Tony Rees (scientist)

Last updated

Dr

Anthony J.J. "Tony" Rees
OBIS team at Rutgers, 2004.jpg
Tony Rees (centre) with members of the Ocean Biogeographic Information System (OBIS) team pictured at Rutgers University, 2004: Fred Grassle (left), Phoebe Zhang (right)
Born1953 (age 69–70)
NationalityBritish, Australian
Known forMarine biology, Biodiversity informatics, software development
Parents
  • Henry Rees (father)
  • Freda Rees (mother)
Awards Ebbe Nielsen Prize (2014)
Scientific career
FieldsBiology, Marine Biology, Biodiversity Informatics
Institutions University College London, CSIRO Division of Fisheries (later CSIRO Marine and Atmospheric Research
Thesis  (1979)
Doctoral advisor Gordon F. Leedale
Author abbrev. (botany) A.J.J.Rees
Website fishbase.de/..

Anthony J. J. ("Tony") Rees (born 1953) is a British-born software developer, data manager and biologist resident in Australia since 1986, and previously a data manager with CSIRO Marine and Atmospheric Research. [1] He is responsible for developing a number of software systems currently used in science data management, including c-squares, Taxamatch, and IRMNG, the Interim Register of Marine and Nonmarine Genera. He has also been closely involved with the development of other biodiversity informatics initiatives including the Ocean Biogeographic Information System (OBIS), AquaMaps, and the iPlant Taxonomic Name Resolution Service (TNRS).

Contents

Biography

Rees was born in Coventry, UK to an academic family [lower-alpha 1] and studied for a degree in Plant Sciences at the University of Leeds from 1971-1974, publishing one paper on the description of a new chrysophyte alga from his undergraduate work. [5] Subsequently he obtained a Ph.D. from the same University, with a thesis entitled "The phytoplankton of a eutrophic lake: community dynamics and ultrastructural studies". [6] [lower-alpha 2] In the 1980s he worked for the Micropalaeontology Unit of the Geology Department at University College London [7] before migrating to Australia where he managed the electron microscope facility for the CSIRO Division of Fisheries until that facility's closure in 1996, whereupon he transitioned into the area of marine data management for the same science agency. In that position he combined oceanographic and marine biological data management [8] and developed an interest in the emerging field of biodiversity informatics, also including a role assisting the technical development of the Ocean Biogeographic Information System (OBIS) being developed by J. Frederick Grassle in the U.S.A. From 2009-2014 he managed the Australian node of OBIS, located at CSIRO, [9] and also collaborated with other national and international biodiversity informatics and data sharing initiatives including the Encyclopedia of Life, the Global Biodiversity Information Facility, the Atlas of Living Australia, the Open Tree of Life project, FishBase, and others. Rees left CSIRO in 2014, since when his Interim Register of Marine and Nonmarine Genera project has been hosted on data infrastructure at the Flanders Marine Institute (VLIZ) in Belgium, with which he continues an involvement as at 2022.

Development of data management tools

June 2004 version of the OBIS front page (www.iobis.org) incorporating "click on a map" spatial search based on c-squares representations of data distributions in the OBIS Index, designed by Rees and implemented by Rees and Y. Zhang Obis-June 2004.jpg
June 2004 version of the OBIS front page (www.iobis.org) incorporating "click on a map" spatial search based on c-squares representations of data distributions in the OBIS Index, designed by Rees and implemented by Rees and Y. Zhang
AquaMap (computer generated predicted distribution) for Mola mola, the ocean sunfish, produced via a live web call to the c-squares mapper Aquamap-mola-mola-20091106-med-res.png
AquaMap (computer generated predicted distribution) for Mola mola, the ocean sunfish, produced via a live web call to the c-squares mapper
Rees speaking at the 2014 GBIF Science Symposium, New Delhi, India; behind him a slide illustrating the "globe view" capability of the c-squares mapper, as implemented for data from the Ocean Biodiversity Information System Rees-2014-gbif.jpg
Rees speaking at the 2014 GBIF Science Symposium, New Delhi, India; behind him a slide illustrating the "globe view" capability of the c-squares mapper, as implemented for data from the Ocean Biodiversity Information System

