Future Martian explorers might not need to leave the Earth to prepare themselves for life on the Red Planet. The Mars Society have built an analogue research site in Utah, USA, which simulates the conditions on our neighbouring planet.
Practicing the methods needed to collect biological samples while wearing spacesuits, a team of Canadian scientists have studied the diverse local flora. Along with the lessons that one day will serve the first to conquer Mars, the researchers present an annotated checklist of the fungi, algae, cyanobacteria, lichens, and vascular plants from the station in their publication in the open-access journal Biodiversity Data Journal.
Located in the desert approximately 9 km outside of Hanksville, Utah, and about 10 km away from the Burpee Dinosaur Quarry, a recently described bone bed from the Jurassic Morrison Formation, the Mars Desert Research Station (MDRS) was constructed in 2002. Since then, it has been continuously visited by a wide range of researchers, including astrobiologists, soil scientists, journalists, engineers, and geologists.
Astrobiology, the study of the evolution and distribution of life throughout the universe, including the Earth, is a field increasingly represented at the MDRS. There, astrobiologists can take advantage of the extreme environment surrounding the station and seek life as if they were on Mars. To simulate the extraterrestrial conditions, the crew members even wear specially designed spacesuits so that they can practice standard field work activities with restricted vision and movement.
In their present research, the authors have identified and recorded 38 vascular plant species from 14 families, 13 lichen species from seven families, 6 algae taxa including both chlorophytes and cyanobacteria, and one fungal genus from the station and surrounding area. Living in such extreme environments, organisms such as fungi, lichens, algae, and cyanobacteria are of particular interest to astrobiologists as model systems in the search for life on Mars.
However, the authors note that there is still field work to be executed at the site, especially during the spring and the summer so that the complete local diversity of the area can be captured.
“While our present checklist is not an exhaustive inventory of the MDRS site,” they explain, “it can serve as a first-line reference for identifying vascular plants and lichens at the MDRS, and serves as a starting point for future floristic and ecological work at the station.”
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Original source:
Sokoloff P, Hamilton P, Saarela J (2016) The “Martian” flora: new collections of vascular plants, lichens, fungi, algae, and cyanobacteria from the Mars Desert Research Station, Utah.Biodiversity Data Journal 4: e8176. doi: 10.3897/BDJ.4.e8176
As part of the Deep Reef Observation Project (DROP), initiated by the Smithsonian Institution, a new goby fish species was discovered in the southern Caribbean. Living at depths greater than conventional SCUBA divers can access, yet too shallow to be of interest for deep-diving submersibles, the fish will now be known under the common name of the Godzilla goby.
Its discoverers Drs Luke Tornabene, Ross Robertson and Carole C. Baldwin, all affiliated with the Smithsonian Institution, have described the species in the open access journal ZooKeys.
Formally called Varicus lacerta, the species name translates to ‘lizard’ in Latin and refers to the reptilian appearance of the fish. Its prime colors are bright yellow and orange, while the eyes are green.
The new goby also has a disproportionately large head and multiple rows of recurved canine teeth in each jaw. This is also why the research team has chosen the common name of the Godzilla goby.
Apart from its lovely coloration, the new fish stands out with its branched, feather-like pelvic-fin rays and the absence of scales.
The scientists caught the Godzilla goby thanks to the manned submersible Curasub, which had already helped in discovering several species over the course of the project. Last year, Drs Ross Robertson and Carole Baldwin had another new goby published in ZooKeys. That time, they even named it after the submersible. Earlier this year, the DROP team also described nine additional new species, many of which were collected by the Curasub.
The manned submersible Curasub reaches depths up to 300 m in search of tropical marine fishes and invertebrates. As a result, it provides new information on the fauna that inhabits poorly studied deep-reef ecosystems.
The sub relies on two hydraulic arms, one equipped with a suction hose, and the other designed to immobilize the fish with an anaesthetizing chemical. That way, not only do the researchers gather live specimens, which once collected, are deposited into a vented acrylic cylinder attached to the outside of the sub, but also individuals suitable for critical DNA analyses.
