TDWG 2017 Annual Conference: Data Integration in a Big Data Universe: Associating Occurrences with Genes, Phenotypes, and Environments

TDWG 2017 Annual Conference: Data Integration in a Big Data Universe: Associating Occurrences with Genes, Phenotypes, and Environments

The Biodiversity Heritage Library is an institutional member of TDWG. TDWG was formed to:

establish international collaboration among biological database projects. TDWG promoted the wider and more effective dissemination of information about the World's heritage of biological organisms for the benefit of the world at large. Biodiversity Information Standards (TDWG) now focuses on the development of standards for the exchange of biological/biodiversity data.

The TDWG 2017 Annual Conference, the theme of which was "Data Integration in a Big Data Universe: Associating Occurrences with Genes, Phenotypes, and Environments" (see the full program here),  provides the opportunity for bioinformatics professionals to meet and exchange a wide variety of ideas. Held in Ottawa, Ontario, the conference was hosted by Agriculture and Agri-Food Canada and the Canadian Museum of Nature (a BHL Affiliate).

This year, The Biodiversity Heritage Library organized a symposium, "500 Years of Big Data from the Biodiversity Heritage Library" organized by BHL Program Director Martin R. Kalfatovic and BHL Program Manager Carolyn A. Sheffield. In addition to the BHL symposium, BHL web developer Mike Lichtenberg participated in the symposium, "Using Big Data Techniques to Cross Dataset Boundaries - Integration and Analysis of Multiple Datasets" organized by Kalfatovic, Matthew Collins, and Robert Guralnick.

The Biodiversity Heritage Library staff had a significant presence at the TDWG 2017 Annual Conference including organizing two symposium (details below).

BHL Symposium (abstracts found in the links below)

• A path to continuous reindexing of scientific names appearing in Biodiversity Heritage Library data / Dmitry Mozzherin, Alexander A Myltsev. Biodiversity Information Science and Standards 1: e20186 (11 Aug 2017)
• Expanding Access to Biodiversity Literature / Mariah Lewis. Biodiversity Information Science and Standards 1: e20146 (10 Aug 2017)
• BHL’s Feedback Tools and User Surveys: Investigating User Needs for Data in Digital Libraries / Carolyn A. Sheffield, Pamela McClanahan. Biodiversity Information Science and Standards 1: e20003 (03 Aug 2017)
• How Did BHL Get to Big Data / Martin R. Kalfatovic. Biodiversity Information Science and Standards 1: e20002 (03 Aug 2017)
• Scientific Names: Linking the Past to Provide Context for Knowledge / Thomas M. Orrell, David Mitchell. Biodiversity Information Science and Standards 1: e19937 (01 Aug 2017)
• Crowdsourcing Data Enhancements to Improve Named Entity Recognition in the Biodiversity Heritage Library / Katie Mika. Biodiversity Information Science and Standards 1: e17354 (25 Jul 2017)

From left: Lewis, Orrell, Mozzherin, Mika, Sheffield

Symposium: Using Big Data Techniques to Cross Dataset Boundaries - Integration and Analysis of Multiple Datasets

• BHL: A Source for Big Data Analysis / Mike Lichtenberg. Biodiversity Information Science and Standards 1: e20339 (16 Aug 2017). 

Excursion

TDWG also offered the opportunity for excursions. The Canadian Museum of Nature (CMN) provided an amazing tour of their collections facilities located just outside the city. The CMN library is also located at this facility and it was great to meet with the library staff and see their collections.

24th meeting of the Global Biodiversity Information Facility (GBIF) Governing Board

BHL Head of Delegation, Constance Rinaldo

The 24th meeting of the Global Biodiversity Information Facility (GBIF) Governing Board and associated events were held its annual meeting in Helsinki, Finland, 24-29 September. The Biodiversity Heritage Library (BHL) was represented at both the 14th GBIF Nodes Meeting (24-25 September 2017, by BHL Program Director, Martin R. Kalfatovic) and the Governing Board Meeting (26-27 September 2017, by BHL Chair, Constance Rinaldo).