In 2002 Rees devised a grid-based identification system "c-squares" for units of geographic space to which areas of scientific operation by particular research projects in his agency could be allocated; [10] by designing the system to cover any scale from global to local, c-squares was also a good fit for the initial spatial data handling of both the OBIS and the subsequent AquaMaps projects, in addition to its original implementation within CSIRO Fisheries' "MarLIN" metadata system. A 2006 upgrade of the "c-squares mapper" software to produce rotatable and zoomable "globe views" was an early, browser-based, implementation of a virtual globe, [11] pre-dating the eventual availability of the (far better specified) Google Earth software as a user-addressable web application.

In 2003-2004, Rees was responsible for a redesign of the OBIS search and display software utilising both c-squares for rapid spatial search and mapping of the resulting marine species distribution information, and pre-indexing of all distributed content at a central data hub so that reliance on live, distributed queries to remote, federated data suppliers was removed; this redesign went live in the production version of OBIS in 2004. [12] At the same time, he introduced a "backbone taxonomy" for OBIS data holdings based on the then-latest (2003) edition of the Catalogue of Life, with individual names flagged as either marine or nonmarine, since OBIS wished to expose only the marine element of content supplied by external systems which did not always discriminate between records on the basis of habitat.

Aware of taxonomic gaps in this last effort arising from incompleteness in the then Catalogue of Life, in 2006 Rees commenced a new taxonomic data compilation entitled the "Interim Register of Marine and Nonmarine Genera" (IRMNG) which attempted to list all published genera of the world and assign them either a marine, or nonmarine status (later this simple distinction was further broken down into marine/brackish/freshwater and terrestrial states), also an extant/fossil flag for the use of systems that wished in addition to discriminate between extant and fossil taxa. IRMNG, initially conceived as a short term data compilation project, turned out to be more complex to complete than initially envisaged and continues to the present time under the auspices first of CSIRO in Australia, then (2016 onwards) hosted at the Flanders Marine Institute (Dutch: Vlaams Instituut voor de Zee, VLIZ) in Belgium. [13] [14] [15]

IRMNG and Taxamatch, two biodiversity informatics applications developed by Rees in the 2000s-2010s Irmng-taxamatch.jpg
IRMNG and Taxamatch, two biodiversity informatics applications developed by Rees in the 2000s-2010s

An additional software tool developed by Rees is a method for spell checking scientific names of organisms entitled "Taxamatch" that aims for high recall (no candidate correctly spelled names missed) and also good precision (rejection of "false hits"), when an input (potentially misspelled) name is supplied and a list of correctly spelled names is available against which it can be tested. [16] This method has subsequently been adopted as a useful feature in a number of global taxonomic databases including the iPlant Taxonomic Name Resolution Service for plants, [17] the World Register of Marine Species (WoRMS) and its dozens of component individual databases, [18] the Euro+Med PlantBase [19] and the EU-NOMEN portal to the Pan-European Species directories Infrastructure (PESI) [20] in addition to its incorporation into IRMNG.

For his work in the area of biodiversity informatics including that on c-squares, OBIS, IRMNG and Taxamatch, the Global Biodiversity Information Facility (GBIF) awarded Rees the 2014 Ebbe Nielsen Prize. [21] Part of the accompanying 2014 citation from GBIF reads:

Ward Appeltans, OBIS manager at UNESCO's Intergovernmental Oceanographic Commission, said he was glad Rees' life work, dedication and perseverance were rewarded by this prestigious prize. "Tony Rees has successfully combined two of his passions, informatics and biology, and with the right intuition and knowledge he has built solutions that have been used by thousands of scientists all over the world." [21]

