Huge data encompassed into a unique georeferenced macrobenthic assemblages database

A new peer-reviewed data paper offers a comprehensive, open-access collection of georeferenced biological information about the Antarctic macrobenthic communities. The term macrobenthic refers to the visible-for-the-eye organisms that live near or on the sea bottom such as echinoderms, sponges, ascidians, crustaceans. The paper will help in coordinating biodiversity research and conservation activities on species living near the ocean bottom of the Antarctic.
The data paper "Antarctic macrobenthic communities: A compilation of circumpolar information", published in the open access journal Nature Conservation, describes data from approximately 90 different expeditions in the region since 1956 that have now been made openly available under a CC-By license. The paper provides unique georeferenced biological basic information for the planning of future coordinated research activities, for example those under the umbrella of the biology program Antarctic Thresholds – Ecosystem Resilience and Adaptation (AnT-ERA) of the Scientific Committee on Antarctic Research (SCAR). The information collected could be also beneficial for current conservation priorities such as the planning of Marine Protected Areas (MPAs) by the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR).
The expeditions were organised by several famous explorers of the Antarctic. The area covered by the paper consists of almost the entire Southern Ocean, including sites covered by a single ice-shelf. The vast majority of information is from shelf areas around the continent at water depth shallower than 800m. The information from the different sources is then attributed to the classified macrobenthic assemblages. The results are made publicly available via the "Antarctic Biodiversity Facility" (data.biodiversity.aq).
A specific feature of this paper is that the manuscript was automatically generated from the Integrated Publishing Toolkit of the Antarctic Node of the Global Biodiversity Information Facility (AntaBIF IPT) and then submitted to the journal Nature Conservation through a novel workflow developed by GBIF and Pensoft Publishers. (see previous press release). Data are made freely available through the AntaBIF IPT, and sea-bed images of 214 localities through the data repository for geoscience and environmental data, PANGAEA- Data Publisher for Earth and Environmental Science (sample: http://doi.pangaea.de/10.1594/PANGAEA.198682).

Researchers and the public can now have immediate access to data underlying discovery of new species of life on Earth, under a new streamlined system linking taxonomic research with open data publication.

The partnership paves the way for unlocking and preserving a wealth of 'small data' backing up research conclusions, which often become lost within a few years of an article's publication in an academic journal.

In the first example of the new collaboration in action, the Biodiversity Data Journal carries a peer-reviewed description of a new species of spider discovered during a field course in Borneo just one month ago. At the same time, the data showing location of the spider's occurrence in nature are automatically harvested by the Global Biodiversity Information Facility (GBIF), and richer data such as images and the species description are exported to the Encyclopedia of Life (EOL).

This contrasts with an average 'shelf life' of twenty-one years between field discovery of a new species and its formal description and naming, according to a recent study in Current Biology.

A group of scientists and students discovered the new species of spider during a field course in Borneo, supervised by Jeremy Miller and Menno Schilthuizen from the Naturalis Biodiversity Center, based in Leiden, the Netherlands. The species was described and submitted online from the field to the Biodiversity Data Journal through a satellite internet connection, along with the underlying data . The manuscript was peer-reviewed and published within two weeks of submission. On the day of publication, GBIF and EOL have harvested and included the data in their respective platforms.

The new workflow established between GBIF, EOL and Pensoft Publishers' Biodiversity Data Journal, with the support of the Swiss NGO Plazi, automatically exports treatment and occurrence data into a Darwin Core Archive, a standard format used by GBIF and other networks to share data from many different sources. This means GBIF can extract these data on the day of the article's publication, making them immediately available to science and the public through its portal and web services, further enriching the biodiversity data already freely accessible through the GBIF network. Similarly, the information and multimedia resources become accessible via EOL's species pages.

One of the main purposes of the partnership is to ensure that such data remain accessible for future use in research. A recent study published in Current Biology found that 80 % of scientific data are lost in less than 10 years following their creation.