14th Global Nodes Meeting

At the Nodes meeting, the delegates were welcomed by Finnish GBIF Nodes Manager, Tapani Lahti. Following this, André Heughebaert, Chair, Nodes Committee, provided an introduction to the structure of the meeting and outlined the key goals:

• Share information on progress in the nodes
• Establish new collaboration models
• Set priorities for the next 2 years

Heughebaert also outlined some elements of the GBIF 2018 Work Programme and noted that there are plans to include regional meetings as in the past. The GBIF Secretariat provide an overview of their activities, led by Tim Hirsch (Deputy Director, GBIF Secretariat). Hirsch's talk, "GBIF International landscape & New regions" was an overview of the GBIF international landscape, including participation by area and how different metrics can be used to measure participation and/or coverage of biodiversity data in GBIF. Some key things that GBIF is addressing are:

• Address major geospacial gaps
• Mobilize sampling-event data
• Digitize natural history collections

Areas are being focused on include the Caribbean (formation of an Atlas of Living Caribbean), Pacific Islands (creating new participant options, including a meeting in Samoa).

Hirsch also noted that GBIF is the key reporting structure for Aichi Target 19  f the Convention on Biological Diversity. He also discussed GBIF's relation to  Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) and how GBIF can engage in filling gaps in knowledge through data mobilization priorities.

Other Secretariat updates included:

• Capacity Enhancement Support Programme (CESP) / Aisha Lolila Jensen (Program Officer for Participation and Engagement, GBIF Secretariat)
• Biodiversity Information for Development (BID) / Laura Russell (Program Officer for Participation and Engagement, GBIF Secretariat)
• Biodiversity Fund for Asia (BIFA) / Maofang Luo (Visiting Scientist from the Chinese Academy of Sciences, GBIF Secretariat)
• IPT GBIF API and other tools / Laura Russell  (Program Officer for Participation and Engagement, GBIF Secretariat)
• Presentation of the new GBIF Portal / Morten Høfft & Thomas S. Jeppesen (Web Developers, GBIF Secretariat)

Swan wings

The second session were short talks by members of the GBIF node community and included:

• Description of the Antarctic Thematic GBIF Node, Strength & Weaknesses / Anton Van de Putte, Node manager, Scientific Committee on Antarctic Research (SCAR) 
• SiB Colombia role as a referent in the Latino American initiatives through GBIF (e.g. workshops, projects, mentoring) / Leonardo Buitrago, Node manager, Colombia 
• Data management: Stable identifiers for collection specimens: What could the Nodes do to spread the use of this practice? / Walter Berendsohn & Anton Güntsch, Node manager, Germany 
• Olaf Banki on the @catalogueoflife CoL+ which provides extended taxonomic catalogue & other goals other partners incl @NLBIF @GBIF @Naturalis_Sci Species2000 ITIS 
• GBIF Norway: Software tools for online citizen science volunteer digitization of museum herbaria collections, https://data.gbif.no/dugnad  By Christian Svindseth, Node staff, Norway
• GBIF Norway: Terms selection tool for data publishers, https://data.gbif.no/dwcexcel By Christian Svindseth, Node staff, Norway 

A tour of the Finnish Museum of Natural History's herbarium scanning project was also provided at the lunch break. The day concluded with a reception at the Finnish Museum of Natural History. Delegates were also privileged to get a behind-the-scenes tour of the museum's collections areas.

Reception with dinosaurs

Global Nodes meeting group photo
(Photo by Anne Mette Nielsen, CC BY-NC 4.0)

* * * * * 

24th GBIF Governing Board Meeting

GBIF Governing Board Chair Peter Schalk (Naturalis Biodiversity Center, Leiden) and Donald Hobern (GBIF Executive Secretary) led the meeting and provided an overview of the past year. There was also a discussion of the GBIF Strategic Plan Goals and Work Programme updates. The plan goals were discussed in detail:

• Strategic Plan Goal 1 – Empower Global Network
  “Ensure that governments, researchers and users are equipped and supported to share, improve and use data through the GBIF network, regardless of geography, language or institutional affiliation.” 
• Strategic Plan Goal 2 – Enhance Biodiversity Information Infrastructure
  “Provide leadership, expertise and tools to support the integration of all biodiversity information as an interconnected digital knowledgebase.” 
• Strategic Plan Goal 3 – Fill Data Gaps
  “Prioritize and promote mobilization of new data resources which combine with existing resources to maximize the coverage, completeness and resolution of GBIF data, particularly with respect to taxonomy, geography and time.” 
• Strategic Plan Goal 4 – Improve Data Quality
  “Ensure that all data within the GBIF network are of the highest-possible quality and associated with clear indicators enabling users to assess their origin, relevance and usefulness for any application.” 
• Strategic Plan Goal 5 – Deliver Relevant Data
  Ensure that GBIF delivers data in the form and completeness required to meet the highest priority needs of science and, through science, society.” 

