July 2, 2019
NamesforLife recently published a white paper contrasting the precision of 16S classification using the NamesforLife HQ16S data product, non-redundant Silva and Greengenes 16S databases.
This study demonstrates two lines of concrete evidence of the dangers of using incorrectly annotated data:
- Both Silva and Greengenes were found to contain 16S sequences for type strains that had not been updated with the correct nomenclature and yield incorrect identifications, even when sequence similarity was > 99%.
- Even after reannotation of both data sets the error rates in identification remain high due to incomplete taxonomic coverage.
These problems can only be overcome by continuously revising the underlying reference data and re-evaluating old or existing data in light of new information, including new names. Subscribers to NamesforLife data and nomenclature services are protected from these problems, as these accumulated changes are integrated into all of our services and data products.
January 11, 2019
NamesforLife is pleased to announce the publication of a new edition of the International Code of Nomenclature of Prokaryotes (ICNP). This endeavor started in 2013 and represents hundreds of hours of work by the editors: Charles Parker (NamesforLife, LLC), Brian Tindall (DSMZ) and George M. Garrity, Sc.D. (Michigan State University and NamesforLife, LLC). Many thanks to the editorial team (especially Hebba Beech, Fiona Mitchell and Justin Clark) at the Microbiology Society for all of their hard work and to everyone who had a hand in producing this new edition of the Code.
The Microbiology Society has written a news story on the Society web site.
A new edition of the complete Code has been long overdue. It is hoped that this attempt to produce the Code in both electronic and print format greatly reduces the burden of future editors while retaining the original vision of Buchanan.
October 16, 2018
State Key Laboratory of Infectious Disease Prevention and Control (SKLID), Beijing, China October 16-17, 2018
George Garrity will be delivering a seminar on Tuesday, regarding observations on the impact of rapid changes in prokaryotic taxonomies and nomenclature. This talk highlights recent findings in taxon calling and strain classification based on NamesforLife data.
Changes in the prokaryotic taxonomy over eight months incur statistically significant changes for some test metagenomes.
August 23, 2018
The August release of the NamesforLife taxonomy contains an updated 16S rRNA data set that includes 15,500 sequences of validly published species and subspecies of Bacteria and Archaea, including new species, new combinations and corrections to nomenclature. Also, 8,473 genome assemblies have been linked to 6,987 of the type strains.
There were a total of 83 changes as compared to Release 20180717, including 47 novel taxa, no replacement names, 13 rank elevations, no rank reductions, 5 new combinations, no corrections, no neotypes/proxy types, no transfers of taxa, 18 deprecated names.
August 21, 2018
ATCC Headquarters, Manassas, Virginia August 21-23, 2018
George Garrity will be delivering a presentation at 1pm on Tuesday, during the session on persistent identifiers. The topic of this talk involves making persistent connections betweens culture collections and research artifacts using the NamesforLife Information Architecture and web services.
These services provide a novel and direct means of assessing the impact of research products by individuals and research institutions that are used by the community but rarely cited. NamesforLife provides a way to correct this deficiency and objectively assess the impact of curators and resource providers.
July 17, 2018
The July release of the NamesforLife taxonomy contains an updated 16S rRNA data set that includes 15,461 sequences of validly published species and subspecies of Bacteria and Archaea, including new species, new combinations and corrections to nomenclature. Also, 8,179 genome assemblies have been linked to 6,827 of the type strains.
There were a total of 153 changes as compared to Release 20180612, including 76 novel taxa, no replacement names, no rank elevations, 1 rank reduction, 36 new combinations, no corrections, 1 neotype/proxy type, 2 transfers of taxa, 37 deprecated names.
June 28, 2018
Korean Society for Microbiology & Biotechnology — KMB 2018 45th Annual Meeting & International Symposium
Yeosu, South Korea June 27-29, 2018
George Garrity will be delivering the opening lecture, “Taxonomic Inference vs. Ground Truth” at this year’s KMB meeting. The lecture will be Thursday June 28th from 2:05 to 3:35pm in Rm1.
The idea of change in microbiology and other fields is nothing new. Our methods are continuously evolving, but ultimately, we need to be able to place our new findings into a frame of reference; to define our findings and to interpret the meaning of those findings.
June 12, 2018
The June release of the NamesforLife taxonomy contains an updated 16S rRNA data set that includes 15,406 sequences of validly published species and subspecies of Bacteria and Archaea, including new species, new combinations and corrections to nomenclature. Also, 8,024 genome assemblies have been linked to 6,713 of the type strains.
There were a total of 60 changes as compared to Release 20180517, including 51 novel taxa, 1 new combination, no replacements, no elevations in rank, 2 reductions in rank, no neotype/proxy types recognized, no corrections and 3 transfers of subspecies, species or genera to alternative higher taxa and 3 deprecated DOIs.
May 23, 2018
You may have noticed some changes to the NamesforLife Abstracts. We have updated the look and feel of the abstracts to match the style of our main web site.
Additionally, the NamesforLife DOIs (prefix 10.1601) now resolve to www.namesforlife.com instead of doi.namesforlife.com. There may have been up to 48 hours of availability issues while we updated CrossRef with the new resolution and completed the deployment of this update.
As always, if you encounter any issues with the Abstracts or any other service we provide, please contact us at email@example.com.
May 17, 2018
The May release of the NamesforLife taxonomy contains an updated 16S rRNA data set that includes 15,363 sequences of validly published species and subspecies of Bacteria and Archaea, including new species, new combinations and corrections to nomenclature. Also, 7,861 genome assemblies have been linked to 6,588 of the type strains.
There were a total of 142 changes as compared to Release 20180421, including 107 new taxa, 4 new combinations, no replacements, no elevations in rank, no reductions in rank, 10 neotype/proxy types recognized, no corrections and 21 transfers of subspecies, species or genera to alternative higher taxa and no deprecated DOIs.
May 1, 2018
Read the full text of the new policy.
April 21, 2018
The April release of the NamesforLife taxonomy contains an updated 16S rRNA data set that includes 15,116 sequences of validly published species and subspecies of Bacteria and Archaea, including new species, new combinations and corrections to nomenclature. Also, 7,705 genome assemblies have been linked to 6,456 of the type strains.