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Original source:
Tornabene L, Robertson DR, Baldwin CC (2016) Varicus lacerta, a new species of goby (Teleostei, Gobiidae, Gobiosomatini, Nes subgroup) from a mesophotic reef in the southern Caribbean. ZooKeys 596: 143-156. doi: 10.3897/zookeys.596.8217
iSimangaliso Wetland Park, a UNESCO World Heritage Site in the sub-tropical north-eastern corner of South Africa has become famous for its birdlife, crocodiles and hippopotamuses that frolic in the warm estuarine waters of Lake St Lucia. However, there’s more to the park than the “big and hairy”, according to aquatic ecologist Prof Renzo Perissinotto at Nelson Mandela Metropolitan University (NMMU) in Port Elizabeth, whose research is published in the open access journal ZooKeys.
“Although we have spent several decades focusing on life in the estuary, we only recently came to realise that much of the wealth of biodiversity in the park exists in the small freshwater ponds that are adjacent to, but disconnected from, the main lake,” he says.
The St Lucia lake itself is generally brackish and is located on a large sandy expanse known as the Maputaland coastal plain. Dotted across the landscape of this coastal foreland are numerous temporary freshwater ponds, seeps and small streams that are disconnected from the brackish lake body.
A team of self-proclaimed “beetle nerds”, led by Prof Perissinotto, got together from NMMU and Plymouth University (UK) and uncovered more species of water beetles in these tiny water bodies than is known for any other similar-sized region in southern Africa.
The beetle collection trips were done over a 16-month period and revealed 68 species of predaceous water beetles alone, termed more formally as the “Hydradephaga”. The iSimangaliso Wetland Park houses approximately 20% of the total number of known species for this beetle group in the whole of southern Africa. Of the species collected during their expeditions, five have never been recorded in South Africa before, highlighting our poor understanding of aquatic insect distributions in this part of the world.
Most of the species collected (almost 80%) belonged to the family Dytiscidae, more commonly known as “diving beetles” due to their lifestyle that involves coming up for air and immediately diving back down to the depths to carry on hunting unsuspecting prey, which can be as large as small fish and amphibians.
Prof Perissinotto and his NMMU colleague Dr Matthew Bird, together with water beetle specialist Prof David Bilton (Plymouth University), collected specimens ranging from 1 mm to almost 5 cm in length (the tadpole eaters). According to Prof Bilton, “Irrespective of size, these water beetles are a crucial component of the iSimangaliso ecosystem in that they are the primary predators in these temporary wetlands, which generally lack fish. Their abundance and diversity can be used to gauge the overall health of wetland ecosystems as they are sensitive to pollution, for instance”.
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Original source:
Perissinotto R, Bird MS, Bilton DT (2016) Predaceous water beetles (Coleoptera, Hydradephaga) of the Lake St Lucia system, South Africa: biodiversity, community ecology and conservation implications. ZooKeys 595: 85-135. doi: 10.3897/zookeys.595.8614
Several individuals of P. pluvialis were found during nocturnal surveys near Manu National Park, a region recognized as having the highest diversity of reptiles and amphibians of any protected area.
The species has also been collected within the private conservation area Bosque Nublado, owned by the Peruvian NGO Perú Verde, and within the Huachiperi Haramba Queros Conservation Concession, the first such type of concession granted to a native community in Peru.
The new species is likely found within the park as well, bringing the number of known amphibian species in this area to 156. Similarly to other species within its genus, which is among the largest vertebrate genera, the new rain frog exhibits direct development. This means that it is capable of undergoing its entire life cycle without a free-living tadpole stage.
It can be distinguished from other members of its genus by call, skin texture, and the presence of a rostral papilla. It was given the name “pluvialis”, translatable to “rainy” from Latin, to denote the incredibly rain-soaked habitat it lives in (>8 meters of rain yearly), and because it was found calling only after heavy rains.
Unfortunately, when a fungal disease, known as the amphibian chytrid fungus, arrived in the area back in the early 2000s, many frog species in and around the region began to decline. Out of the studied ten individuals of the presently described new species, four were found to be infected. However, the impact of the disease on these particular rain frogs is still unknown, and their numbers do not seem to have decreased.
