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uBio News

uBio latest news releases

Published: Tue, 20 Mar 2018 00:30:45 -0400


uBio creates new XML Web Services

Tue, 15 Aug 2006 00:00:00 -0400

A new set of webservices was added to the current collection. The new XML webservices can be called via HTTP GET and POST requests and will return XML data structures. This new version of web services can be easily embedded within any web-based application without having to deal with setting up SOAP clients.

Missouri Botanical Garden's Tropicos database is indexed in NameBank

Tue, 01 Aug 2006 00:00:00 -0400

uBio has indexed The Missouri Botanical Garden's (MOBOT) Tropicos database within NameBank. Indexing Tropicos allows uBio to provide a variety of tools and services to MOBOT such as enhanced LinkIT and FindIT applications as well as linkages to Tropicos from the uBio Portal. "W3TROPICOS provides new and improved access to the Missouri Botanical Garden's VAST nomenclatural database and associated authority files."

uBio RSS is integrated within FishBase

Tue, 27 Jun 2006 00:00:00 -0400

uBio has partnered with FishBase to produce an application that monitors current publications available via Real Simple Syndication (RSS) for references to fish species. A link to this application is provided within FishBase species summaries.

MBLWHOI Library incorporates uBioRSS

Tue, 27 Jun 2006 00:00:00 -0400

The MBLWHOI Library has uBioRSS functions built into it's web architecture. Model organisms used at the MBL are cross-referenced to current literature within the application and provided to the library as an RSS feed where it is formatted and displayed on the home page.

uBioRSS referenced in Nature discussion article

Wed, 21 Jun 2006 00:00:00 -0400

An article in the current issue of Nature entitled "Technical solutions: Evolving peer review for the internet" features uBioRSS.

uBio in Elsevier Library Connect newsletter

Fri, 19 May 2006 00:00:00 -0400

Cathy Norton, MBLWHOI Library director and director of uBio, appears in this months issue of Library Connect, a newsletter circulated in the library community. The uBio section appears on page 8 in a section titled "Librarians speak up - How your library is adding value" and features a description of uBioRSS.

uBio mention in Economist Zoobank article (Feb. 2006)

Wed, 17 May 2006 00:00:00 -0400

An article titled "Today we have naming of parts" in the Feb. 9, 2006 edition of the Economist focused on the establishment of ZooBank, a proposed registry for new species names. uBio was mentioned as one of the potential collaborators in this effort.

European Register of Marine Species is indexed in NameBank

Fri, 28 Apr 2006 00:00:00 -0400

MarBef has provided uBio with access to a taxonomic list of ERMS records which makes them available within the uBio portal, NameBank, uBioRSS, LinkIt and other tools. This provides us with the means to selectively link uBio resources and services to ERMS. The European Register of Marine Species (ERMS) is an authoritive taxonomic list of species occuring in the European marine environment.

Taxonomic intelligence presentation to Sylvia Earle, Gustavo Fonseca, and Tom Lacher

Wed, 26 Apr 2006 00:00:00 -0400

David Remsen and David Patterson of uBio made a presentation to Dr. Sylvia Earle of Global Marine Conservation, and Drs. Gustavo Fonseca and Thomas Lacher of Conservation International. The presentation focused on the use of taxonomic intelligence in biological content management and retrieval.

IUCN classification in uBioRSS

Fri, 21 Apr 2006 00:00:00 -0400

uBioRSS was updated to provide more effective use of the IUCN redlist. Browsing by the IUCN classification limits results only to the IUCN Redlst of Threatened Species. A species-only limit prevents results from being returned that match higher taxon names.

Java SOAP classes updates

Fri, 21 Apr 2006 00:00:00 -0400

We updated some java classes to our newer SOAP methods and provide some example code.