Donald Hobern, GBIF's Executive Secretary, commented: "A great volume of extremely important information about the world's species is effectively inaccessible, scattered across thousands of small datasets carefully curated by taxonomic researchers. I find it very exciting that this new workflow will help preserve these 'small data' and make them immediately available for re-use through our networks."

"Re-use of data published on paper or in PDF format is a huge challenge in all branches of science", said Prof. Lyubomir Penev, managing director of Pensoft and founder of the Biodiversity Data Journal. "This problem has been tackled firstly by our partners from Plazi who created a workflow to extract data from legacy literature and submit it to GBIF. The workflow currently launched by GBIF, EOL and the Biodiversity Data Journal radically shortens the way from publication of data to their sharing and re-use and makes the whole process cost efficient", added Prof. Penev.

The elaboration of the workflow from BDJ and Plazi to GBIF through Darwin Core Archive was supported by the EU-funded project EU BON (Building the European Biodiversity Observation Network, grant No 308454). The basic concept has been initially discussed and outlined in the course of the pro-iBiosphere project (Coordination and policy development in preparation for a European Open Biodiversity Knowledge Management System, addressing Acquisition, Curation, Synthesis, Interoperability and Dissemination, grant No 312848).

Original source:

Miller J, Schilthuizen M, Burmester J, van der Graaf L, Merckx V, Jocqué M, Kessler P, Fayle T, Breeschoten T, Broeren R, Bouman R, Chua W, Feijen F, Fermont T, Groen K, Groen M, Kil N, de Laat H, Moerland M, Moncoquet C, Panjang E, Philip A, Roca-Eriksen R, Rooduijn B, van Santen M, Swakman V, Evans M, Evans L, Love K, Joscelyne S, Tober A, Wilson H, Ambu L, Goossens B (2014) Dispatch from the field: ecology of micro web-building spiders with description of a new species. Biodiversity Data Journal 2: e1076. DOI: 10.3897/BDJ.2.e1076

Data collection and analysis are at the core of modern research, and often take months or even years during which researchers remain uncredited for their contribution. A new plugin to a workflow previously developed by the Global Biodiversity Information Facility (GBIF) and Pensoft, and tested with datasets shared through GBIF and DataONE, now makes it possible to convert metadata into a manuscript for scholarly publications, with a click of a button.

Pensoft has currently implemented the feature for biodiversity, ecological and environmental data. Such records are either published through GBIF or deposited at DataONE, from where the associated metadata can be converted directly into data paper manuscripts within the ARPHA Writing Tool, where the authors may edit and finalize it in collaboration with co-authors and peers and submit it to the Biodiversity Data Journal (BDJ) with another click. Until now, the GBIF metadata have been exported into an RTF file. The new feature will be also part of future Pensoft projects, including the recently announced Research Ideas & Outcomes (RIO) Journaland the forthcoming Ecology and Sustainability Data Journal.

The concept of the data paper was introduced in the early 2000's by the Ecological Society of America in order to solve issues of handling big data and to make the metadata and the corresponding datasets discoverable and citable. It was then brought to the attention of the biodiversity community in 2011 as a result of a joint GBIF and Pensoft project and later implemented in the routine publishing process in all Pensoft journals.

Since then, Pensoft has been working with GBIF, and subsequently DataONE to automate the process of converting metadata into a human-readable data paper format. The novel workflow means that with only a couple of clicks, publishers of datasets on either GBIF, DataONE or any other portal storing metadata in the same format, may submit a manuscript for peer-review and open access citable publication in BDJ.

The process is simple, yet it brings a lot of benefits. Publishing data does not only mean a citable publication and, thus, credit to the authors and the repository itself, but it also provides the option to improve your work and collect opinion though peer-review. BDJ also shortens the distance between "narrative (text)" and "data" publishing.