“This discovery highlights the need for increased study throughout the tropics, for example Manu NP and its surrounding areas have been well studied, but despite these efforts, new species are being continuously discovered,” points out first author Alex Shepack, a PhD student in the laboratory of co-author Dr Alessandro Catenazzi at Southern Illinois University.
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Original source:
Shepack A, von May R, Ttito A, Catenazzi A (2016) A new species of Pristimantis (Amphibia, Anura, Craugastoridae) from the foothills of the Andes in Manu National Park, southeastern Peru. ZooKeys 594: 143-164. doi: 10.3897/zookeys.594.8295
Inaccessibility and mysticism surrounding the mist-veiled mountains of the central Andes make this region promising to hide treasures. With an area of 2197 km2, most of the Llanganates National Park, Ecuador, is nearly unreachable and is traversed only by foot. However, fieldwork conducted by researchers from the Museo de Zoología at Catholic University of Ecuador resulted in the discovery of a more real and tangible gem: biodiversity.
Among other surprises, during their expeditions the researchers discovered two new species of rain frogs, formally named P. llanganati and P. yanezi. The new species are characterized by the spiny appearance typical of several species inhabiting montane forests. The study was published in the open access journal ZooKeys.
The new rain frogs belong to the megadiverse genus Pristimantis. They are direct-developing frogs, which means that they lack a tadpole stage and therefore do not undergo metamorphosis.
The Neotropical Andes houses a spectacular radiation of Pristimantis, especially in the Montane Forests of the eastern slopes of the Ecuadorian Andes. The species richness of this genus is still underestimated as a consequence of their cryptic morphology and the still sparse amphibian inventories in unexplored regions such as the Llanganates National Park.
The discovery reminds the authors of a mystic local legend dating from the 16th century, when the Inca Empire fell into the hands of Spanish conquerors. Word has it that in exchange for the young emperor’s life, Atahualpa, Incas offered to fill an entire room with tons of gold. However, the Spaniards broke their promise and the emperor was executed. A small group of loyal Incas led by General Rumiñahui decided to hide both, the mummy of Atahualpa and the gold, in the depths of the jungle of the Llanganates National Park.
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Original source:
Navarrete MJ, Venegas PJ, Ron SR (2016) Two new species of frogs of the genus Pristimantis from Llanganates National Park in Ecuador with comments on the regional diversity of Ecuadorian Pristimantis (Anura, Craugastoridae). ZooKeys 593: 139-162. doi: 10.3897/zookeys.593.8063
Innovation in ‘Big Data’ helps address problems that were previously overwhelming. What we know about organisms is in hundreds of millions of pages published over 250 years. New software tools of the Global Names project find scientific names, index digital documents quickly, correcting names and updating them. These advances help “Making small data big” by linking together to content of many research efforts. The study was published in the open access journal Biodiversity Data Journal.
The ‘Big Data’ vision of science is transformed by computing resources to capture, manage, and interrogate the deluge of information coming from new technologies, infrastructural projects to digitise physical resources (such as our literature from the Biodiversity Heritage Library), or digital versions of specimens and records about specimens by museums.
Increased bandwidth has made dialogue among distributed data centres feasible and this is how new insights into biology are arising. In the case of biodiversity sciences, data centres range in size from the large GenBank for molecular records and the Global Biodiversity Information Facility for records of occurrences of species, to a long tail of tens of thousands of smaller datasets and web-sites which carry information compiled by individuals, research projects, funding agencies, local, state, national and international governmental agencies.
The large biological repositories do not yet approach the scale of astronomy and nuclear physics, but the very large number of sources in the long tail of useful resources do present biodiversity informaticians with a major challenge – how to discover, index, organize and interconnect the information contained in a very large number of locations.