The meeting also presented the winners of the 2017 Young Researchers Award:

• Nora Escribano Compains, a Ph.D candidate at the University of Navarra (UNAV)
• Itanna Oliveira Fernandes, a Ph.D candidate at the National Institute of Amazonian Research (INPA)

In official business, the various GBIF Committee chairs (Science, Nodes, Budget) all reported. Hobern also presented the 2018 budget and work programme. Ireland was selected as the host for the 2018 GBIF 25th meeting of the Global Biodiversity Information Facility (GBIF) Governing Board and Governing Board positions were voted on. Results of the elections were:

• Chair, Governing Board: Tanya Abrahamse, South Africa
• 2nd Vice Chair, Governing Board: Mark Graham, Canada
• Chair, Budget Committee: Peter Schalk, Netherlands
• 1st Vice-Chair, Budget Committee: Liam Lysaght, Ireland
• 2nd Vice-Chair, Budget Committee: Joanne Daly, Australia
• Chair, Science Committee: Thomas M. Orrell, United States
• 2nd Vice-Chair, Science Committee: Anders G. Finstad, Norway
• 3rd Vice-Chair, Science Committee: Philippe Grandcolas, France

Governing Board meeting group photo
(Photo by Linda Tammisto, CC0 2017)

* * * * * 

Finnish National Seminar

Professor Leif Schulman

All delegates and other guests were invited to the Finish National Seminar, "Finnish Biodiversity Information for the Benefit of Society".  The national seminar is a full-day event with talks from invited international and Finnish guest speakers including researchers of various fields as well as representatives of the natural resources administration. The programme gives broad insight into the various uses of openly available biodiversity data in research, governance, and teaching, and introduces the newly established Finnish Biodiversity Information Facility (FinBIF).

Professor Leif Schulman, Director of the Finnish Museum of Natural History (and GBIF Head of Delegation for Finland) provided a brilliant opening to the Seminar (which was held in the beautiful Great Hall of the University of Helsinki) by pacing four meters across the stage and noting that it was this distance that birds in Finland are moving north due to climate change. Schulman also introduced Finnish Member of Parliment Ville Niinistö (Minister of the Environment in 2011-2014, led to the funding of FinBIF) who provided a governmental perspective on biodiversity.

Executive Secretary Donald Hobern

GBIF Executive Secretary Donald Hobern provided an overview of GBIF's activities and goals and was followed by FinBIF Manager Kari Lahti who contextualized this work within the Finnish context. Dr. Vincent Smith (Head of Diversity & Informatics Division, Natural History Museum, London), provided a keynote talk, "The Digital Transformation of Biodiversity Institutions - a Changing Intellectual Business Model".

Researchers from across Finland then provided a series of talks that delved deeper into programs and investigations that FinBIF, GBIF, and other global biodiversity research organizations are facilitating. The talks included:

• Research Director Atte Moilanen (University of Helsinki & FinBIF)
• Associate Professor Tuuli Toivonen (University of Helsinki)
• University Researcher Sami Aikio (University of Oulu)
• Post Doc Researcher Andrea Santangeli (Finnish Museum of Natural History)
• Research Director Ilari Sääksjärvi (University of Turku)
• Senior Curator Marko Mutanen (University of Oulu Biodiversity Unit)
• Professor Jouko Rikkinen (Finnish Museum of Natural History & Faculty of Biosciences, University of Helsinki)
• Ministerial Adviser Johanna Niemivuo-Lahti , Ministry of Agriculture and Forestry
• Dr. Aino Juslén , Unit Director at the Finnish Museum of Natural History

* * * * * 

Other Meetings

Xu & Kalfatovic

The meetings also provided BHL staff to meet with a number of our partners. Dr. Zheping Xu (BHL China) Patricia Koleff (BHL México). Discussions with Michelle Price (Conservatoire et Jardin botaniques de la Ville de Genève) and Chair of Consortium of European Taxonomic Facilities (CETAF AISBL) provided an opportunity to explore possible collaborations.

Rinaldo, Koleff, Kalfatovic

Rinaldo and Kalfatovic were also able to spend time with outgoing GBIF Science Committee Chair and BHL power user Rod Page to discuss ongoing work with the BHL portal. The GBIF meetings also provided a good opportunity to catch up with staff from iDigBio, including Deb Paul (Digitization and Technology Specialist).

