Announcements


 
Mathematical, Statistical and Computational Aspects of the New Science of Metagenomics
Isaac Newton Institute for Mathematical Sciences, University of Cambridge
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Genomic Science 2014
Contractors-Grantees Meeting XII
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 (47kB PDF)
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 (6.0MB PDF)
 
Society for Industrial Microbiology and Biotechnology
RAFT X: Recent Advances in Fermentation Technology
George Garrity and Charles Parker will be presenting posters ("Global commercialization trends of microbial products and processes" and "A semantic index of phenotypic and genotypic data") at the RAFT X conference. The posters will also be available to attendees on the RAFT-X meeting site.
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 (30kB PDF)
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 (4.7MB PDF)
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 (31kB PDF)
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 (477kB PDF)
 
BioCreative IV Challenge and Workshop
BioCreative: Critical Assessment of Information Extraction in Biology
George Garrity presented an overview of the text mining approaches employed by NamesforLife during the DOE Panel on October 8th, 2013.
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 (9.4MB PDF)
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 (88kB PDF)
 
Intellectual Property Rights Workshop
University of Arizona
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 (446kB PDF)
 
Genomic Science 2013
Contractors-Grantees Meeting XI
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 (645kB PDF)
 
NamesforLife Phenotypic Ontology
Argonne National Laboratory
Dr. George Garrity presents NamesforLife's progress toward a phenotpyic ontology for bacteria and archaea.
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 (28.9MB KeyNote)
 
DOI mediated semantic services
Scientific, Technical and Medical Publishers New Technologies Meeting
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A potential semantic service layer for DOI RAs
International DOI Foundation Board Meeting
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 (36kB PDF)
 
Phenotypic Dark Matter
Danish Technical University
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Phenotypic Dark Matter
Deutsche Sammlung fur Mikroorganismen und Zellkulturen
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DOIs, Kbase and NamesforLife
Webinar
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Genomic Science 2012
Contractors-Grantees Meeting
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 (2.1MB PDF)
 
eXtyles User Group Meeting
Dr. George Garrity will be presenting a case study of NamesforLife at the 2011 XUG Meeting.
This case study will discuss integration of NamesforLife's DOI-based semantic resolution services with eXtyles. The NamesforLife tool is designed to provide editors and authors with direct access to expertly maintained information about biological names and other dynamic terminologies as a part of the editorial process, to automatically resolve any instances of ambiguity, and to embed DOIs directly into XML instances so that readers have direct access to rich contextual information associated with each name, without having to leave the article they are reading.
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 (3.2MB PDF)
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 (7.5MB PowerPoint)
 
SyMBIOTA: Synergy in Microbiota Research Workshop
Methods to Study the Human Microbiome
Dr. George M. Garrity will be presenting the keynote lecture, "Distorted Realities", during the Bioinformatics session on Monday at 9:15am.
Workshop Agenda
 (88kB PDF)
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 (72.1MB KeyNote)
 
NamesforLife founder is awarded the van Niel International Prize
The Senate of The University of Queensland, on the recommendation of a panel of experts of the International Committee on Systematics of Prokaryotes, is pleased to present the van Niel International Prize for Studies in Bacterial Systematics for the triennium 2009-2011 to Professor George M. Garrity in recognition of his contribution made to the field of bacterial systematics. The award, established in 1986 by Professor V. B. D. Skerman of The University of Queensland, honours the contribution of scholarship in the field of microbiology by Professor Cornelis Bernardus van Niel.
Busse H-J, Labeda DP, Oren A, Tindall BJ. The van Niel International Prize for Studies in Bacterial Systematics, awarded by The University of Queensland Awarded in 2011 to George M. Garrity. Int J Syst Evol Microbiol 2011; 61:2328-2329. doi:10.1099/ijs.0.035907-0 [PubMed].
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 (40kB PDF)
 
IUMS Bacteriology and Applied Microbiology Congress
The Unlimited World of Microbes
Dr. George M. Garrity will be presenting Plenary Lecture 4 for this conference on September 7th.
Dr. Garrity presents the plenary lecture, "The Beginning of Wisdom...".
Photo from the lecture
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Intellogist article on NamesforLife
Kristin Whitman from Landon IP has written about NamesforLife from the perspective of the patent community.
Whitman K. Biotech patents and their pitfalls: NamesforLife adds value to your biology searches. Intellogist 2011.
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 (external site)
 