There were a total of 191 changes as compared to Release 20180314, including 73 new taxa, 19 new combinations, no replacements, no elevations in rank, 1 reduction in rank, 0 neotype/proxy types recognized, 32 corrections and 35 transfers of subspecies, species or genera to alternative higher taxa and 59 deprecated DOIs.
March 14, 2018
The March release of the NamesforLife taxonomy contains an updated 16S rRNA data set that includes 15,053 sequences of validly published species and subspecies of Bacteria and Archaea, including new species, new combinations and corrections to nomenclature. Also, 7,529 genome assemblies have been linked to 6,329 of the type strains.
There were a total of 385 changes as compared to Release 20180216, including 92 new taxa, 117 new combinations, no replacements, no elevations in rank, 3 reductions in rank, 6 neotype/proxy types recognized, no corrections and 110 transfers of subspecies, species or genera to alternative higher taxa and 57 deprecated DOIs.
February 16, 2018
The February release of the NamesforLife taxonomy contains an updated 16S rRNA data set that includes 14,954 sequences of validly published species and subspecies of Bacteria and Archaea, including new species, new combinations and corrections to nomenclature. Also, 7,333 genome assemblies have been linked to 6,206 of the type strains.
There were a total of 172 changes as compared to Release 20180113, including 38 new taxa, 1 new combination, 1 replacement, no elevations in rank, 4 reductions in rank, no neotypes recognized, no corrections and 127 transfers of subspecies, species or genera to alternative higher taxa.
January 13, 2018
The January release of the NamesforLife taxonomy contains an updated 16S rRNA data set that includes 14,956 sequences of validly published species and subspecies of Bacteria and Archaea, including new species, new combinations and corrections to nomenclature. Also, 7,101 genome assemblies have been linked to 6,028 of the type strains.
There were a total of 1,070 changes as compared to Release 20171217, including 99 new taxa, 1 new combination, no replacements, five elevations in rank, no reductions in rank, no neotypes recognized, no corrections and 965 transfers subspecies, species or genera to from the Cytophagacaea to the Flavobacteriacea.
January 8, 2018
The founder of NamesforLife, George M. Garrity, Sc.D. has been elected elected to Fellowship in the American Academy of Microbiology. The Academy, the honorific leadership group within the American Society for Microbiology, recognizes excellence, originality, and leadership in the microbiological sciences.
George Garrity and Beronda Montgomery, Michigan State University professors of the College of Natural Science, were elected fellows of the American Academy of Microbiology, or AAM, for their excellence, originality and leadership in the microbiological sciences. Garrity, a professor in the Department of Microbiology and Molecular Genetics, was elected for his work in a range of important areas of microbial biology, knowledge mining and industrial microbiology.
Natural Science is proud to have two of its faculty members elected as AAM fellows this year. Professors Garrity and Montgomery are recognized not only for their outstanding contributions to microbial research, but also for extending fundamental research to human applications and for leadership in advancing the next generation of microbiologists. Their distinction as AAM fellows is richly deserved.
The mission of the Academy is to recognize scientists for outstanding contributions to microbiology and provide microbiological expertise in the service of science and the public. The American Academy of Microbiology is honored to welcome these Fellows, elected in recognition of their records of scientific achievement and original contributions that have advanced microbiology. Each elected Fellow has built an exemplary career in basic and applied research, teaching, clinical and public health, industry or government service. Election to Fellowship indicates recognition of distinction in microbiology by one’s peers.
December 17, 2017
The December release of the NamesforLife taxonomy contains an updated 16S rRNA data set that includes 14,878 sequences of validly published species and subspecies of Bacteria and Archaea, including new species, new combinations and corrections to nomenclature arising primarily from the placement of a small number of species/subspecies in enumerated unnamed intermediate taxa. Also, 6,982 genome assemblies have been linked to 5,941 of the type strains.
We now include a changelog of taxonomic changes from the previous release.
There were a total of 266 changes to the as compared to Release 20171113, including 164 new taxa, 5 new combinations, two replacements, five elevations in rank, four reductions in rank, two neotypes recognized, 1 correction and 63 transfers subspecies, species or genera to new parent taxa.
November 13, 2017
The November release of the NamesforLife taxonomy contains an updated 16S rRNA data set that includes 14,726 sequences of validly published species and subspecies of Bacteria and Archaea, including new species, new combinations and corrections to nomenclature arising primarily from the placement of a small number of species/subspecies in enumerated unnamed intermediate taxa. Also, 6,773 genome assemblies have been linked to 5,740 of the type strains.
This month, we have introduced a new strain-to-genome resolution method that performs nightly data integration with the NamesforLife prokaryotic database and NCBI genome assemblies.
October 30, 2017
The October release of the NamesforLife taxonomy contains an updated 16S rRNA data set that includes 14,611 sequences of validly published species and subspecies of Bacteria and Archaea, including new species, new combinations and corrections to nomenclature. Also, 6,693 genome assemblies have been linked to 5,672 of the type strains.
September 13, 2017
As you may have noticed, we have re-designed our web site. We will be making a few minor changes here and there over the next month or so as we refresh our content. Our services have been merged into a single platform, so please update your bookmarks if needed and feel free to contact us if you have any trouble finding things.
September 10, 2017
Congress Center, Basel, Switzerland September 10-13, 2017
George Garrity will be presenting on two topics during the Innovating MedComms panel: How to ensure content quality in a world of overwhelming scientific complexity, 1:30pm-2:30pm (Machine learning-based tools for peer review) and Scientific discovery In the Machine Age: New tools for competitive advantage, 3:30pm-4:30pm (Machine learning tools for discovering scientific content). Both sessions are in the Shanghai 1 room, and videos will be made available after the event.
The first session (Machine learning tools for discovering scientific content) will showcase how novel semantic tagging and document classification methods can be used to enrich content by unobtrusively integrating externally curated resources and references. Further discussion will explore how these curated resources can serve as hidden metrics that provide a supplementary measure regarding the significance of various research artifacts or concepts in a given field of study.
The following session focuses on applying machine learning tools to the peer review process.
George Garrity reasons that most people underestimate the amount of work that goes into the process. “The publisher distributes your content, they polish it, they make sure there’s an archival version, but they also provide all the necessary quality control, and this is typically done by peer review,” he said.