For a period in the 2010s, Rees was a member of the Global Team of the Catalogue of Life, taking part in discussions regarding that projects's ongoing functionality and evolution. He is currently (2021) a member of the Catalogue of Life Taxonomy Group. [22] He was also a member of the international teams responsible for designing and implementing the biodiversity-related AquaMaps (global predictive maps for aquatic organisms) and iPlant TNRS (Taxonomic Name Resolution Service) projects, described in the scientific literature in 2010 and 2013, respectively. [23] [17] Five-degree global "c-squares" cells were also used as the fundamental reporting and analysis units for the first standardized data analysis and mapping of global marine biogeographic realms by M. Costello et al. in 2017. [24] In 2020, data from IRMNG were used to release as a data table, and provide summary statistics on, all of the known genera of the world and their synonyms, as held in IRMNG at that time. [15] Meanwhile, the International Council for the Exploration of the Sea (ICES) have most recently been using c-squares as the underlying spatial grid for managing all of their vessel monitoring systems (VMS) and fishing logbook data, and have also built several applications around this including "FishFrame" (refer C-squares article for more information), and the EU-funded Horizon 2020 ATLAS Project which studied vulnerable marine ecosystems (VMEs) in the North-East Atlantic also adopted c-squares as the underlying spatial grid for its main data structure, the VME Index. [25]

See also

Notes

  1. ↑ Rees' family was academically, but not specifically scientifically inclined; his mother Freda Rees (née Bennett) attended St Hilda's College, Oxford in 1938 [2] while his father Henry Rees obtained a Ph.D. in economic geography in 1955 following a first degree at the London School of Economics, lectured in geography, authored a number of textbooks on the subject, and was involved in the early stages of the creation of the University of Warwick. [3] [4]
  2. ↑ Gordon F. Leedale, supervisor of Rees' postgraduate studies, was formerly a colleague of the previous professor of Botany at Leeds University Irene Manton, whose electron microscope facility in the basement of "Botany House" was a continuing resource for future students, including Rees and a number of his near-contemporaries.

Related Research Articles

Genus is a taxonomic rank used in the biological classification of living and fossil organisms as well as viruses. In the hierarchy of biological classification, genus comes above species and below family. In binomial nomenclature, the genus name forms the first part of the binomial species name for each species within the genus.

<span class="mw-page-title-main">Charales</span> Order of green algae in the division Charophyta

Charales is an order of freshwater green algae in the division Charophyta, class Charophyceae, commonly known as stoneworts. Depending on the treatment of the genus Nitellopsis, living (extant) species are placed into either one family (Characeae) or two. Further families are used for fossil members of the order. Linnaeus established the genus Chara in 1753.

<span class="mw-page-title-main">Integrated Taxonomic Information System</span> Authoritative taxonomic information on plants, animals, fungi, and microbes

The Integrated Taxonomic Information System (ITIS) is an American partnership of federal agencies designed to provide consistent and reliable information on the taxonomy of biological species. ITIS was originally formed in 1996 as an interagency group within the US federal government, involving several US federal agencies, and has now become an international body, with Canadian and Mexican government agencies participating. The database draws from a large community of taxonomic experts. Primary content staff are housed at the Smithsonian National Museum of Natural History and IT services are provided by a US Geological Survey facility in Denver. The primary focus of ITIS is North American species, but many biological groups exist worldwide and ITIS collaborates with other agencies to increase its global coverage.

Biodiversity informatics is the application of informatics techniques to biodiversity information, such as taxonomy, biogeography or ecology. It is defined as the application of Information technology technologies to management, algorithmic exploration, analysis and interpretation of primary data regarding life, particularly at the species level organization. Modern computer techniques can yield new ways to view and analyze existing information, as well as predict future situations. Biodiversity informatics is a term that was only coined around 1992 but with rapidly increasing data sets has become useful in numerous studies and applications, such as the construction of taxonomic databases or geographic information systems. Biodiversity informatics contrasts with "bioinformatics", which is often used synonymously with the computerized handling of data in the specialized area of molecular biology.

Leptomitales are an order of water moulds within the class Oomycetes that contains the genus Apodachlya.