N4L::Guide updated for new versions of Firefox
N4L::Guide has been updated to support Firefox versions 5 through 8. The add-on will continue to work with older versions, back to Firefox 2.0. As always, if you encounter any issues or have any suggestions for improvements, please let us know.
Install N4L::Guide
 (Firefox Add-on)
 
The NamesforLife Abstracts
The NamesforLife Abstracts are now available. These are citable micropublications containing up-to-date information about all validly published names under the Prokaryotic Code of Nomenclature. Each abstract can be accessed via a Digital Object Identifier, which resolves to the NamesforLife Anchor for that object. If you are logged in with your NamesforLife account, you can view the full abstract. You can search for specific bacteria or archaea using the sidebar on this page, or you can start browsing the complete taxonomy using the links to the Archaea or Bacteria here. We will continue to refine the content in the coming months. Please let us know what you think.
Taxon Abstract for the domain “Archaea”. NamesforLife, LLC 2011. doi:10.1601/tx.1.
Taxon Abstract for the domain “Bacteria”. NamesforLife, LLC 2011. doi:10.1601/tx.419.
 
PIUG 2011 Annual Conference
Best Practices Beyond Free-text: The Value of Indexing and Classification when Searching and Analyzing Patents
George M. Garrity will be presenting a lecture on applying NamesforLife semiotic analysis to Fairview's Alexandria database during the Tuesday morning session (Indexing Patent Literature Using Semiotic Fingerprints).
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 (5.3MB KeyNote)
 
Genomic Science 2011
Awardee Meeting IX and USDA-DOE Plant Feedstock Genomics for Bioenergy Awardee Meeting
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 (828kB PDF)
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 (89kB PDF)
 
Volume 3 of SIGS is NamesforLife-enabled.
SIGS Vol. 3, Issue 3
 (external site)
 
Microbial Earth
The first version of Microbial Earth is now available.
Microbial Earth
 (external site)
 
BioSystematics 2011
Charles Parker will be presenting a poster and demonstrating the N4L system at the software bazaar. George Garrity will be presenting during the evening session on April 13th.
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 (806kB PDF)
 
PIUG 2010 Northeast Conference
NamesforLife will be attending the Patent Users Information Group Northeast conference.
 
Biocuration 2010
The Conference of the International Society for Biocuration
Moving towards an Extensible and Interoperable System for Naming.
Parker CT, Taylor NO, Mannor KM, Wigley SW, Osier N, Lyons C, Garrity GM. NamesforLife Semantic Resolution Services for the Life Sciences. Nat Pre 2010. doi:10.1038/npre.2010.5137.1.
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 (1.4MB PDF)
 
DOI News mentions NamesforLife
NamesforLife has a mention in the May 2010 DOI News. See “DOI-based Tool for Taxonomy”.
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 (external site)
 
ASM 2010
American Society for Microbiology 110th General Meeting
NamesforLife will be attending the ASM 2010 Meeting. Stop by the Society for General Microbiology booth for a demonstration of N4L::Guide and grab a brochure. We are excited to show our new work.
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 (682kB PDF)
 
Society for General Microbiology Spring 2010 Meeting
NamesforLife will have a booth at the SGM Spring 2010 meeting.
SGM Spring 2010 Agenda
 (4.3MB PDF)
 
Microbiology Today
NamesforLife has a full page write-up in Microbiology Today.
Garrity GM. NamesforLife: BrowserTool takes expertise out of the database and puts it right in the browser. Microbiology Today 2010; 2:9.
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 (1.1MB PDF)
View Entire Issue
 (external site)
 
Genomic Science 2010
Awardee Workshop VIII and USDA-DOE Knowledgebase Workshop
NamesforLife Semantic Resolution Services for the Life Sciences
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 (2.4MB PDF)
 
Annual Collaboration for Entrepreneurship 2010
NamesforLife will have a booth at ACE'10: The Annual Collaboration for Entrepreneurship in Ann Arbor, Michigan.
 