The peer review process is essential for checking that valid arguments and conclusions are present, with appropriate priority, provenance and originality. However, it can be costly and very time-consuming, thus there is great interest in automating as much of the process as possible.
Hoping to do just that, a suite of tools from NamesforLife allows processing of a raw manuscript in mere minutes, validating facts, structure, terminology and cited resources, and annotating any “red flags”. The automation can then extend to the peer review stage, cross-checking the intended submission with a pool of some 40,000 documents in order to identify candidate reviewers based on relevant publication records.
The process removes selection bias, screens for conflicts of interest, and tracks ongoing reviewer performance. What’s more, it keeps up-to-date contact information for reviewers, and constructs a compelling email to send to the reviewer to encourage their participation.
June 28, 2017
Korean Society for Microbiology & Biotechnology — KMB 2017 44th Annual Meeting & International Symposium
BEXCO, Busan, South Korea June 28-30, 2017
George Garrity will be delivering the opening lecture, “Some Thoughts and Observations on ‘Taxon Calling’” at this year’s KMB meeting. The lecture will be Wednesday June 28th from 12:30 to 1:10pm at APEC Hall.
The focus of this lecture will be to demonstrate the value of a well-curated and carefully annotated reference database that can be used to evaluate existing and new methods of identifying and assigning names to prokaryotic taxa which can serve as a standard and be used for routine re-annotate and updating of existing metagenomes and microbiomes at a much finer grain of resolution that is currently used.
June 6, 2017
East Lansing, Michigan June 6, 2017
NamesforLife, LLC has been awarded U.S. Patent Grant No. 9,672,293 for Systems and Methods for Automatically Identifying and Linking Names in Digital Resources.
This expands the company’s IP portfolio to 5 granted US patents, including two patents exclusively licensed from Michigan State University.
June 6, 2017
The present invention provides systems and methods for automatically identifying name-like-strings in digital resources, matching these name-like-string against a set of names held in an expertly curated database, and for those name-like-strings found in said database, enhancing the content by associating additional matter with the name, wherein said matter includes information about the names that is held within said database and pointers to other digital resources which include the same name and it synonyms.
May 31, 2017
Society for Scholarly Publishing 39th Annual Meeting — Striking a Balance: Embracing Change While Preserving Tradition in Scholarly Communications
Westin Boston Waterfront, Boston, Massachusetts May 31-June 2, 2017
NamesforLife has a booth at the SSP 2017 annual meeting this year. Stop by booth number TT7 for a demonstration of how our tools are being used by early adopters, how our approach might meet your needs for semantic enrichment of your content, and how you can help us shape forthcoming features.
Our software architect, Charles Parker, and our founder, George Garrity will be available every day of the conference for questions and product demonstrations.
Online tools have improved the efficiency of many parts of the editorial workflow, but also place pressure on publishers to perform new tasks in the service of authors and readers. These include identifying suitable editors and peer-reviewers and ensuring technical accuracy of published content. These tasks require a high level of domain knowledge that is often in short supply. We offer services to fill these gaps that can be integrated into existing editorial platforms.
May 23, 2017
East Lansing, Michigan May 23, 2017
NamesforLife, LLC (East Lansing, Michigan) and NUtech Ventures (Lincoln, Nebraska), have been jointly awarded U.S. Patent Grant No. 9,659,145 for classification of nucleotide sequences by Latent Semantic Analysis (LSA).
This expands the NamesforLife’s IP portfolio to 4 granted US patents, including two patents exclusively licensed from Michigan State University.
May 23, 2017
DNA sequences are analyzed using latent semantic analysis. A set of nucleotide sequences is received in which the set has a first number of sequences. A set of basis vectors is determined, in which the set has a second number of basis vectors, the second number being smaller than the first number. Each basis vector represents a specific combination of predetermined nucleotide segments. For each of the nucleotide sequences, an approximate representation of the nucleotide sequence is determined based on a combination of the basis vectors. For each pair of nucleotide sequences, a distance between the pair of nucleotide sequences is determined according the distance between the approximate representation of the pair of nucleotide sequences. The set of nucleotide sequences are classified based on the distances between the pairs of nucleotide sequences.
March 8, 2017
London Book Fair 2017 — Advancing Editorial Productivity with NamesforLife Production Workflow Solutions
Olympia, London, England, United Kingdom March 14-16, 2017
NamesforLife has a booth at the London Book Fair this year. Please stop by Stand 3B36 for product demonstrations and join George Garrity at the Tech Theater on Tuesday March 14th at 12:15pm for a seminar on how our tools are being used by early adopters to improve editorial efficiency. The presentation will be posted here after the seminar.
NamesforLife semantic services provide scientific and technical publishers with standards-based editorial workflow solutions that enhance the value of content to readers while reducing the efforts of authors, peer-reviewers and editors to produce technically accurate content.
Our semantic annotation services save time at each stage of the editorial process and continue to add value after publication. Detection and correction of errors at the earliest possible stage of content production results in significant improvement of document throughput and substantial cost savings.
November 29, 2016
Austin, Texas November 29-December 1, 2016
Charles Parker and George Garrity will be attending the Defense Innovation Summit this year. We will be presenting an overview of our recent work on poster 313, “Knowledge Extraction from Mixed-Precision Information”, during Poster Session I Tuesday afternoon from 2:30pm-3:15pm. We are actively seeking commercial partners to bring this technology to market.
A fundamental barrier to effective human-machine communication is the lack of a shared, unambiguous language that is understandable to humans and precise enough for machine reasoning. The knowledge of domain experts is aggregated from a variety of information sources, ranging from raw text or data to structured and normalized databases (Mixed Precision Information; MPI).
We introduce a novel standards-based method for extracting knowledge from MPI to provide knowledge workers and machine reasoners with verifiable interpretations of observational data.
Our approach combines semantic and semiotic methods to represent information at multiple levels in concept hierarchies, “slice” and aggregate concepts to represent information consistently for ambiguous human language and reasoners, provide multiple entry points for information (term, concept, data), provide attachment points for reasoning over rules and axioms and accommodate multiple interpretations of information.
April 12, 2016
Olympia, London, England, United Kingdom April 12-14, 2016
NamesforLife will be attending the London Book Fair this year. Although we are not presenting this year, we have demonstrations available for our upcoming reviewer services.