* * * * * 

Biodiversity Excursions

Vallisaari and Suomenlinna
Vallisaari is just 20 minutes by boat from the Market Square in Helsinki. The island was opened for the public last year – before that it was decades abandoned and the nature took its place. Vallisaari is the most diverse nature destination in the metropolitan area. The island’s fortifications, buildings, and a record-breaking range of species tell a tale of coexistence between humans and wild nature. The other attraction, fortress of Suomenlinna is one of Finland’s UNESCO World Heritage Sites. Suomenlinna was built during the Swedish era as a maritime fortress and a base for the Archipelago Fleet.

Excursion to Vallisaari

Nuuksio National Park
The Nuuksio National Park is located in the border of the oak forest zone and the southern boreal forest zone. The landscape is dominated by valleys and gorges formed by the Ice Age, and barren rocky hills covered by lichen and sparse pine forest. At some places the hills reach the height of 110 metres above the sea level.

* * * * * 

Other Resources

• Meeting Page
• GBIF Meeting Documents
• GBIF Presentations
• Videos

Amanita muscaria, Vallisaari, Finland

Report from the Digital Data in Biodiversity Research Conference, University of Michigan

University of Michigan

The Digital Data in Biodiversity Research Conference was sponsored by iDigBio, the University of Michigan Herbarium, the University of Michigan Museum of Paleontology, and the University of Michigan Museum of Zoology. The conference was attended by about 185 people from a variety of institutions. I attended to participate in the GBIF North American Nodes Workshop and was joined by Alicia Esquivel (BHL NDSR Resident based at the Chicago Botanic Garden).

After a welcome from Dean Andrew D. Martin of the College of Literature, Science, and the Arts, the opening series of plenary talks began with Stephen Smith (University of Michigan) speaking on "The Utility of Large-scale Phylogenetic Analyses for Understanding the Evolution of Biodiversity." The detailed talk covered the promise of a comprehensive view of the tree of life, whether for a particular clade or the entire tree of life which has been a major motivation of the systematics community for decades. Smith described new efforts and new ways for combining the resources from the Open Tree of Life with other phylogenetic analyses to construct a dated and comprehensive tree and discussed construction of a comprehensive tree for seed plants containing 80,037 taxa from GenBank and 356,807 total taxa.

Maureen Kearney

Maureen Kearney, Associate Director for Science, National Museum of Natural History (Smithsonian Institution) spoke next. Kearney's talk, "Expanding the Power of Natural History Knowledge: Frontiers in Research and Collections at the Smithsonian’s National Museum of Natural History," was an inspiring overview of the role of natural history museums in this era of rapid global change to mobilize collections data and natural history knowledge for science and society.

Kearney spoke of how Natural history scientists help us comprehend the fundamental nature of the planet, of organisms (including humans), and of evolutionary and ecological interactions throughout the history of life on Earth. The enormous potential exists for natural history museums in the 21st century if they highlight their unique niche as irreplaceable research and data centers for the study of global change. Kearney also noted that this can only be realized, though, if museums build large-scale pipelines and open-source, dynamic platforms to digitize, structure, link, and share our natural history data and knowledge. She spoke of key partners inside the National Museum of Natural History (such as the Global Genomics Initiative and the Encyclopedia of Life) and other partners at the Smithsonian, including the Biodiversity Heritage Library and the Smithsonian's Digitization Program Office and its 3D imaging team.

Donald Hobern

Donald Hobern, GBIF Executive Secretary, spoke on "Preserving Evidence of Biodiversity Patterns: GBIF and Persistent Biodiversity Data Management." Hobern gave an overview of GBIF as well as the goals of the GBIF implementation plan include simplifying and supporting data publishing and assisting with delivery of the most detailed version possible for each data source.

Other plenary talks included:

• Linking Heterogeneous Data in Biodiversity Research by Pam Soltis, Florida Museum of Natural History, University of Florida
• Using “Digital Specimens” to explore the behavioral phenotype by Mike Webster, Cornell Laboratory of Ornithology

Dan Fisher

DAY 1: CONCURRENT SESSIONS
Full abstracts and details at of the Concurrent Sessions is online here. Sessions attended were:

• 3D Surface Models in Paleontology and Archaeology by Dan Fisher, University of Michigan Museum of Paleontology. Used the Buesching mastodon (now at University of Michigan) as a case study for the talk. Walked through the excavation and the 3D imaging process. Digital data on the external form of specimens are central to many paleontological and archaeological analyses. Digital models minimize handling of fragile and/or heavy specimens, facilitate access and collaboration, allow complex measurements, enhance visualization of surface topography, and simplify inspection of multi-object assemblies. 
• Paleobiology Database: A Community Based Data Service for Research, Education, and Museums by Mark Uhen, George Mason University
• MorphoSource: A Virtual Museum and Digital Repository for 3D Specimen Data by Doug Boyer, Duke University
• ePANDDA: enhancing Paleontological and Neontological Data Discovery API by Susan Butts, Yale University; Seth Kaufman, Whirligig Inc.
• The Importance and Challenges of Database Integration: MorphoBank, MorphoSource, and the Paleobiology Database by Julie Winchester, Duke University

Macklin, Hanner, Bruneau

AFTERNOON WORKSHOP
In the afternoon, the meeting offered focused workshops. The Biodiversity Heritage Library was invited to participate in the Digital Data and the North American Nodes of the Global Biodiversity Information Facility session led by Bob Hanner, Stinger Guala, and James Macklin. A goal of the workshop was to discuss the current status of the GBIF North American Nodes, current activities and collaborations.

Attended by about 50 participants, the presentations at the workshop included:

• National and Regional Coordination Roles within GBIF (Donald Hobern)
• Biodiversity Information Serving Our Nation (BISON): Connections and Cooperation (Stinger Guala)
• The Canadian Biodiversity Information Facility (CBIF) (James Macklin)
• Canadensys: revealing the biodiversity of Canada (Anne Bruneau)
• Overview of the Biodiversity Heritage Library Recent Activities (Martin Kalfatovic)
• The Catalogue of Life: Infrastructure for Science (Tom Orrell)
• Global Genome Biodiversity Network – Infrastructure for Genomic Research (Jon Coddington)
• iDigBio, National Coordinating Center for NSF's ADBC Program (Larry Page)

The BHL talk, "Overview of the Biodiversity Heritage Library: Recent Activities" covered:

As the world’s largest open access digital library for biodiversity literature, the Biodiversity Heritage Library (BHL) is an unparalleled resource that has forever changed the way researchers around the globe understand, describe, and conserve life on Earth. BHL has become not only a model for digital libraries but also a fundamental resource for taxonomic literature aggregation, discovery, and presentation by engaging the taxonomic community and responding to user needs. To achieve this, BHL relies on many standards and tools, such as Digital Object Identifiers (DOIs), Application Programming Interfaces (APIs), and Global Names Architecture (GNA). These standards and tools help ensure that data in and about the literature matches the needs and expectations of the scientific community and is readily available for widespread reuse. To meet the evolving needs and expectations of researchers, we must continually innovate and adapt to the changing technological landscape.  BHL is in the process of organizing widespread user needs analysis and an environmental scan of information resources to define requirements for a next generation digital library. 

The presentations were followed by a panel discussion and a conversation with the audience.

EVENING RECEPTION AND TOUR OF THE RESEARCH MUSEUMS CENTER
After the day's meetings, attendees were bused to the Research Museums Center, located about 7.5 kilometers from the center of the University of Michigan campus. Participants were given the opportunity of guided tours of the University of Michigan Herbarium, collections areas of the Museum of Paleontology, and the wet and dry collections of the Museum of Zoology.

 

 

 

 

Adam Summers

DAY 2: PLENARY TALKS
The second day again opened with plenary talks which included:

• Big Data, Museum Specimens, Access and Archiving - Lessons from #scanAllFish by Adam Summers, University of Washington. Amazing high energy talk about Summers' project #scanAllFish, over 1,991 species, 3,094 specimens from 109 collections. Expects to store over half a petabyte of data for 30,000 vertebrates. Storing and backing these data up is an issue. It is also interesting to consider what collections plan to do when these data are returned to them with the specimens. 
• Video Data and Motion Analysis in Comparative Biomechanics Research by Beth Brainerd, Brown University. "Film or video recordings have long been important primary data for research in comparative biomechanics. Innovations have included the use of two or more cameras to capture 3D motion, and the use of two X-ray video cameras (fluoroscopes) to capture 3D motion of bones in vivo. Over the past decade we have developed X-ray Reconstruction of Moving Morphology (XROMM), which combines  dual-fluoroscopy with bone models from CT scans to produce accurate animations of 3D bones moving in 3D space."
• The PREDICTS Project: Projecting Responses of Ecological Diversity In Changing Terrestrial Systems by Adriana De Palma, Natural History Museum, London. "PREDICTS is a collaborative project that aims to produce global models of how local biodiversity responds to land use and related human impacts, in order to make projections under possible future scenarios."
• Field Collections to Digital Data: A Workflow for Fossils and the Use of Digital Data for Reconstructing Ancient Forests by Dori Contreras, University of California Museum of Paleontology. "The integration of curation and digitization with project-focused data collection is a key component to performing time-efficient studies from new fossil collections. Standard workflows for processing fossil specimens starting from initial field collection and continuing through digital analysis/measurement are not widely established. Here I present my workflow for reconstruction of a diverse Late Cretaceous flora from plant macrofossils preserved in an extensive recrystallized volcanic ashfall deposit."
• Natural History Data Pipelines: The Good, the Bad, and the Ugly by Andy Bentley, University of Kansas Biodiversity Institute. "Collections, aggregators, data re-packagers, publishers, researchers, and external user groups form a complex web of data connections and pipelines that form the natural history knowledge base essential for collections use by an ever increasing and diverse external user community.  We have made great strides in developing the individual parts of this knowledge base and we are now well poised to integrate these capabilities to address big picture questions.  Although we need to continue work on the individual pieces, the focus now needs to be on integration of these disparate sources of data that create the pipeline."

Esquivel

DAY 2: CONCURRENT SESSIONS
Sessions attended included:

• Using Statistical Analysis to Calculate the Size of Biodiversity Literature by Alicia Esquivel, Chicago Botanic Garden
• Illustrating Value Added in Databasing Historical Collections: Entered, Proofed, and Done (or Not!) by Tony Reznicek, University of Michigan Herbarium
• The Encyclopedia of Life v3: constructing a linked data model by Jennifer Hammock, National Museum of Natural History, Encyclopedia of Life, Smithsonian Institution
• Encyclopedia of Life Version 3: New Tools for the Exploration of Biodiversity Knowledge by Katja Schulz, National Museum of Natural History, Encyclopedia of Life, Smithsonian Institution
• How do People see Biodiversity? Using a Digital Identification Key in a Citizen Science Program by Mathilde Delaunay, Muséum national d'Histoire naturelle, Paris, France
• Taxonomic Data Quality in GBIF: A Case Study of Aquatic Macroinvertebrate Groups by Joan Damerow, Field Museum of Natural History
• Hole-y Plant Databases! Understanding and Preventing Biases in Botanical Big Data by Katelin D. Pearson, Florida State University

Alicia Esquivel's talk was an excellent overview of the BHL NDSR Resident program and the important work being done by the group as BHL looks forward to BHL Version 2. Esquivel's work focuses on looking for gaps in the BHL collections and other collections analysis. In addition to her talk, she also presented a poster (co-authored by Constance Rinaldo, BHL Chair / Museum of Comparative Zoology, Harvard University).

CAPSTONE SESSION

• Prospects for the Use of Digitized Specimens in Studies of Plant Diversity and Evolution by Michael Donoghue, Yale University
• A Vision for a National Cyberinfrastructure for Biodiversity Research and what NSF can do Enable it by Peter McCartney, National Science Foundation

OTHER RESOURCES

• Link to Abstracts for Plenary Talks | Concurrent Sessions | GBIF Workshop | Poster Sessions
• Conference Information Page | Conference Wiki Page
• iDigBio Blog Post
• Link to Twitter Hashtag: #digibiodata

Research Museums Center, University of Michigan

BHL Annual Meeting. BHL Open Day Symposium talk on the @BioDivLibrary

Here's my presentation at the BHL Open Day Symposium at the Singapore Botanic Gardens (15 March 2017).

Empowering Global Research in Biodiversity: The Biodiversity Heritage Library. Martin R. Kalfatovic. BHL Annual Meeting. BHL Open Day Symposium. Singapore Botanic Gardens. Singapore. 15 March 2017.

TDWG 2016 meeting, La Fortuna & Alajuela Province, San Carlos, Costa Rica #TDWG16

Official Photo by Denisse Vargas

The 2016 TDWG Biodiversity Information Standards meeting was held at the Centro de Transferencia Tecnológica y Educación Continua (CTEC) in San Carlos, Costa Rica. Hotels and other activities were in La Fortuna, about a 45 minute bus ride from CTEC.