In this regard, biology is fortunate that, from the middle of the 18th Century, the community has accepted the use of latin binomials such as Homo sapiens or Ba humbugi for species. All names are listed by taxonomists. Name recognition tools can call on large expert compilations of names (Catalogue of Life, Zoobank, Index Fungorum, Global Names Index) to find matches in sources of digital information. This allows for the rapid indexing of content.
Even when we do not know a name, we can ‘discover’ it because scientific names have certain distinctive characteristics (written in italics, most often two successive words in a latinised form, with the first one – capitalised). These properties allow names not yet present in compilations of names to be discovered in digital data sources.
The idea of a names-based cyberinfrastructure is to use the names to interconnect large and small distributed sites of expert knowledge distributed across the Internet. This is the concept of the described Global Names project which carried out the work described in this paper.
The effectiveness of such an infrastructure is compromised by the changes to names over time because of taxonomic and phylogenetic research. Names are often misspelled, or there might be errors in the way names are presented. Meanwhile, increasing numbers of species have no names, but are distinguished by their molecular characteristics.
In order to assess the challenge that these problems may present to the realization of a names-based cyberinfrastructure, we compared names from GenBank and DRYAD (a digital data repository) with names from Catalogue of Life to assess how well matched they are.
As a result, we found out that fewer than 15% of the names in pair-wise comparisons of these data sources could be matched. However, with a names parser to break the scientific names into all of their component parts, those parts that present the greatest number of problems could be removed to produce a simplified or canonical version of the name. Thanks to such tools, name-matching was improved to almost 85%, and in some cases to 100%.
The study confirms the potential for the use of names to link distributed data and to make small data big. Nonetheless, it is clear that we need to continue to invest more and better names-management software specially designed to address the problems in the biodiversity sciences.
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Original source:
Patterson D, Mozzherin D, Shorthouse D, Thessen A (2016) Challenges with using names to link digital biodiversity information. Biodiversity Data Journal, doi: 10.3897/BDJ.4.e8080.
Among the eight new bee species that Spencer K. Monckton has discovered as part of his Biology Master’s degree at York University, there is one named after a popular draconic creature from the Japanese franchise Pokémon. Called the stem-nesting Charizard, the new insect belongs to a subgenus, whose 17 species are apparently endemic to Chile, yet occupy a huge variety of habitats.
The young scientist, who is currently a PhD student at the University of Guelph, studying sawfly systematics and phylogeography, has his work published in the open access journal ZooKeys.
Known as polyester bees, the family to which the new species belong is characterized by the curious secretions these bees produce. Once applied to the walls of their nest cells, the secretion dries into a smooth, cellophane-like lining.
The new bee species are endemic to Chile, yet they occupy a huge variety of habitats ranging from the hyper-arid Atacama Desert in the north, to moist forests of monkey puzzle trees in the south, spanning elevations from the Pacific coast to more than 3200 metres above sea level. All of them are also solitary and nest in hollow plant stems.
Although the new bee species might lack the fiery breath of the dragon-like Pokémon, much like its namesake, it is normally found around mountains. Also, like the fictional species, the new bee has a distinctively long, snout-like face and broad hind legs, with antennae in place of horns.
However, the stem-nesting Charizard bee, as well as the other new species, are tiny creatures that measure between 4 and 7 mm in length. Unlike the predominantly orange colouration of the Pokémon, both males and females are mostly dark brown to black, patterned with variable yellow markings.
Yet, sometimes these yellow markings can turn orange when specimens are preserved, as was the case for the first specimen that Spencer Monckton observed of this species, which, he says, “cemented the comparison”.
In his research paper Spencer Monckton not only describes eight new endemic polyester bees, but he also provides thoroughly illustrated keys for identification of both the males and females of each of the species.
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Original source:
Monckton SK (2016) A revision of Chilicola (Heteroediscelis), a subgenus of xeromelissine bees (Hymenoptera, Colletidae) endemic to Chile: taxonomy, phylogeny, and biogeography, with descriptions of eight new species. ZooKeys 591: 1-144. doi: 10.3897/zookeys.591.7731
The Australian small carpenter bee populations appear to have dramatically flourished in the period of global warming following the last Ice Age some 18,000 years ago.