March 1, 2016
Tysons, Virginia March 6-9, 2016
Charles Parker and George Garrity will be presenting poster 147 (“Semantic Index of Phenotypic and Genotypic Data”, Abstract Book, pages 256-257) highlighting their team’s recent work during the Monday evening mixer (5:00pm-7:00pm) in Tyson’s Ballroom.
During the course of this project we developed many software components that overcome specific technical barriers in terminology management, text mining, information extraction, knowledge transformation, entity recognition, document classification and annotation. The individual tools (N4L::Guide, N4L::Scribe, the Taxonomic Abstracts, Taxomatic, the KWIC Index and the Semantic Desktop) were implemented using W3C standards and recommendations (SPARQL, RDFS, RDF, OWL2, SKOS, SKOS-XL, XML, XSL, XSD, SPIN, OWL RL, DOI/CrossRef, CORS) and commercially-compatible FOS frameworks (Java, Apache, PostgreSQL, Virtuoso OSE, Jena/ARQ, SPIN Reasoner). We are integrating these components into a single software suite that can support a variety of document analysis needs.
Backed by the Fairview Research Alexandria platform (CLAIMS Global Patent Database), this analysis suite has access to the full text of the worldwide patent literature. We have demonstrated the ability to reverse-engineer the diagnostic phrases that human indexers use to classify large corpora of technical documents, and to measure both the quality of previously annotated documents and the cohesion of individual document classifications. Our software provides a novel way to navigate and bridge multiple classification systems.
Our continued collaborations with the Joint Genome Institute, Fairview Research/IFI Claims and Oak Ridge National Laboratories provide excellent opportunities to test and refine the capabilities of this analysis suite while raising the visibility of other federal funded projects by completing the semantic linking between projects, entities and publications.
June 1, 2015
There is a known compatibility issue with the N4L::Guide Firefox Add-on that affects the bookmarks toolbar and other features in Firefox 38.0. We are working to address this issue and will deploy a fix as soon as possible.
May 1, 2015
17th Workshop of the Genomic Standards Consortium (GSC17) — Standards for the Microbial Dark Matter (uncultured microbial life)
Department of Energy Joint Genome Institute, Walnut Creek, California May 4-6, 2015
Charles Parker will be presenting a poster at the GSC Workshop on May 5th.
Despite significant improvements in genome annotation, many assertions are hypothetical and may lack experimental support. The taxonomic literature for prokaryotes contains a wealth of experimental phenotypic data, but that knowledge is currently in a form that does not lend itself to integration with databases or ontologies.
Our knowledge base is designed to address these problems by providing reference phenotypic data for nearly all type strains of Bacteria and Archaea, based on concepts and observational data drawn from the primary taxonomic literature (the corpus of literature that supports our up-to-date taxonomy and strain database).
We developed software (Semantic Desktop) to extract putative feature domain vocabularies from this corpus, we have since developed this vocabulary into a precise thesaurus of phenotypic terms, which will ultimately conform to W3C SKOS-XL semantics, providing a link between the language of microbial phenotype, the semantic web and existing NamesforLife services.
April 30, 2015
Patent Users Information Group Annual Conference and USPTO-EPC CPC Annual Meeting — From Search Strategy to Business Strategy: Domestic and International Practices, Styles, and Viewpoints
Westin Lombard Yorktown Center, Lombard, Illinois May 1-7, 2015
NamesforLife is attending the USPTO-EPO CPC Annual Meeting with Industry Users on May 1st, as well as the PIUG Annual Conference from May 2-7.
Our company has developed several innovative software components to overcome technical barriers in text mining, information extraction, document classification and annotation.
Our technology arose from a need to support thesaurus construction, vocabulary integration and ontology development. As a result, we have created bridges between document analytics and important industry standards for knowledge representation. Our patented technology produces high-quality data sets from scientific, medical and legal literature via its partnerships with the academic publishers, and Fairview Research, LLC.
Our classification tools provide novel ways to navigate and bridge various patent classification systems, enabling more precise classification and integration with additional proprietary classifications.
These individual software components have been integrated into a single platform that can support a variety of document analysis needs. Our software may be deployed in a web service container, as a desktop application, or extended/integrated with third party software via our developer API.
Backed by the Fairview Research Alexandria platform (CLAIMS Global Patent Database), this analysis suite has access to the full text of the worldwide patent literature.
February 20, 2015
Tysons, Virginia February 22-25, 2015
Charles Parker and George Garrity will be presenting poster 222 (“Semantic Index of Phenotypic and Genotypic Data”, Abstract Book, page 333) during Tuesday evening’s mixer (5:00pm-7:00pm) in Tyson’s Ballroom. We will be highlighting our team’s recent work on Knowledge Extraction from scientific literature.
Our core technical objectives are to: (1) build a database of normalized phenotypic descriptions using the primary taxonomic literature of bacterial and archaeal type strains, (2) construct an ontology capable of making accurate phenotypic and environmental inferences based on that data, and (3) improve the visibility and accessibility of publicly-available research data.
This project is tightly coupled with ongoing DOE projects (the Genomic Encyclopedia of Bacteria and Archaea, the Microbial Earth Project, the Community Science Program) and with two key publications, Standards in Genomic Sciences (SIGS) and the International Journal of Systematic and Evolutionary Microbiology (IJSEM).
The scope of this project covers many technical fields, including text-mining, Information Extraction, Natural Language Processing, indexing & search, terminology & ontology development, machine reasoning, semantic analysis, sequence analysis and taxonomic classification.
December 2, 2014
East Lansing, Michigan December 2, 2014
NamesforLife, LLC has been awarded U.S. Patent Grant No. 8,903,825 for Semiotic Indexing of Digital Resources.
This expands the company’s IP portfolio to 3 granted US patents, including two patents exclusively licensed from Michigan State University.
December 2, 2014
A method of classifying a plurality of documents. The method includes steps of providing a first set of classification terms and a second set of classification terms, the second set of classification terms being different from the first set of classification terms; generating a first frequency array of a number of occurrences of each term from the first set of classification terms in each document; generating a second frequency array of a number of occurrences of each term from the second set of classification terms in each document; generating a first similarity matrix from the first frequency array; generating a second similarity matrix from the second frequency array; determining an entrywise combination of the first similarity matrix and the second similarity matrix; and clustering the plurality of documents based on the result of the entrywise combination.