BioOne Journals added to uBioRSS

Thu, 23 Mar 2006 00:00:00 -0500

RSS feeds from the BioOne journals were added to uBioRSS. The following titles have been added. (AMBIO: A Journal of the Human Environment), (The American Biology Teacher), (American Fern Journal), (The American Midland Naturalist), (American Museum Novitates), (American Zoologist), (Annals of the Entomological Society of America), (Applied Vegetation Science), (The Arabidopsis Book), (Arctic, Antarctic, and Alpine Research), (The Auk), (Avian Diseases), (BIOS), (BIOTROPICA), (BioScience), (Biology of Reproduction), (The Botanical Review), (Brittonia), (The Bryologist), (Bulletin of the American Museum of Natural History), (Castanea), (Cell Stress & Chaperones), (The Coleopterists Bulletin), (Comparative Parasitology), (The Condor), (Copeia), (Economic Botany), (Environmental Entomology), (Evolution), (Florida Entomologist), (Herpetologica), (Herpetological Monographs), (In Vitro Cellular & Developmental Biology - Animal), (In Vitro Cellular and Developmental Biology - Plant), (Integrative and Comparative Biology), (Journal of Arachnology), (Journal of the Arizona-Nevada Academy of Science), (Journal of Avian Medicine and Surgery), (Journal of Coastal Conservation), (Journal of Coastal Research), (Journal of Crustacean Biology), (Journal of Economic Entomology), (The Journal of Eukaryotic Microbiology), (Journal of Field Ornithology), (Journal of Herpetology), (Journal of Insect Science), (Journal of the Kansas Entomological Society), (Journal of Mammalogy), (Journal of Medical Entomology), (Journal of the New York Entomological Society), (Journal of the North American Benthological Society), (Journal of Orthoptera Research), (Journal of Paleontology), (Journal of Parasitology), (Journal of Vegetation Science), (Journal of Vertebrate Paleontology), (Journal of Wildlife Management), (Journal of Zoo and Wildlife Medicine), (Mammalian Species), (Micropaleontology), (Mountain Research and Development), (Northeastern Naturalist), (Northwestern Naturalist), (PALAIOS), (Paleobiology), (Palynology), (Photochemistry and Photobiology), (Proceedings of the Academy of Natural Sciences of Philadelphia), (Radiation Research), (Rangeland Ecology & Management), (Rangelands), (The Society of Wetland Scientists Bulletin), (Southeastern Naturalist), (The Southwestern Naturalist), (Systematic Botany), (Transactions of the Kansas Academy of Science), (Ursus), (Waterbirds), (Weed Science), (Weed Technology), (Wetlands), (Wildlife Society Bulletin), (The Wilson Bulletin)

micro*scope version 6 released.

Thu, 16 Mar 2006 00:00:00 -0500

micro*scope is the first star*site. Star*software uses uBio Namebank content, a unifying classification, and taxonomically intelligent algorithms to create web sites that organize local and distributed information about organisms.

uBio Portal and website update

Wed, 15 Mar 2006 00:00:00 -0500

The uBio Portal is an experimental search aggregating tool that seeks to bring together distributed knowlege sources that enhance information retrieval and elevate the visibility and efforts of authoritative informatics efforts in biology. uBio has also updated it's website to a more modular system written in PHP.

Keyword search feature revised in uBioRSS

Tue, 14 Mar 2006 00:00:00 -0500

Keyword search in uBioRSS has been integrated with taxonomic viewing as we prepare for more integrated cross-referencing between taxonomic intelligence methods and standard subject taxonomies. A keyword search for "genome," for example lists the matching RSS feeds while at the same time, the taxonomic lists changes to reflect the taxonomic coverage of the results set.

uBioRSS.Novum monitors RSS feeds for new names

Tue, 07 Mar 2006 00:00:00 -0500

uBioRSS.Novum is derived from uBioRSS, an application that parses scientific names from RSS feeds to allow RSS titles to be browsed by taxonomies. The new application monitors the same RSS feed list for nomenclatural statements such as "nov. sp., nov. comb., etc." and other nomenclatural conventions for designating new additions to biological nomenclature. The new names are then identified using uBio Taxonomic Name Recognition (TNR) algorithms. uBio utilizes this application to update the dictionaries used by it's TNR algorithms as well as to add new names to NameBank.

National Marine Fisheries Service uses X:ID for shipboard fish identification

Fri, 03 Mar 2006 00:00:00 -0500

uBio has developed a version of X:ID, an XML-based taxonomic key software that will be used in shipboard trawler surveys conducted by the National Marine Fisheries Service in Woods Hole, MA. The software will help users identify trawler-caught species and link to species-specific information containing video, images and handling protocols.

Zootaxa added to uBioRSS

Tue, 28 Feb 2006 00:00:00 -0500

[] uBio created an RSS feed for Zootaxa, "A rapid international journal for animal taxonomists". New publications are indexed and available for taxonomic browsing through uBioRSS or can be accessed via RSS at:

uBioRSS is a taxonomic RSS aggregator that allows taxonomic browsing of thousands of articles from hundreds of journals.

uBio and developing uBio OWL.

Mon, 13 Feb 2006 00:00:00 -0500

FreshwaterLife is using uBio data to test our model of taxonomy in the Web Ontology Language (OWL) and to test scale and performance in their new ontology based Ecological Database system

uBio joins Smithsonian Library in the digital conversion of Index Animalium

Wed, 01 Feb 2006 00:00:00 -0500

The Smithsonian Institution Libraries have contracted with uBio to parse Index Animalium, a compilation of zoological species names published between 1801-1850. The text has been digitially converted to raw unparsed text. uBio is drawing upon lexical and taxonomic parsing tools to convert this raw form to a relational data model.

uBioRSS, a taxonomically intelligent feed reader.

Sat, 28 Jan 2006 00:00:00 -0500

uBio releases a demonstration version of a taxonomically intelligent RSS aggregator.

Author Abbreviation Resolver SOAP methods.