The bee species is found in sub-tropical, coastal and desert areas from the north-east to the south of Australia. Researchers Rebecca Dew and Michael Schwarz from the Flinders University of South Australia teamed up with Sandra Rehan, the University of New Hampshire, USA, to model its past responses to climate change with the help of DNA sequences. Their findings are published in the open access Journal of Hymenoptera Research.
“It is really interesting that you see very similar patterns in bees around the world,” adds Rebecca. “Different climate, different environment, but the bees have responded in the same way at around the same time.”
In the face of future global warming these finding could be a good sign for some of our bees.
However, the news may not all be positive. There are other studies showing that some rare and ancient tropical bees require cool climate and, as a result, are already restricted to the highest mountain peaks of Fiji. For these species, climate warming could spell their eventual extinction.
“We now know that climate change impacts bees in major ways,” says Rebecca, “but the challenge will be to predict how those impacts play out. They are likely to be both positive and negative, and we need to know how this mix will unfold.”
Bees are major pollinators and are critical for many plants, ecosystems, and agricultural crops.
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Original source:
Dew RM, Rehan SM, Schwarz MP (2016) Biogeography and demography of an Australian native bee Ceratina australensis (Hymenoptera, Apidae) since the last glacial maximum. Journal of Hymenoptera Research 49: 25-41. doi: 10.3897/JHR.49.8066
We want to stress at this point that the import functionality itself is agnostic of the data source and any metadata file in EML 2.1.1 or 2.1.0 can be imported. We have listed these three most likely sources of metadata to illustrate the workflow.
In the remainder of the post, we will go through the original post from October 13, 2015 and highlight the latest updates.
At the time of the writing of the original post, the Biodiversity Information Standards conference, TDWG 2015, was taking place in Kenya. Data sharing, data re-use, and data discovery were being brought up in almost every talk. We might have entered the age of Big Data twenty years ago, but it is now that scientists face the real challenge – storing and searching through the deluge of data to find what they need.
As the rate at which we exponentially generate data exceeds the rate at which data storage technologies improve, the field of data management seems to be greatly challenged. Worse, this means the more new data is generated, the more of the older ones will be lost. In order to know what to keep and what to delete, we need to describe the data as much as possible, and judge the importance of datasets. This post is about a novel way to automatically generate scientific papers describing a dataset, which will be referred to as data papers.
The common characters of the records, i.e. descriptions of the object of study, the measurement apparatus and the statistical summaries used to quantify the records, the personal notes of the researcher, and so on, are called metadata. Major web portals such as DataONE, the Global Biodiversity Information Facility(GBIF), or the Long Term Ecological Research Network store metadata in conjunction with a given dataset as one or more text files, usually structured in special formats enabling the parsing of the metadata by algorithms.
To make the metadata and the corresponding datasets discoverable and citable, the concept of the data paper was introduced in the early 2000’s by the Ecological Society of America. This concept was brought to the attention of the biodiversity community by Chavan and Penev (2011) with the introduction of a new data paper concept, based on a metadata standard, such as the Ecological Metadata Language, and derived from metadata content stored at large data platforms, in this case the Global Biodiversity Information Facility (GBIF). You can read this article for an in-depth discussion of the topic.
Therefore, in the remainder of this post we will explain how to use an automated approach to publish a data paper describing an online dataset in Biodiversity Data Journal. The ARPHA system will convert the metadata describing your dataset into a manuscript for you after reading in the metadata. We will illustrate the workflow on the previously mentioned DataONE and GBIF.
The Data Observation Network for Earth (DataONE) is a distributed cyberinfrastructure funded by the U.S. National Science Foundation. It links together over twenty five nodes, primarily in the U.S., hosting biodiversity and biodiversity-related data, and provides an interface to search for data in all of them(Note: In the meantime, DataONE has updated their search interface).