September 6, 2014
International Union of Microbiological Societies Conference 2014 — International Congress of Bacteriology and Applied Microbiology
Convention centre (Palais des congrès), Montréal, Québec, Canada July 27-August 1, 2014
George Garrity and Charles Parker will be attending the International Congress of Bacteriology and Applied Microbiology at the IUMS 2014 conference. We will be submitting a draft of the next edition of the International Code of Nomenclature of Prokaryotes.
May 19, 2014
Second Workshop of the United States Culture Collections Network — Fusarium Research Laboratory, Penn State University
State College, Pennsylvania, United States May 19-21, 2014
George Garrity presents “Standards to Promote Data Interchange in the Life Sciences”.
This discussion will focus on emerging data, metadata, publishing and web standards and explore how collections might adopt these standards as part of their strategy in developing and delivering interoperable information products to the market.
...these issues are ultimately dependent upon accurate and properly curated reference material, further discussion included the use of standards in managing collection materials. Different standards were described including self imposed standards such as nomenclature and also external standards for reference material, process optimization, and data management.
April 8, 2014
We have partnered with the Michigan State University to develop commercial applications of our semiotic technology to Information Extraction for Phenotypic and Genotypic data.
January 16, 2014
Mathematical, Statistical and Computational Aspects of the New Science of Metagenomics — Isaac Newton Institute for Mathematical Sciences, University of Cambridge
Cambridge, England, United Kingdom March 24-28, 2014
George Garrity presents “Reasonable names and reasonable terms for Bacteria and Archaea”.
This presentation will focus on the development of a generalized semantic model that has been developed to disambiguate biological nomenclature and to provide both humans and machines with direct access to the correct information about all of the validly named prokaryotic taxa. Current research efforts on developing an ontology of microbial phenotypes, which supports machine reasoning, will also be discussed.
January 15, 2014
Arlington, Virginia February 9-12, 2014
Charles Parker and George Garrity will be presenting poster 170 (“Semantic Index of Phenotypic and Genotypic Data”, Abstract Book, pages 297-298) during Tuesday evening’s mixer (5:00pm-7:00pm) in Independence Center. We will be highlighting our team’s recent research on Information Extraction (IE), reasoning and ontology query.
This project has presented technical challenges that require creative solutions across several areas of information science.
Many ontologies consist of a large thesaurus of terms in a narrowly-defined domain and do not contain any reasoning capability beyond the taxonomic structure of the vocabulary and relations among concepts. Our objective is to develop an ontology that covers many broad feature domains and contains axioms encoded in first order logic that enable reasoning and inference over sparse phenotypic data, even in feature domains that contain partially-overlapping concepts and terms that map to undefined ranges of environmental conditions. In order to accomplish this, we have developed a core ontology model that maps between imprecise phenotypic features and precise environmental data.
In our current work, we are applying these novel modeling techniques to encode Tbox axioms for automatically resolving ambiguity attributed to the semantic equivalence and imprecision of phenotypic terms arising in literature. These axioms will enable reasoners to make appropriate inferences over the ontology and phenotypic data. We are also developing a query and retrieval service linked to the ontology that will provide researchers with consistent, accurate interpretations of these data that are usable for predictive modeling and in other research and commercial applications.
Several additional software components were developed to overcome technical barriers that arose during this project. Originally implemented as command-line utilities for vocabulary extraction, annotation and document analysis, we are now developing these into a commercial semantic desktop application for document/corpus analysis and for bootstrapping terminology/ontology development.
October 15, 2013
Society for Industrial Microbiology and Biotechnology — RAFT X: Recent Advances in Fermentation Technology
Marco Island, Florida November 3-6, 2013
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 poster session will be in the Capri Ballroom from 5:00pm-7:30pm Monday evening. The posters are also available to attendees on the RAFT-X meeting site.
Our objective is to make the connections between strains and the patent literature easy to navigate and to make the information about patented microbial products and processes more readily discoverable. We recently completed a first pass through the USDA ARS Patent Collection (NRRL Collection, Peoria, IL). Using proprietary text mining methods, we were able to identify global commercialization trends in 162 technology classes over a 70 year time span by following more than 4,000 distinct NRRL strains referenced by over 16,000 US and foreign patents drawn from a corpus of over 80 million patent documents.
October 7, 2013
BioCreative IV Challenge and Workshop — BioCreative: Critical Assessment of Information Extraction in Biology
Bethesda, Maryland October 7-9, 2013
George Garrity presented an overview of the text mining approaches employed by NamesforLife during the DOE Panel on October 8th, 2013.
How might one maintain quality, consistency and usability of stored observational data over time, knowing that both the information and the underlying data are fluid and often inconsistent or even contradictory?
While text mining, natural language processing and machine reasoning are all thought of as computational problems, our experience teaches that the human element, provided by Subject Matter Experts and data curators is crucial if one is to obtain useable and meaningful results. Subject Language Terminologies (SLTs) are dynamic and may contain terms that have many nuanced meanings.
We have developed a generalized process to mitigate these challenges that includes a flexible data model, document analysis methods, and a workflow.
March 24, 2013
Tucson, Arizona April 26, 2013
George Garrity presents an overview of NamesforLife technology, services and data products.
NamesforLife provides web services for editorial offices. These services are designed to have minimal impact on production workflows, by providing multiple access points that can be integrated at any point in a content production workflow.
We also offer consulting services in terminology and taxonomy development, including management of Subject Language Terminology, QA/QC, data cleaning, linking and annotation, and ab-initio development of vocabularies.
We have several professionally curated data products available for licensing, as well as a patented method for serving terms, names and associated information over unique identifiers.
February 24, 2013
Bethesda, Maryland February 24-27, 2013
Charles Parker and George Garrity will be presenting a poster (“The NamesforLife Semantic Index of Phenotypic and Genotypic Data”) during the evening mixers (5:00pm-7:00pm) on Monday and Tuesday. We will be highlighting our team’s recent research on Information Extraction (IE) and automated thesaurus construction.
Please note that due to federal travel restrictions, this meeting’s attendance and scope will be limited, and no abstracts document will be published. We appreciate the folks from Oak Ridge National Labs, who took a bus all the way from Tennessee to attend this meeting!