"Metadata descriptions (e.g., data about the data) are of primary importance for data dissemination, sharing and re-use, as they give essential information on content, scope, purpose, fitness for use, authorship, usage rights, etc. to any potential user. Authoring detailed metadata in repositories can seem a tedious process, however DataONE users will now benefit from direct export of already created metadata into data paper manuscripts and have even better exposure of their work through discoverability mechanisms and scholarly citations," commented Dr Amber Budden, DataONE Director for Community Engagement and Outreach

"It is great to reap the fruits of a process that started back in 2010. The automated streamlining of biodiversity data between repositories and publisher is an elegant feature that makes publishing a data paper an easy and rewarding process to crown scientists data collection efforts and ensure its use and re-use," added Prof. Lyubomir Penev, Managing Director of Pensoft.

More detailed information on how data authors could use the workflow can be found on the Pensoft blog.

References:

Chavan V, Penev L (2011) The data paper: a mechanism to incentivize data publishing in biodiversity science. BMC Bioinformatics. 12(Suppl 15):S2. DOI: 10.1186/1471-2105-12-S15-S2

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. 542241.

Substantial amount of documented occurrence records is awaiting publication stored in repositories and data indexing platforms, such as the Global Biodiversity Information Facility (GBIF), Barcode of Life Data Systems (BOLD Systems), or Integrated Digitized Biocollections (iDigBio). In order to streamline the authoring process, save taxonomists time, and provide a workflow for peer-review and quality checks, Pensoft has introduced an innovative feature that makes it possible to easily import occurrence records into a taxonomic manuscript.

Prior to this development, Pensoft's ARPHA Writing Tool (AWT) only used the "upload from Excel" approach for this workflow. Although this method significantly simplified the process of importing materials and is actively used by the authors, it still required one extra transposition step.

Now, we added a new even more user-friendly option. By simply specifying an identifier (ID) in the relevant box, the new import plugin allows for occurrence data, stored at GBIF, BOLD systems, or iDigBio, to be be directly inserted into the manuscript. It all happens in the user-friendly environment of the AWT, where the imported data can be then edited before submission to the Biodiversity Data Journal.

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 be easily downloaded from the article text into structured data by anyone who needs the data for reuse after publication.

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 and iDigBio.

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. 542241.

The 5th edition of the DEST course "Basics of Taxonomy" is co-organised with the Scandinavian Research School in Biosystematics (ForBio). The course will take place from 10 to 21 October 2016 at the Sven Lovén Centre for Marine Sciences, Kristineberg.

Course topics covered: DELTA, digital drawing, scientific illustration, scientific writing and communication, Scratchpads.

For more infromation and to register, please go to: http://taxonomytraining.eu/content/basics-taxonomy-describing-illustrating-and-communicating-biodiversity-0

The New England-based author of "Nat Enough" has been able to mine enough humor out of pre-teen trauma for five graphic novels — with a sixth on the way.

The post Maria Scrivan is reliving middle school so you don’t have to appeared first on Boston.com.

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Several former contractors, who did content moderation work for Facebook, are suing in Europe over the psychological trauma they say the work has caused them. The lawsuit is bringing new scrutiny to the content moderation ecosystem that Facebook and other platforms rely on to police what gets posted on their platforms. Author Sarah T. Roberts says that human content moderation isn’t going away anytime soon.

Also, a North Korean cartoon called ‘Bunny Brothers and the Wolf’, may not be the thinly disguised anti-American propaganda it appears to be; Sesame Street, revolutionized children's television in the US, now it’s doing the same and around the world; and Blue’s Clues, an iconic kids TV program in the US has a new host, Filipino actor Josh Dela Cruz. He tells Marco what the reaction has been like among Asian-American kids.

(Woman looking at the internet site of the online network Facebook. Credit: Classen/ullstein bild/Getty Images)

New York Judge Juan M. Merchan had been set to rule Tuesday on an earlier request to throw out Trump's conviction because of a U.S. Supreme Court ruling this summer on presidential immunity.

The post Judge delays ruling on whether to scrap Trump’s conviction in hush money case appeared first on Boston.com.