Since butterflies are neat, let’s search for datasets about butterflies on DataONE! Type “Lepidoptera” in the search field and scroll down to the dataset describing “The Effects of Edge Proximity on Butterfly Biodiversity.” You should see something like this:
As you can notice, this resource has two objects associated with it: metadata, which has been highlighted, and the dataset itself. Let’s download the metadata from the cloud! The resulting text file, “Blandy.235.1.xml”, or whatever you want to call it, can be read by humans, but is somewhat cryptic because of all the XML tags. Now, you can import this file to the ARPHA writing platform and the information stored in it would be used to create a data paper!Go to the ARPHA web-site, and click on “Start a manuscript,” then scroll all the way down and click on “Import manuscript”.
Upload the “blandy” file and you will see an “Authors’ page,” where you can select which of the authors mentioned in the metadata must be included as authors of the data paper itself. Note that the user of ARPHA uploading the metadata is added to the list of the authors even if they are not included in the metadata. After the selection is done, a scholarly article is created by the system with the information from the metadata already in the respective sections of the article:
Now, the authors can add some description, edit out errors, tell a story, cite someone – all of this without leaving ARPHA – i.e. do whatever it takes to produce a high-quality scholarly text. After they are done, they can submit their article for peer-review and it could be published in a matter of hours. Voila!
Let’s look at GBIF. Go to “Data -> Explore by country” and select “Saint Vincent and the Grenadines,” an English-speaking Caribbean island. There are, as of the time of writing of this post, 166 occurrence datasets containing data about the islands. Select the dataset from the Museum of Comparative Zoology at Harvard. If you scroll down, you will see the GBIF annotated EML. Download this as a separate text file (if you are using Chrome, you can view the source, and then use Copy-Paste). Do the exact same steps as before – go to “Import manuscript” in ARPHA and upload the EML file. The result should be something like this, ready to finalize:
To finish it up, we want to leave you with some caveats and topics for further discussion. Till today, useful and descriptive metadata has not always been present. There are two challenges: metadata completeness and metadata standards. The invention of the EML standard was one of the first efforts to standardize how metadata should be stored in the field of ecology and biodiversity science.
Currently, our import system supports the last two versions of the EML standard: 2.1.1 and 2.1.0, but we hope to further develop this functionality. In an upcoming version of their search interface, DataONE will provide infographics on the prevalence of the metadata standards on their site (as illustrated below), so there is still work to be done, but if there is a positive feedback from the community, we will definitely keep elaborating this feature.
Image: DataONE
Regarding metadata completeness, our hope is that by enabling scientists to create scholarly papers from their metadata with a single-step process, they will be incentivized to produce high-quality metadata.
Now, allow us to give a disclaimer here: the authors of this blog post have nothing to do with the two datasets. They have not contributed to any of them, nor do they know the authors. The datasets have been chosen more or less randomly since the authors wanted to demonstrate the functionality with a real-world example. You should only publish data papers if you know the authors or you are the author of the dataset itself. During the actual review process of the paper, the authors that have been included will get an email from the journal.
Additional information:
This project has received funding from the European Union’s FP7 project EU BON (Building the European Biodiversity Observation Network), grant agreement No 308454, and Horizon 2020 research and innovation project BIG4 (Biosystematics, informatics and genomics of the big 4 insect groups: training tomorrow’s researchers and entrepreneurs) under the Marie Sklodovska-Curie grant agreement No. 642241 for a PhD project titled Technological Implications of the Open Biodiversity Knowledge Management System.
On October 20, 2015, we published a blog postabout the novel functionalities in ARPHA that allows streamlined import of specimen or occurrence records into taxonomic manuscripts.
Recently, this process was reflected in the “Tips and Tricks” section of the ARPHA authoring tool. Here, we’ll list the individual workflows:
Based on our earlier post, we will now go through our latest updates and highlight the new features that have been added since then.
Repositories and data indexing platforms, such as GBIF, BOLD systems, iDigBio, or PlutoF, hold, among other types of data, specimen or occurrence records. It is now possible to directly import specimen or occurrence records into ARPHA taxonomic manuscripts from these platforms [see Fig. 1]. We’ll refer to specimen or occurrence records as simply occurrence records for the rest of this post.