Phenotypic data needs to be viewed from an historical perspective to understand not only what was measured but how it was measured (growth on substrate vs. hydrolysis of indicator compound). It is also important to know which methods were applied and whether different methods within an array of data are measuring the same trait, and if so, whether the results are comparable.
The Phenotypic Index will address these issues by tying together observations under specific sets of growth conditions, supporting faceted search, retrieval and comparison of differentiating characteristics between (and within) taxonomic groups. Each phenotypic observation will be linked to a strain via a NamesforLife Exemplar DOI (Digital Object Identifier), which is directly linked to an actively maintained taxonomy and nomenclature.
January 23, 2013
Chicago, Illinois January 23, 2013
Dr. George Garrity presents NamesforLife’s progress toward a phenotypic ontology for Bacteria and Archaea.
December 31, 2012
DOI mediated semantic services — Scientific, Technical and Medical Publishers New Technologies Meeting
London, England, United Kingdom December 1, 2012
George Garrity will be presenting a five-minute overview of the NamesforLife publisher services at the 2012 STM conference.
Our goal is to provide on-demand access to information so your authors, reviewers, readers and editors can read like a Subject Matter Expert.
December 30, 2012
Oxford, England, United Kingdom December 1, 2012
George Garrity will be presenting the NamesforLife semantic annotation services at the 2012 IDF board meeting.
At the core of our services is a proprietary data model using DOIs to deliver semantic services into a publisher’s content, either through embedded links or transient links that are created on-the-fly. This allows us to apply independently managed terminologies to a digital library immediately and to provide real-time content enhancement rather than a posteriori annotation of a body of literature.
December 29, 2012
Lyngby, Denmark December 1, 2012
December 28, 2012
Braunschweig, Germany December 1, 2012
August 8, 2012
We have partnered with the University of Nebraska to develop commercial applications of our semiotic technology to Information Extraction for Phenotypic and Genotypic data.
June 7, 2012
East Lansing, Michigan June 7, 2012
NamesforLife, LLC has completed an agreement with Michigan State University to exclusively license two key patents for terminology management and data classification, U.S. Patent Grant No. 7,925,444 and U.S. Patent Grant No. 8,036,997.
Michigan State University announced today that it has entered into an exclusive license agreement with NamesforLife, LLC for a novel, patented technology that enhances a reader’s ability to locate, retrieve, and understand complex technical information in a digital environment. Until now, when readers came across a technical term on the Web whose definition wasn’t exactly clear, they would have to look it up elsewhere, by visiting a search engine on another page. NamesforLife has changed that. The Company’s technology delivers expertly maintained information about the term and inserts it automatically into the page.
The technology was developed to solve an age-old problem. As a scientific field advances, technical terms, like the names of organisms and chemicals, change rapidly. In some cases, the vocabularies can change daily. This constant change creates uncertainty about the meaning of scientific papers and other electronic resources. Scientists, lawmakers, and businesspeople need to take that uncertainty into account when searching technical literature, or they risk making decisions based on incomplete or out-dated information. Failure to account for this uncertainty has consequences ranging from unnecessary duplication of effort and expense to situations that could endanger public health and safety.
Unlike any other service, NamesforLife secures the meaning of technical terms, wherever they occur, by binding them permanently to a monitoring service that records change in meaning. This technology brings the knowledge of subject experts to end-users, through their web browser, at their point of need. Once the binding is established using this technology, the reader need only click on the term to obtain information about current and prior usage, along with a wealth of related information, in an interface under their control. According to George Garrity, a professor in the Department of Microbiology and Molecular Genetics at Michigan State University and Company co-founder, “NamesforLife utilizes the power of semantic web concepts to understand and analyze technical literature in the face of dynamically changing terminologies and complex subject matter in biology, chemistry and a host of other fields.”
NamesforLife co-founder Catherine Lyons explains, “This patented technology ensures that information about current usage can be found even when multiple terms are in parallel use. NamesforLife’s conceptual precision also supports highly targeted micromarketing. In the past online publishers have relied on overgeneralized advertising. But this new technology supports targeted matching of vendor communities to niche markets.
According to Richard Chylla, Executive Director of MSU Technologies, “We are extremely excited about the NamesforLife technology and the positive impact it will have on solving a difficult problem facing the scientific community and Internet users at large.”
The NamesforLife solution serves as the foundation for N4L Services, developed by the Company in partnership with the Society for General Microbiology (Reading, UK), Inera, Inc. (Belmont, MA), and the International DOI Foundation (Washington, DC, & Oxford, UK) to incorporate professionally edited and self-updating information directly into scientific papers, data feeds, and other documents. N4L Services locate scientific names or technical terms in a document and then use persistent identification to bind the names or terms permanently to the NamesforLife terminology monitoring service. Because of the unique way the patented technology works, even when a name or term has changed in meaning, NamesforLife ensures that it remains bound to up-to-date information. The Company has chosen the Digital Object Identifier System (DOI System) for its persistent identification technology, because it provides ISO-compliant, professional content management.
NamesforLife offers services for authors and editors, publishers, service providers, and readers. Its tools integrate seamlessly into users’ routine workflows and into existing software like word processors and web browsers. NamesforLife also offers expertly edited bacteriological data as well as custom indexing and abstracting services for large document collections and data curation services. Additional licensing opportunities are available. The company is also partnering with IFI CLAIMS Patent Services/Fairview Research (Madison, CT and Barcelona, Spain) to use a novel search method called Semiotic Fingerprinting for patent searching.
About the Company
NamesforLife, LLC is a Michigan based company, located in the East Lansing Technology Innovation Center. Development of the Company’s technology was underwritten by three STTR grants from the U.S. Department of Energy through the Office of Biological and Environmental Research and awards from the Michigan Universities Commercialization Initiative, and the Business Accelerator Fund and the Michigan Emerging Technology Fund which are administered by the Michigan Small Business Development Center. NamesforLife is a general member of the International Digital Object Identifier Foundation and employs ISO Standard DOIs in its products. For additional information about the company please visit namesforlife.com.
April 3, 2012
Belmont, Massachusetts April 3, 2012
NamesforLife, LLC, in partnership with Massachusetts-based Inera, Inc., has launched a new subscription service for academic publishers: the N4L Linking module for eXtyles. This module is based on the N4L Scribe semantic annotation service, which recognizes named entities in text and links them to authoritative resources, providing additional information about technical terms to reviewers and editors.