BHL was represented at the TDWG 2016 conference with a symposium, "BHL: 10 Years of Innovation and Growth". The panel consisted of:

Constance Rinaldo

• BHL - 10 Years and More! (Martin R. Kalfatovic)
• BHL: Grants and Growth (Constance Rinaldo)
• BHL-SciELO Network (Henrique Rodrigues)
• Towards extracting occurrence data from biodiversity literature (Dmitry Schigel)
• Questions: BHL - 10 years of innovation & growth (Discussion led by Constance Rinaldo)

The session was attended by about 70 people. The conclusion of the session was a discussion with the audience about desires for the future direction of BHL and features or services that could be implemented as BHL explores refactoring the BHL platform. Among the topics mentioned by the audience were: integration of visual resources in BHL; expanding in-copyright material,

Dimitris Koureas, Cynthia Parr, Erick Mata

The TDWG organizers, lead by the program committee, Dr. Erick Mata Montero (Professor, School of Computing, Costa Rica Institute of Technology), Gail Kampmeier (Prairie Research Institute, Illinois Natural History Survey, University of Illinois, USA); Francisco ("Paco") Pando (Real Jardín Botánico-CSIC, Spain); Maria Mora Instituto (Nacional de Biodiversidad, Costa Rica); Joel Sachs (Agriculture and Agri-Food, Canada); Manuel Vargas (Instituto Nacional de Biodiversidad, Costa Rica); Stan Blum (ex-officio TDWG Coordinator); and William Ulate (ex-officio TDWG Treasurer, Missouri Botanical Garden), delivered an excellent program.

The keynote, by Dr. Rodrigo Gámez Lobo (founder and former Director General and President of the National Biodiversity Institute) spoke the future of Costa Rican biodiversity as exemplified in his work On Biodiversity, People and Utopias (1999). His talk addressed the them of this work, in which he states, "Our real goal is to make the society come to the understanding that, because of being something that directly affects quality of life, materially, intellectually and spiritually, we must preserve at all costs the rich biodiversity of the country".

Former BHL Technical Director William Ulate led a symposium on Semantics for Biodiversity Science: Challenges & Solutions. Ulate and co-author Riza Batista-Navarro spoke on "Real use cases for Semantic Information from the Mining Biodiversity project."

Other important symposium was Semantics for Biodiversity Science: Text Mining & Semantic Role Tagging. Key papers included:

• Enhancing semantic search through the automatic construction of a Biodiversity Terminological Inventory (Nhung T.H. Nguyen, Georgios Kontonatsios, Axel J. Soto, Riza Batista-Navarro, Sophia Ananiadou)
• Geographic entities extraction from biological textual sources (Moisés Alberto Acuña-Chaves)

Another symposium of note was Semantics for Biodiversity Science: Taxon Names & Traits. Key papers included:

• What's in a name? Sense and reference in digital biodiversity information (Joakim Philipson)
• Creating computable definitions for clades using the Web Ontology Language (OWL) (Gaurav Vaidya, Hilmar Lapp, Nico Cellinese)

Globally Unique Identifiers for Names (organized by Chuck Miller and Richard Pyle) included papers of interest to BHL:

• Reviewing data integration and mobilisation using name reconciliation and identifier services (Nicky Nicolson, Robert Turner, Abigail Barker)
•  Implementing Name Identifiers for the World Flora Online (Chuck Miller)
• Identifiers for Biodiversity Informatics: The Global Names Approach (Dmitry Y. Mozzherin, Richard Pyle)
• The Catalogue of Life Editor's View on Globally Unique Identifiers for Names (Yuri Roskov)
• Names and identifiers in the CyVerse cyberinfrastucture (Ramona L. Walls)
• Utilizing Unique Identifiers for Taxonomic Concepts (Jeff Gerbracht)

Two standout papers in the contributed papers session were:

• TDWG Then and Now (Arturo H. Ariño, Anabel Pérez de Zabalza)
• Nanopublications for biodiversity: concept, formats and implementation (Lyubomir Penev, Éamonn Ó Tuama, Viktor Senderov, Pavel Stoev, Teodor Georgiev)

Volcán Arenal

A highlight of the meeting as the TDWG 2016 Bioblitz at the nearby Texas A&M Soltis Center. The bioblitz helped to create a biodiversity snapshot of TDWG 2016. Participants were encouraged to take the opportunity to observe, to post their pictures of local biodiversity. The event took place in a torrential rainstorm, but the event still provided some observations and camaraderie.