[Fig. 1] Workflow for directly importing occurrence records into a taxonomic manuscript.Until now, when users of the ARPHA writing tool wanted to include occurrence records as materials in a manuscript, they would have had to format the occurrences as an Excel sheet that is uploaded to the Biodiversity Data Journal, or enter the data manually. While the “upload from Excel” approach significantly simplifies the process of importing materials, it still requires a transposition step – the data which is stored in a database needs to be reformatted to the specific Excel format. With the introduction of the new import feature, occurrence data that is stored at GBIF, BOLD systems, iDigBio, or PlutoF, can be directly inserted into the manuscript by simply entering a relevant record identifier.
The functionality shows up when one creates a new “Taxon treatment” in a taxonomic manuscript in the ARPHA Writing Tool. To import records, the author needs to:
Locate an occurrence record or records in one of the supported data portals;
Note the ID(s) of the records that ought to be imported into the manuscript (see Tips and Tricks for screenshots);
Enter the ID(s) of the occurrence record(s) in a form that is to be seen in the “Materials” section of the species treatment;
Select a particular database from a list, and then simply clicks ‘Add’ to import the occurrence directly into the manuscript.
In the case of BOLD Systems, the author may also select a given Barcode Identification Number (BIN; for a treatment of BIN’s read below), which then pulls all occurrences in the corresponding BIN.
We will illustrate this workflow by creating a fictitious treatment of the red moss, Sphagnum capillifolium, in a test manuscript. We have started a taxonomic manuscript in ARPHA and know that the occurrence records belonging to S. capillifolium can be found on iDigBio. What we need to do is to locate the ID of the occurrence record in the iDigBio webpage. In the case of iDigBio, the ARPHA system supports import via a Universally Unique Identifier (UUID). We have already created a treatment for S. capillifolium and clicked on the pencil to edit materials [Fig. 2].
[Fig. 2] Edit materialsIn this example, type or paste the UUID (b9ff7774-4a5d-47af-a2ea-bdf3ecc78885), select the iDigBio source and click ‘Add’. This will pull the occurrence record for S. capillifolium from iDigBio and insert it as a material in the current paper [Fig. 3].
[Fig. 3] Materials after they have been importedThis workflow can be used for a number of purposes. An interesting future application is the rapid re-description of species, but even more exciting is the description of new species from BIN’s. BIN’s (Barcode Identification Numbers) delimit Operational Taxonomic Units (OTU’s), created algorithmically at BOLD Systems. If a taxonomist decides that an OTU is indeed a new species, then he/she can import all the type information associated with that OTU for the purposes of describing it as a new species.
Not having to retype or copy/paste species occurrence records, the authors save a lot of efforts. Moreover, they automatically import them in a structured Darwin Core format, which can easily be downloaded from the article text into structured data by anyone who needs the data for reuse.
Another important aspect of the workflow is that it will serve as a platform for peer-review, publication and curation of raw data, that is of unpublished individual data records coming from collections or observations stored at GBIF, BOLD, iDigBio and PlutoF. Taxonomists are used to publish only records of specimens they or their co-authors have personally studied. In a sense, the workflow will serve as a “cleaning filter” for portions of data that are passed through the publishing process. Thereafter, the published records can be used to curate raw data at collections, e.g. put correct identifications, assign newly described species names to specimens belonging to the respective BIN and so on.
Additional Information:
The work has been partially supported by the EC-FP7 EU BON project (ENV 308454, Building the European Biodiversity Observation Network) and the ITN Horizon 2020 project BIG4 (Biosystematics, informatics and genomics of the big 4 insect groups: training tomorrow’s researchers and entrepreneurs), under Marie Sklodovska-Curie grant agreement No. 642241.
Located in the desert approximately 9 km outside of Hanksville, Utah, and about 10 km away from the Burpee Dinosaur Quarry, a recently described bone bed from the Jurassic Morrison Formation, the Mars Desert Research Station (MDRS) was constructed in 2002. Since then, it has been continuously visited by a wide range of researchers, including astrobiologists, soil scientists, journalists, engineers, and geologists.