This service is designed to save editorial time and improve peer review by adding context and performing automatic fact-checking on terminology use.
The module is available as a subscription-based add-on to Inera’s eXtyles editorial software.
The eXtyles NamesforLife (N4L) Linking module is now available. N4L Linking automatically identifies biological names in Word documents (currently, validly published names of Bacteria and Archaea at all ranks, from domain to subspecies, as well as names for which a published genome exists; other terminologies are in the works) and provides DOI-based links to the N4L service.
February 24, 2012
Bethesda, Maryland February 26-29, 2012
Charles Parker and George Garrity will be presenting poster 228 (“The NamesforLife Semantic Index of Phenotypic and Genotypic Data”, Abstracts Book, pages 183-184) during the Monday evening mixer (5:30pm-8:00pm) in the Grand Ballroom. We will be highlighting our team’s recent research on text mining and automated vocabulary extraction.
The long-term objective of this STTR project is to develop a semantic index of bacterial and archaeal phenotypes that can be used to augment annotation efforts and to provide a basis for predictive modeling of microbial phenotype. The index is based on published descriptions of taxonomic type and non-type strains that have been the subject of ongoing genome sequencing efforts as this will provide a mechanism whereby hypotheses can be tested and reproducibility verified. This project is tightly coupled with ongoing DOE projects (Genomic Encyclopedia of Bacteria and Archaea, the Microbial Earth Project, the Community Sequencing Project) and with two key publications, Standards in Genomic Sciences and the International Journal of Systematic and Evolutionary Microbiology. The first step towards accomplishing this goal, and the primary objective of this Phase I project is the development of a draft vocabulary.
November 7, 2011
Boston, Massachusetts November 11, 2011
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.
November 2, 2011
East Lansing, Michigan November 2, 2011
The East Lansing City Council held a special presentation on November 1st, marking the graduation of the inaugural tenants of the East Lansing Technology Innovation Center (TIC). Mayor Loomis highlighted the TIC which began three years ago to advance the culture of entrepreneurship throughout the East Lansing community. Jeff Smith, Project Manager for New Economic Initiatives, recognized graduating tenants of TIC and thanked the Downtown Development Association, Planning Department, city residents, and tenants of TIC for their efforts. Smith said the City has been nationally recognized for its support of entrepreneurship.
The council approved a resolution celebrating the graduation of the first East Lansing Technology Innovation Center tenants. As one of the inaugural tenants, Charles Parker of NamesforLife, LLC was asked to share a few words on his experiences with the center since its launch. He stated, “We sincerely appreciate all of the assistance provided by the TIC, and in particular I’d like to thank Jeff Smith and Amy Schlusler, whose dedication since the launch in October 2008 really brought this center to life. Every time we needed anything, they were there for us without fail. The resources the TIC provided and the mix of companies they’ve brought together have been an enormous help to us over the past three years, and I’m not sure where we’d be now without that help. Although our lease is up at the TIC, we intend to stay right here in East Lansing. Since we’re a spinoff from Michigan State University, the proximity to campus makes downtown the perfect location for us.”
On November 2nd, the City of East Lansing hosted an event at the TIC, presenting signed copies of the resolution to NamesforLife and the other graduating companies.
October 17, 2011
University of Toronto, Ontario, Canada October 17-18, 2011
Dr. George M. Garrity will be presenting the keynote lecture, “Distorted Realities”, during the Bioinformatics session on Monday at 9:15am.
October 11, 2011
East Lansing, Michigan October 11, 2011
U.S. Patent Grant No. 8,036,997 has been awarded to Michigan State University, covering a method for data classification using self-organizing, self-correcting heatmaps. NamesforLife, LCC holds a worldwide exclusive license to the patent.
October 11, 2011
The present invention provides methods for classifying data and uncovering and correcting annotation errors. In particular, the present invention provides a self-organizing, self-correcting algorithm for use in classifying data. Additionally, the present invention provides a method for classifying biological taxa.
September 10, 2011
George Garrity, professor in the Department of Microbiology and Molecular Genetics, was recently awarded the Van Niel International Prize for Studies in Bacterial Systematics. He was recognized for the contribution he has made to the field of bacterial systematics. He will receive the award at the 13th International Congress of Bacteriology and Applied Microbiology Sept. 6-10 in Japan.
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.
[George’s] work centres on the use of bioinformatics and computational biology in prokaryote systematics, the development of algorithms for the classification and identification of microorganisms and microbial products, nomenclature/annotation, data visualization and knowledge mining.
He was instrumental in developing the technology for the NamesforLife project, established to resolve the ambiguity between nomenclature and biological objects and concepts, providing a new approach to the retrieval of information from diverse sources, based upon the use of nomenclature to link content. NamesforLife models the evolution of changes in biological nomenclature and terminology, resolves instances of synonymy and homonymy, and provides mapping to the underlying concepts that can be viewed in a temporal context. Using Digital Object Identifiers, names or terms are linked to permanent unique identifiers, can provide a direct path through the literature, and link to a variety of databases and other contextually relevant services. The project has also developed a Firefox add-on that can identify taxonomic names in online articles and provide up-to-date nomenclatural and taxonomic information.
Busse, H.-J., Labeda, D.P., Oren, A. and Tindall, B.J. The van Niel International Prize for Studies in Bacterial Systematics, awarded by The University of Queensland Awarded in 2011 to George M. Garrity; 2011. International Journal of Systematic and Evolutionary Microbiology 61:2328-2329.
September 6, 2011
Sapporo, Japan September 6-10, 2011
Dr. George M. Garrity will be presenting Plenary Lecture 4 for this conference on September 7th.
June 22, 2011
Kristin Whitman from Landon IP has published an article about how NamesforLife adds value to your searches, from the perspective of the patent community.
..there are a number of patents in the green technology collection that include long lists of named species (in some cases redundantly), but fail to specify a given strain that actually performs the claimed invention…Patents that include “laundry lists” of organisms that may or may not perform according to claims (and in fact, may not even exist) open the door to what could be some interesting challenges and counter-claims in the courts dealing with both non-enablement and prior art.
