, so any other institute can profit from models trained by others.
Mock-up of a Central Library of Algorithms.
A central library of datasets accessing images of collection specimens that have recently been identified by experts. This will provide an indispensable source of images for training new algorithms.
Mock-up of a Central Library of Datasets.
A digital workbench that provides an easy-to-use interface for inexperienced users to customise the algorithms and datasets to the particular needs in their own collections.
As the entire system depends on international collaboration as well as sharing of algorithms and datasets, a user forum is essential to discuss issues, coordinate, evaluate, test or implement novel technologies.
How would this work on a daily basis for curators? We provide two examples of use cases.
First, let’s zoom in to a case where a curator needs to identify a box of insects, for example bush crickets, to a lower taxonomic level. Here, he/she would take an image of the box and split it into segments of individual specimens. Then, image recognition will identify the bush crickets to a lower taxonomic level. The result, which we present in the table below – will be used to update object-level registration or to physically rearrange specimens into more accurate boxes. This entire step can also be done by non-specialist staff.
Mock-up of box with grasshoppers mentioned in the above table
Results of automated image recognition identify specimens to a lower taxonomic level.
Another example is to incorporate image recognition tools into digitisation processes that include imaging specimens. In this case, image recognition tools can be used on the fly to check or confirm the identifications and thus improve data quality.
Mock-up of an interface for automated taxon identification.
Using image recognition tools to identify specimens in museum collections is likely to become common practice in the future. It is a technical tool that will enable the community to share available taxonomic expertise.
Using image recognition tools creates the possibility to identify species groups for which there is very limited to none in-house expertise. Such practises would substantially reduce costs and time spent per treated item.
Image recognition applications carry metadata like version numbers and/or datasets used for training. Additionally, such an approach would make identification more transparent than the one carried out by humans whose expertise is, by design, in no way standardised or transparent.
Greeff M, Caspers M, Kalkman V, Willemse L, Sunderland BD, Bánki O, Hogeweg L (2022) Sharing taxonomic expertise between natural history collections using image recognition. Research Ideas and Outcomes 8: e79187. https://doi.org/10.3897/rio.8.e79187