Ok. It’s Christmas. It’s the weird time of year where everyone seems so jolly, kids are all well-behaved and the money flows like we are all Bill Gates. It can also be a stressful time of year for parents, teachers, leaders and especially Santa. It becomes super easy to complain and tell everyone how BAD things are...BUT! We can make this the best time of year for people everywhere! This truly is a magical season (and let’s all be reminded of WHY...hint: it’s Jesus), so lets make it so. Help spread the good cheer, so to speak.

So, here are James’ 5 simple ways NOT to be a scrooge (or insert appropriate adjective here) this year.

BE FRIENDLY.

Oh boy, I literally just felt you roll your eyes. Seriously though, this can be overlooked in so many ways. For instance; when was the last time you texted a friend for no reason but to say “I’m thinking about you and praying for your family this season!”. Ok, some of you do that, but what about to people that aren’t really your friends? Take a moment and scroll through your contacts list and see who you can reach out to just as a friendly person to say your thinking about them. You’ll be surprised at how quickly you’ll make more friends and you’ll be giving someone a much needed boost during the day.

BUY STUFF.

Ok, this one is mainly for me. I LOVE presents. Who doesn’t? But, we all know someone around who might need something. Might be clothes, shoes, a jacket...or food. Maybe a neighbor you’ve seen who just moved in, or a friend you know would love a candle for their home. These little things add up and can express value to those around you.

GET TOGETHER.

C'mon people! Have people over to your house! ‘Tis the season for big meals! Hey, and if your house isn’t big enough, then meet at someone else's’! Getting together regularly strengthens friendships and keeps you out of isolation in a season when it's easy to hide away. Force yourself to be with other people on a regular basis.

LAUGH.

For the benefits of this, see my article on “Medicinal Laughter”. Trust me, laughing is good for you. For those of you that aren't funny (I know who you are), practice some jokes! Yes, practice. And practice bad jokes too. It sounds weird but even a poorly told joke, around good people, can lighten up the room and show you are willing to go the extra mile so those around you can laugh and have a good time.  For those of you that are funny, unleash the crazy.

NO COMPLAINING.

This is tough in today's society and culture. Complaining is almost a given. From politics to sports, family to work, we can cover the whole gamut. Make a conscious effort to try focusing on positives in regular conversations. Write down 5 good things that are happening in the world, or at work, or in your family and focus on those things in conversation. Not only will people respond favorably toward you, you’ll feel better too.

There you go. Some good starters for the season, and you might as well carry them through to the new year too. We can have enough battles to face ourselves over Christmas, we might as well not be a battle to someone else. Kapish? ...Kaposh.

Remember, all in all, that we are called to love people and love God. So be a good example of that moving forward!

I hope you all have a wonderful Christmas and New Year!

This week Zorba and Karl talk about why it takes so long to get a doctor appointment, and they examine new research showing screen time is linked to delayed development […]

We take a look at the romantic tropes of modern love and how they’re changing. Do the old dreams of true love and happiness ever after fit our new lives and new identities?

Original Air Date: February 13, 2021

Guests: 

Logan Ury — Angelo Bautista — Jane Ward — Angela Chen — Bara Jichova Tyson

Interviews In This Hour: 

The New Coffee Date: COVID-19 Pushes The Dating World To Zoom — Are Straight People Okay? — Love Without Touch, Desire Without Sex — Learning To Believe In Monogamy 

Never want to miss an episode? Subscribe to the podcast.

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The Rainscreen Association in North America announced the launch of the RAiNA Awards, an annual program celebrating outstanding achievements in rainscreen design, innovation and construction. The awards aim to recognize projects that exemplify the highest standards of excellence, technical performance, sustainability and aesthetic design in rainscreen systems across North America.

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Silver Spring, MD — Employers in the construction industry need to promote “effective, non-opioid pain-management methods” for injured workers, a nonprofit safety group is saying after two of its recent studies found construction workers with musculoskeletal disorders are three times more likely than their co-workers to use prescription opioids.

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