Introducing N4L::Guide
This NamesforLife Firefox Add-on brings expertise from the database into the browser.
At present, the list of validly published names of Bacteria and Archaea changes roughly fifteen times each week. Invalid and trivial names appear in the literature and public databases at a rate that if more than three fold higher. While a small number of experts diligently work to keep pace with these changes the rest of the scientific, medical, and allied communities are left on their own to make sense of a never-ending onslaught of names. While all agree that using the correct name is essential for accurate communication, but what name is it? What was it? If a name changed, why did it change? What does this mean to you as you read the literature? Do you interrupt your reading to check on the taxonomic state of play. Do you break what you are doing and look up related information or do it later? Are you sure that your knowledge is current? Keeping up with this could be a full-time job.
There is a solution to this problem. NamesforLife, in partnership with the SGM and the International Committee on the Systematics of Prokaryotes, has been working to extract all of the relevant information from the taxonomic literature for Bacteria and Archaea. This information is then served up, along with rich annotation, for any text that is readable in a web browser (starting with Firefox, but expanding to other browsers in the near future), on-demand. Never again will a reader have to feel ill-informed about the status or meaning of a name.
The NamesforLife philosophy is that online annotation services must be sufficiently authoritative and persistent that other systems can rely on them rather than attempting to duplicate them. Those services must work not only for the ad hoc human user, who after all has fail-safe alternatives, but also when incorporated in third-party applications. NamesforLife identifies these objects using now familiar digital object identifiers (DOIs) and makes them reliably citeable. The objects then become formally structured micropublications. How is it done? NamesforLife employs a team of expert curators to index the taxonomic literature as a sequence of interrelated taxonomic, nomenclatural and organismal events that are tied to all previously recorded events and the underlying literature.
N4L::Guide moves expertise from the database into the browser. The events that NamesforLife captures are presented via a menu that collocates with the occurrence of a name on a web page. The menu provides links out to other resources and to NamesforLife Abstracts, which aggregate names and key biological information with our Name, Taxon, and Exemplar objects.
Install N4L::Guide
 (Firefox Add-on)
 
ASM 2009
American Society for Microbiology 109th General Meeting
NamesforLife will be attending the ASM 2009 Meeting. Stop by the Society for General Microbiology booth for a live demonstration of the N4L system.
 
United Nations Convention on Biological Diversity
Seventh Meeting: Ad hoc Open-Ended Working Group on Access and Benefit Sharing
Excerpts from: Studies on the Identification, Tracking and Monitoring of Genetic Resources
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 (2.6MB PowerPoint)
 
Genomics 2009
GTL Awardee Workshop VII and USDA-DOE Plant Feedstock Genomics for Bioenergy Awardee Workshop
NamesforLife Semantic Resolution Services for the Life Sciences
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 (2.6MB PDF)
 
Annual Collaboration for Entrepreneurship 2009
NamesforLife will have a booth at ACE'09: The Annual Collaboration for Entrepreneurship in Ann Arbor, Michigan.
 
NamesforLife opens an office in downtown East Lansing
NamesforLife has opened a commercial office at the new Technology Innovation Center in downtown East Lansing. We are proud to be an Inaugural Tenant and the first company to move into this new space.
East Lansing TIC
 (external site)
 
Society for Scholarly Publishing 2008 Annual Meeting
George Garrity will be presenting on NamesforLife during Seminar 4.
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 (5.8MB PowerPoint)
 
Genomics 2008
GTL Awardee Workshop VI and Metabolic Engineering Working Group Interagency Conference on Metabolic Engineering
NamesforLife Semantic Resolution Services for the Life Sciences
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 (1.9MB PDF)
 
Garrity named AAAS Fellow
American Association for the Advancement of Science Annual Meeting
George M. Garrity, ScD has been elected among the 2007 Fellows of the American Association for the Advancement of Science.
 
Mid-Michigan Entrepreneur's Day
George Garrity presents "NamesforLife: Bringing meaning to life".
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 (1.5MB PowerPoint)
 
Taxonomic Outline of Bacteria and Archaea 7.7
The Taxonomic Outline of Bacteria and Archaea (TOBA) 7.7 has been published.
External Site
 (external site)
 
Food and Agriculture Organization of the United Nations
IT Support for SMTA implementation
George Garrity presents "An Overview of Persistent Identifiers".
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 (1.5MB PowerPoint)
 