C-squares is a system of spatially unique, location-based identifiers (geocodes) for areas on the surface of the earth, represented as cells from a latitude- and longitude-based Discrete Global Grid at a hierarchical set of resolution steps, obtained by progressively subdividing 10×10 degree World Meteorological Organization squares; the term "c-square" is also available for use to designate any component cell of the grid. Individual cell identifiers incorporate literal values of latitude and longitude in an interleaved notation, together with additional digits that support intermediate grid resolutions of 5, 0.5, 0.05 degrees, etc.

The World Register of Marine Species (WoRMS) is a taxonomic database that aims to provide an authoritative and comprehensive list of names of marine organisms.

Darwin Core is an extension of Dublin Core for biodiversity informatics. It is meant to provide a stable standard reference for sharing information on biological diversity (biodiversity). The terms described in this standard are a part of a larger set of vocabularies and technical specifications under development and maintained by Biodiversity Information Standards (TDWG).

Parechelus is an extinct genus of prehistoric bony fish that lived during the Ypresian. The genus was circumscribed by Edgard Casier in 1967 for his description of P. parechelus.

A taxonomic database is a database created to hold information on biological taxa – for example groups of organisms organized by species name or other taxonomic identifier – for efficient data management and information retrieval. Taxonomic databases are routinely used for the automated construction of biological checklists such as floras and faunas, both for print publication and online; to underpin the operation of web-based species information systems; as a part of biological collection management ; as well as providing, in some cases, the taxon management component of broader science or biology information systems. They are also a fundamental contribution to the discipline of biodiversity informatics.

<span class="mw-page-title-main">AquaMaps</span>

AquaMaps is a collaborative project with the aim of producing computer-generated predicted global distribution maps for marine species on a 0.5 x 0.5 degree grid of the oceans based on data available through online species databases such as FishBase and SeaLifeBase and species occurrence records from OBIS or GBIF and using an environmental envelope model in conjunction with expert input. The underlying model represents a modified version of the relative environmental suitability (RES) model developed by Kristin Kaschner to generate global predictions of marine mammal occurrences.

<i>Diachrysia balluca</i>

Diachrysia balluca, commonly known as the green-patched looper or hologram moth, is a moth of the family Noctuidae. The species was first described by scientific illustrator Carl Geyer in 1832.

<i>Iguanodectes</i> Genus of fishes

Iguanodectes is a genus of freshwater fish found in tropical South America, with eight currently described species. They are all small tetras, none longer than 5 inches, and often have attractive silvery or striped scales, which makes them a target for the ornamental fish industry. Alongside the genus Piabucus, it is in the subfamily Iguanodectinae, which in turn is in the family Iguanodectidae. The genus Bryconops, which is also in Iguanodectidae, makes up a sister clade to Iguanodectinae.

<span class="mw-page-title-main">Flanders Marine Institute</span> Organization in Flanders, northern Belgium that supports marine research

The Flanders Marine Institute provides a focal point for marine scientific research in Flanders, northern Belgium.

<span class="mw-page-title-main">Interim Register of Marine and Nonmarine Genera</span> Taxonomic database

The Interim Register of Marine and Nonmarine Genera (IRMNG) is a taxonomic database which attempts to cover published genus names for all domains of life from 1758 in zoology up to the present, arranged in a single, internally consistent taxonomic hierarchy, for the benefit of Biodiversity Informatics initiatives plus general users of biodiversity (taxonomic) information. In addition to containing over 490,000 published genus name instances as at March 2020, the database holds over 1.7 million species names, although this component of the data is not maintained in as current or complete state as the genus-level holdings. IRMNG can be queried online for access to the latest version of the dataset and is also made available as periodic snapshots or data dumps for import/upload into other systems as desired.

<i>× Oncostele</i> Genus of orchids

× Oncostele, abbreviated Ons., is a hybrid genus of orchids, used for greges containing at least one ancestor species from the genera Oncidium (Onc.) and Rhynchostele (Rst.). The nothogenus was defined in 2003 by J. M. H. Shaw.