Thu, 17 Nov 2005 00:00:00 -0500

The Author Abbreviation Resolver is a web service and database of variations within the recording of authors of taxonomic names.

Volume 10 of Nomenclator Zoologicus online

Thu, 22 Sep 2005 00:00:00 -0400

[] The uBio project, in collaboration with the Zoological Society of London, have updated the online Nomenclator Zoologicus with an electronic Volume 10 that covers zoological genera published between 1994-2004. This supplement adds approximately 20,400 records to the 340,000+ records contained within the original nine volumes.

Nomenclator Zoologicus is a continuous record of the bibliographical origins of the names of every genus and subgenus in zoology published since the 10th ed. of Linnaeus' Systema Naturae in 1758 up to 1994 in nine volumes. (Now 2004 and 10 volumes). Names are listed alphabetically, with a bibliographic reference to the original description of each one and an indication of the animal group to which it belongs.

We would like to extend thanks to those who have helped to review the conversion of the original nine volumes. Over 20,000 records (or 864,000 characters) have been reviewed. Of these, 264 corrections have been required of which only 33 represent actual typographical errors. The remainder are parsing errors where content intended for one column was in another. We have calculated the typographical accuracy currently as 99.997%. We continue to seek volunteer reviewers.

We would like to acknowledge the efforts of Nigel Robinson and the Thompson Publishing Group for their collaboration with the ZSL.

uBio releases name processing tools.

Fri, 05 Aug 2005 00:00:00 -0400

uBio is developing a variety of taxonomic name recognition tools, name parsing tools and text-crawling applications.

Name-aware Google Client

Fri, 01 Jul 2005 00:00:00 -0400

This web application combines the Google SOAP API with the uBio API to create a taxonomic names interface to Google.

Charles Hussey first to review 100 pages of Nomenclator Zoologicus

Tue, 07 Jun 2005 00:00:00 -0400

Charles Hussey of the Library of the Natural History Museum in London reviewed 100 pages of the digital conversion of Nomenclator Zoologicus. We are indebted to him for helping ensure the quality of the online version of this important referent work.

uBio welcomes Dr. Adorian Ardelean

Mon, 23 May 2005 00:00:00 -0400

[] May 23, 2005 - uBio welcomes Dr. Adorian Ardelean who has started a new position within uBio as a bioinformatics taxonomist. Dr. Ardelean arrives from West University in Timisoara, Romania. He earned a Ph.D. in invertebrate zoology at Kansas University under Dr. Daphne Fautin.

Adorian is the author of SynGraph, an application the allows linkage of any published name to any other using a lexicon of modifiers that are conventional in taxonomy, anchoring each use to its bibliographic reference. He hosts a biodiversity site and combines a background in taxonomy with programming and informatics skills.

Adorian will be working within uBio in the technical development of NameBank.

Nomenclator Zoologicus available online

Tue, 30 Nov 2004 00:00:00 -0500

Nomenclator Zoologicus is a continuous record of the bibliographical origins of the names of every genus and subgenus in zoology published since the 10th ed. of Linnaeus' Systema Naturae in 1758 up to 1994 in nine volumes.

Multiple concept review of Francolinus afer and related taxa demonstrates taxon concept service

Wed, 06 Oct 2004 00:00:00 -0400

uBio recently collaborated with an AMNH ornithologist to review a small group of African francolins within multiple catalogs to examine the relationships between different interpretations. The purpose additionally was to explore the utility of the TNS data model in accurately mapping multiple classificatons and the WSDL service calls in retrieving them.

uBio receives GBIF funding for names digitization project

Wed, 07 Jul 2004 00:00:00 -0400

uBio has received funding from the Global Biodiversity Information Facility to assist in the digital conversion of Nomenclator Zoologicus, a compilation of zoological genera from the time of Linnaeus to 1991.

WSDL added to the uBio Service.

Mon, 07 Jun 2004 00:00:00 -0400

the uBio SOAP service was upgraded to include a full service description using the Web Services Description Language. A WSDL file provides a standardized and machine-readable means to qualify a SOAP service.

X:ID development focuses on employing the SDD standard.

Tue, 01 Jun 2004 00:00:00 -0400

The uBio taxonomic key software, X:ID, now supports the SDD (Structure of Descriptive Data) standard that is maintained by the Taxonomic Databases Working Group (TDWG)

uBio upgrades it's web services

Thu, 15 Apr 2004 00:00:00 -0400

uBio has upgraded it's web services from XML-RPC to SOAP and has expanded the web service methods available through this interface.

uBio and GBIF to develop Memo of Cooperation

Tue, 27 Jan 2004 00:00:00 -0500

David Remsen named to GBIF ECAT names subcommittee

Mon, 22 Dec 2003 00:00:00 -0500

David Remsen was named to become a member of the Science Subcommittee of the Electronic Catalog of Names of Known Organisms (ECAT) of the Global Biodiversity Information Facility (GBIF) in Copenhagen, Denmark.