The ABS Dialogues
The Role of Documentation in ABS and TK Governance
George Garrity presents the lecture "An Overview of Persistent Identifiers" in the afternoon meeting, "New approaches to documentation of genetic resources".
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 (1.3MB PowerPoint)
 
eGenomics 2006
eGenomics III: Cataloguing our complete genome collection
George Garrity discusses NamesforLife and Phenbank at Cambridge. He will also chair Monday's second session: "Databases and Metadata capture and Exchange efforts".
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 (5.2MB PowerPoint)
 
FEMS Meeting 2006
2nd FEMS Congress of European Microbiologists
George Garrity presents "Knowledge bleed, PhenBank, and NamesforLife" during Symposium 20 (Biodiversity).
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 (250kB PDF)
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 (8.7MB PowerPoint)
 
Computational aspects of systematic biology
Lilburn, Harrison, Cole and Garrity discuss the resources currently available to systematic biologists.
Lilburn TG, Harrison SH, Cole JR, Garrity GM. Computational aspects of systematic biology. Brief Bioinform 2006; 7:186-195. doi:10.1093/bib/bbl005 [PubMed].
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 (135kB PDF)
 
Taxonomic Databases Working Group GUID-1 Workshop
First International Workshop on Globally Unique Identifiers (GUIDs) for Biodiversity
George Garrity presents "Digital Object Identifiers as a technology implementation of a full working prototype the NamesforLife model".
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 (2.5MB PowerPoint)
 
eGenomics 2005
eGenomics II: Cataloguing our complete genome collection
George Garrity discusses NamesforLife and Phenbank at Cambridge.
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 (3.0MB PowerPoint)
 
International workshop (IUAP V/23)
Exploring and exploiting microbiological commons: contributions of bio-informatics and intellectual property rights in sharing biological information
George Garrity presents the N4L system in "Automating the Quest for Novel Prokaryotic Diversity (revisited)".
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 (38kB PDF)
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 (8.4MB PowerPoint)
 
Bioinformatics Forum
Names and Objects for Unambiguous Data Access amongst Biodiversity Data Entities
Catherine Lyons presents "An Introduction to igital Object Identifiers as background to Names for Life".
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 (1.3MB PowerPoint)
 
19th International CODATA Conference
Digital Object Identifiers for scientific data
Norman Paskin has published an article regarding the use of DOIs for scientific data. A description of the NamesforLife system is given on page 7.
Paskin N. Digital Object Identifiers for scientific data. Data Science Journal 2005; 4:12-20. doi:10.2481/dsj.4.12.
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 (211kB PDF)
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 (52kB PDF)
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 (557kB PowerPoint)
 
Annual International DOI Foundation Members Meeting
Session 4: Uses of identifiers - Identifiers for data
Catherine Lyons presents the NamesforLife concept at the IDF Members Meeting.
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 (532kB PowerPoint)
 
GBIF/WFCC/SPO Expert Workshop
Towards a Global Infrastructure for Microbial Information
George Garrity presents "Biological nomenclature in the postgenomic era: Biological and computational issues".
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 (1.8MB PowerPoint)
 
Genomes to Life Contractor–Grantee Workshop I
Workshop Breakout Session — Comparative Genomics: New Approaches & Insights
George Garrity presents "Carolus Linnaeus in the postgenomic era".
This discussion will focus on a problem that plagues us all to some degree or another – biological nomenclature. Ideally, our formalized system of nomenclature is supposed to improve communication among biologists. In reality, it seems to be a major obstacle, especially when misapplied. Although the problem is evident in the literature, it is most severe in the sequence databases, which now serve as the principal source and repository of data used in comparative biology. Moreover, the sequence databases tend to propagate such errors for a variety of reasons. As biological data proliferates and interconnects, it depends increasingly on software infrastructure, and it becomes increasingly obvious that biological names do not meet the requirements of a good identifier, in strict computing terms. A good identifier should be unique and persistent. As an outgrowth of my current DOE funded project, we have been exploring a practical and workable solution that we believe will help solve the problem in a future-proof fashion.
 
Workshop on Data Management for Molecular and Cell Biology
George Garrity will be present to discuss the white paper, "Future-proofing biological nomenclature".
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 (external site)
 
Future-proofing biological nomenclature
The original white paper behind the NamesforLife concept.
Garrity GM, Lyons CL. Future-proofing biological nomenclature. OMICS 2003; 7:31-33. doi:10.1089/153623103322006562 [PubMed].