<i>Nomenclator Zoologicus</i>

Nomenclator Zoologicus is one of the major compendia in the field of zoological nomenclature, compiled by Sheffield Airey Neave and his successors and published in 9 volumes over the period 1939–1994, under the auspices of the Zoological Society of London; a tenth, electronic-only volume was also produced before the project ceased. It contains over 340,000 published name instances with their authorities and details of their original publication, certain nomenclatural notes and cross references, and an indication of the taxonomic group to which each is assigned. An electronic (digitised) version of volumes 1-10 was released online by the uBio project, based at the Marine Biological Laboratory, Woods Hole, in 2004–2005.

<span class="mw-page-title-main">Ocean Biodiversity Information System</span> Online marine biology database

The Ocean Biodiversity Information System (OBIS), formerly Ocean Biogeographic Information System, is a web-based access point to information about the distribution and abundance of living species in the ocean. It was developed as the information management component of the ten year Census of Marine Life (CoML) (2001-2010), but is not limited to CoML-derived data, and aims to provide an integrated view of all marine biodiversity data that may be made available to it on an open access basis by respective data custodians. According to its web site as at July 2018, OBIS "is a global open-access data and information clearing-house on marine biodiversity for science, conservation and sustainable development." 8 specific objectives are listed in the OBIS site, of which the leading item is to "Provide [the] world's largest scientific knowledge base on the diversity, distribution and abundance of all marine organisms in an integrated and standardized format".

Compsosaurus is an extinct genus of phytosaur, a crocodile-like reptile that lived during the Triassic. Its fossils have been found in North Carolina. The type species, Compsosaurus priscus, was named by American paleontologist Joseph Leidy in 1856, although other sources say 1857. Compsosaurus may have been the same animal as the related Belodon.

<i>Laxta friedmani</i> Species of cockroach

Laxta friedmani, the flat cockroach, is a species of Blaberidae occurring in Australia. The habitat is under loose back of eucalyptus trees, and fallen leaf litter on the ground. Length is up to 25 mm, a flattened creature, resembling a trilobite, sometimes found in small groups. Females are wingless, adult males with wings.