There were other opportunities to see some of Costa Rica's amazing biodiversity, among those sighted were:

Two-toed Sloth
(Choloepus hoffmanni)

Mammals

• Three-toed Sloth (Bradypus variegatus)
• Two-toed Sloth (Choloepus hoffmanni)
• White-nosed Coati (Nasua narica)
• Mantled Howler Monkey (Alouatta palliata)
• Spider Monkey (Ateles geoffroyi)
• White-throated Capuchin (Cebus capucinus)
• Long-nosed bat (Rhynchonycteris naso)

Yellow-throated Toucan
(Ramphastos ambiguus)

Birds

• Wood Stork (Mycteria americana)
• Little Blue Heron (Egretta caerulea)
• Cattle Egret (Bubulcus ibis)
• Snoy Egret (Egretta thula)
• Northern Jacana (Jacana spinosa)
• Turkey Vulture (Cathartes aura)
• Groove-billed Ani (Crotophaga sulcirostris)
• Yellow-throated Toucan (Ramphastos ambiguus)
• Green Kingfisher (Chloroceryle americana)
• Anhinga (Anhinga anhinga)
• White Ibis (Eudocimus albus)

American Crocodile
(Crocodylus acutus)

Reptiles

• Spectacled Caiman (Caiman crocodilus)
• American Crocodile (Crocodylus acutus)
• Emerald Basilisk (Basiliscus plumifrons)
• Black River Turtle (Rhinoclemmys funerea)
• Common Snapping Turtle (Chelydra serpentina)
• Green Iguana (Iguana iguana)

BHL participates in meetings at the Muséum national d’Histoire naturelle (Paris)

From left:
Bruno David, Martin R. Kalfatovic,
Laurence Bénichou, Nancy E. Gwinn, Gildas Illien
photo by Jean-Christophe Domenech

I was honored to participate in the signing ceremony on 2 December 2016 where the Museum officially joined the Biodiversity Heritage Library. Accompanying Dr. Nancy E. Gwinn (Smithsonian Libraries Director and Chair of the BHL Executive Committee), the ceremony was held in the amphitheater of the Galeries d'Anatomie comparée et de Paléontologie. Attending on behalf of the MNHN were Dr. Bruno David (Director), Gildas Illien (head of the MNHN library), and Laurence Bénichou (Head, Publications Scientifiques).

Immediately before the meeting, I gave a presentation ("Increasing Access, Promoting Progress: Empowering Global Research through the BHL") on BHL to representatives from a number of large natural history museums from around the world (including BHL partners American Museum of Natural History, The Field Museum of Natural History, Muséum national d’Histoire naturelle, Natural History Museum (London), National Museum of Natural History (Smithsonian Libraries), Natural History Museum Los Angeles County, and Naturalis Biodiversity Center.

Earlier, on 30 November, I was treated to a tour of the MNHN library by the M. Illien and had the opportunity to meet with key staff (Alice LeMaire, Anaïs Rameaux, Chloé Besombes, and Vincent Detienne) who will be participating in BHL. The following day, I met with Laurence Bénichou and the staff of the Publications Scientifiques. Topics included BHL metadata models and best practices to be reviewed for ingest of MNHN publications into BHL.

A tour of the Grand Hall of Evolution and the special exhibition, Espèces d’ours! was also arranged. The Grande Galerie de l'Évolution is an amazing four level exhibition that documents life on our planet. The installation is an outstanding re-envisioning of an older space for the 21st century. Of personal interest was the La salle des espèces menacées et disparues and a nice display of artifacts related to Raphus cucullatus.

On 2 December, before the signing ceremony, the Museum arranged for a tour of the Jardin des Plantes for me and Nancy E. Gwinn. Our host, Fabien Dupuis, Desk Officer from the office of International and European Affairs provided an excellent tour of the gardens and greenhouses that are under the auspices of the Museum.

 

Herbarium (left) and Galeries d'Anatomie comparée et de Paléontologie (right)

Gwinn (left) and Illien (right)

My special thanks to the staff of the Museum for arranging our visit. Gildas Illien was a superb host who juggled multiple high-profile events during this brief visit. It was a pleasure to meet him in person after many emails and phone calls. All of us at BHL and the Smithsonian look forward to working with him in the years to come. And at last, I was able to meet with Laurence Bénichou in France after seeing her in many other places around the world. Seeing her office, located in the 18th century home of noted naturalist  Georges-Louis Leclerc, Comte de Buffon, made one appreciate the over 200 year history of scientific publishing at the Museum.

And yes, good food was had by all ...

Raphus cucullatus