References

  1. ↑ ORCID record: Tony Rees
  2. ↑ University of Oxford Gazette, 6 February 2014: Obituaries, p. 302
  3. ↑ VIAF entry: Rees, Henry, 1916-2006
  4. ↑ warwick.ac.uk: Obituary: Henry Rees - 1916 - 2006
  5. ↑ Rees, Anthony J.J.; Leedale, Gordon F.; Cmiech, Helena A. (1974). "Paraphysomonas faveolata sp. nov. (Chrysophyceae), a fourth marine species with meshwork body-scales". British Phycological Journal. 9 (3): 273–283. doi: 10.1080/00071617400650331 .
  6. ↑ Rees, Anthony John Joseph, 1979. The phytoplankton of a eutrophic lake: community dynamics and ultrastructural studies. Ph. D. Thesis, University of Leeds, 152 pp. Available online via https://etheses.whiterose.ac.uk/153/
  7. ↑ Lord, A.R.; Cooper, M.K.E.; Corbett, P.W.M.; Fuller, N.G.; Rawson, P.R.; Rees, A.J. (1987). "Microbiostratigraphy of the Volgian Stage (Upper Jurassic), Volga River, USSR". Neues Jahrbuch für Geologie und Paläontologie - Monatshefte. 1987 (10): 577–605. doi:10.1127/njgpm/1987/1987/577.
  8. ↑ Finney, Kim & Rees, Tony, 2000. "Metadata and data management activities at CSIRO Marine Research, Australia." in: Hiscock, K. (Ed.) Using marine biological information in the electronic age. Proceedings of the Conference held on 19–21 July 1999. Occasional Publication. Marine Biological Association of the United Kingdom, 7: pp. 35-4. Available at http://www.vliz.be/en/imis?module=ref&refid=338963
  9. ↑ OBIS Australia: About Us (archived version, April 2013)
  10. ↑ Rees, Tony (2003). "'C-squares', a new spatial indexing system and its applicability to the description of oceanographic datasets". Oceanography. 16 (1): 11–19. doi: 10.5670/oceanog.2003.52 .
  11. ↑ "C-squares Mapper Help". CSIRO Marine & Atmospheric Research. Retrieved 21 September 2021.
  12. ↑ Rees, Tony & Zhang, Phoebe. 2007. "Evolving concepts in the architecture and functionality of OBIS, the Ocean Biogeographic Information System". in Vanden Berghe, E. et al. (ed.) Proceedings of Ocean Biodiversity Informatics: an international conference on marine biodiversity data management Hamburg, Germany, 29 November-1 December 2004. IOC Workshop Report, 202, VLIZ Special Publication 37: pp. 167-176.(PLEN-18-03)]. Publications Office of the European Union, Luxembourg, 95 pp. ISBN   978-92-79-98374-0, doi : 10.2760/335280
  13. ↑ Rees, Tony (2008). "18.8. IRMNG—the Interim Register of Marine and Nonmarine Genera" (PDF). The Proceedings of TDWG. 2008: 72–73.
  14. ↑ Rees, Tony; Vandepitte, Leen; Decock, Wim; Vanhoorne, Bart (2017). "IRMNG 2006–2016: 10 years of a global Taxonomic Database". Biodiversity Informatics. 12: 1–44. doi: 10.17161/bi.v12i0.6522 .
  15. 1 2 Rees, Tony; Vandepitte, Leen; Vanhoorne, Bart; Decock, Wim (2020). "All genera of the world: an overview and estimates based on the March 2020 release of the Interim Register of Marine and Nonmarine Genera (IRMNG)". Megataxa. 1 (2): 123–140. doi: 10.11646/megataxa.1.2.3 .
  16. ↑ Rees, Tony (2014). "Taxamatch, an algorithm for near ('fuzzy') matching of scientific names in taxonomic databases". PLOS ONE. 9 (9): e107510. Bibcode:2014PLoSO...9j7510R. doi: 10.1371/journal.pone.0107510 . PMC   4172526 . PMID   25247892.
  17. 1 2 Boyle, Brad; Hopkins, Nicole; Lu, Zhenyuan; et al. (2013). "The taxonomic name resolution service: an online tool for automated standardization of plant names". BMC Bioinformatics. 14: 16. doi: 10.1186/1471-2105-14-16 . PMC   3554605 . PMID   23324024. S2CID   2731008.
  18. ↑ Vandepitte, Leen; Vanhoorne, Bart; Decock, Wim; et al. (2018). "A decade of the World Register of Marine Species – General insights and experiences from the Data Management Team: Where are we, what have we learned and how can we continue?". PLOS ONE. 13 (4): e0194599. Bibcode:2018PLoSO..1394599V. doi: 10.1371/journal.pone.0194599 . PMC   5889062 . PMID   29624577.
  19. ↑ the Euro+Med PlantBase - the information resource for Euro-Mediterranean plant diversity,
  20. ↑ http://www.eu-nomen.eu: PESI Taxon Match tool. Accessed 15 August 2021.
  21. 1 2 "CSIRO's Tony Rees named 2014 Ebbe Nielsen Prize winner". GBIF . Retrieved 10 December 2018.
  22. ↑ Catalogue of Life: COL Governance. Accessed 15 August 2021.
  23. ↑ Ready, Jonathan; Kaschner, Kristin; South, Andy B.; et al. (2010). "Predicting the distributions of marine organisms at the global scale". Ecological Modelling. 221 (3): 467–478. doi:10.1016/j.ecolmodel.2009.10.025.
  24. ↑ Costello, Mark J.; Tsai, Peter; Wong, Pui Shan; et al. (2017). "Marine biogeographic realms and species endemicity". Nature Communications. 8 (1): 1057. Bibcode:2017NatCo...8.1057C. doi: 10.1038/s41467-017-01121-2 . PMC   5648874 . PMID   29051522.
  25. ↑ Turner, Phillip J.; Gianni, Matthew; Kenchington, Ellen; Valanko, Sebastian; Johnson, David E. (2021). "New scientific information can help to inform the evaluation of EU deep-sea fisheries regulations". The International Journal of Marine and Coastal Law. 36 (4): 627–646. doi:10.1163/15718085-bja10074. S2CID   240257476.


This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.