Based on this initial analysis from the NamesforLife team, the challenges faced by biological taxonomists directly affect the work of inventors and patent searchers. I think it’s likely that their data may become integrated into more patent and non-patent databases as the value of their work becomes more obvious.
June 17, 2011
Michigan State University will continue to be our research partner as we investigate applications of our semiotic technology to Information Extraction for Phenotypic and Genotypic data.
May 21, 2011
The NamesforLife Abstracts are now available, replacing our earlier Monographs on Bacteria and Archaea. 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.
May 1, 2011
PIUG 2011 Annual Conference — Best Practices Beyond Free-text: The Value of Indexing and Classification when Searching and Analyzing Patents
Cincinnati, Ohio May 21-26, 2011
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).
April 12, 2011
East Lansing, Michigan April 12, 2011
U.S. Patent Grant No. 7,925,444 been awarded to Michigan State University, covering systems and methods for resolving ambiguity in Named Entities using a semiotic approach over persistent identifiers. NamesforLife, LCC holds a worldwide exclusive license to the patent.
April 12, 2011
The present invention provides systems and methods that utilize an information architecture for disambiguating scientific names and other classification labels and the entities to which those names are applied, as well as a means of accessing data on those entities in a networked environment using persistent, unique identifiers.
April 1, 2011
Crystal City, Virginia April 10-13, 2011
Charles Parker and George Garrity will be presenting poster 117 (“Semantic Indexing of the Green Technology Patent Literature”, Abstracts Book, page 90) during the Tuesday evening mixer (5:30pm-8:00pm) on the Independence Level (Independence Center B). We will be highlighting our team’s recent research on semiotic document classification.
As DOE research on biofuels, bioremediation and carbon sequestration moves from the laboratory into production or commercial environments, a number of important policy and business decisions must be made that demand correct information.
An awareness of developments in the field requires a thorough review of both bodies of literature. NamesforLife is building tools to simplify such searches, using its proven approach to indexing through the creation of persistent links to externally managed terminologies that common to both bodies of literature. This approach integrates well with existing commercial, academic and USPTO data mining capabilities.
March 20, 2011
February 1, 2011
Berlin, Germany February 21-27, 2011
Charles Parker will be presenting a poster and demonstrating the NamesforLife services at the software bazaar on Thursday from 10:30am-3:00pm in the Yale-Princeton room. George Garrity will be present a 20 minute talk on Standards in Genomic Sciences on Friday evening from 6:00pm-6:20pm in the Princeton room.
Our semantic tagging web service, N4L Scribe, is now available. It tags bacterial names in any well-formed XML document with forward-linking Digital Object Identifiers. The service sits at the core of the server-side content enablement for N4L Guide, and is intended for integration into existing publication workflows. Plug-ins are currently in development for several ubiquitous word processing and desktop publishing applications as well. The service can be tested out for free on our web site with a NamesforLife account.
The N4L Guide browser add-on detects and links bacterial names to the N4L database, providing up-to-date nomenclature, strain and genome information, and a full bibliography. The screenshots below demonstrate the use of this tool on an IJSEM article. Instructions for installing and using this tool can be found at the NamesforLife website.
October 1, 2010
Hyatt Regency, New Brunswick, New Jersey October 11-15, 2010
Charles Parker from NamesforLife will be attending the main meeting and exhibition for the Patent Users Information Group Northeast conference on Tuesday, October 12th. The PIUG Northeast Conference brings together experts in the area of chemistry/biology, non-chemistry/biology and legal topics relating to patent information.
October 1, 2010
Odaiba, Tokyo, Japan October 11-14, 2010
To assist those confronted with ambiguous names (which not only includes researchers but clinicians, manufacturers, patent attorneys, and others who use biological data in their routine work), we developed a generalizable semantic model that represents names, concepts, and exemplars (representations of biological entities) as distinct objects. By identifying each object with a Digital Object Identifier (DOI), it becomes possible to place forward-pointing links in the published literature, in databases, and vector graphics that can be used as part of a mechanism for resolving ambiguities, thereby “future proofing” a nomenclature or terminology. A full implementation of the N4L model for the Bacteria and Archaea was released in April, 2010. The system is professionally curated and represents a Tier III resource in Parkhill’s view of bioinformatic services (Genomic information infrastructure after the deluge, Parkhill et al. 2010). A variety of tools and web services have been developed for readers, publishers, and others (N4L Guide, N4L Autotagger, N4L Semantic Search, N4L Taxonomic Abstracts) and we are incorporating other taxonomies into the N4L data model, as well as adding additional phenotypic, genotypic, and genomic information to the existing exemplars to add greater value to end users.
May 7, 2010
San Diego, California May 23-27, 2010
NamesforLife will be attending the ASM 2010 Meeting. Stop by the Society for General Microbiology booth, grab a brochure, sign up for a free account and try live demonstrations of the NamesforLife document annotation and rich content services for publishers.
May 6, 2010
NamesforLife has a mention in the DOI News. See ‘DOI-based Tool for Taxonomy’.
IDF member NamesforLife, in partnership with the Society for General Microbiology and the International Committee on the Systematics of Prokaryotes, has announced the launch of a specialist browser tool which provides current information on taxonomic nomenclature of Bacteria and Archaea, through DOI name links providing authoritative and persistent online annotation. This allows authors to obtain current data from the rapidly changing taxonomic literature easily, and allows third party re-use of the information as persistent and reliable current data. Expert annotation is presented via a menu that collocates with the occurrence of a name on a web page and links to other resources.
March 22, 2010
Edinburgh, Scotland, United Kingdom March 29-April 1, 2010
NamesforLife will have a booth at the SGM Spring 2010 meeting. Please stop by in between sessions to sign up for a free account and try live demonstrations of the NamesforLife document annotation and rich content services for publishers.
February 13, 2010
NamesforLife has a full page write-up in the February 2010 issue of Microbiology Today.
George Garrity explains the philosophy behind the new NamesforLife BrowserTool, developed in partnership with the SGM and ICSP to help the wider microbiological community keep in touch with and understand the changes in bacterial and archaeal systematics. Never again need a reader be ill-informed about the status or meaning of a name.
February 1, 2010
Crystal City, Virginia February 7-10, 2010
Charles Parker will be presenting poster number 231 (“NamesforLife Semantic Resolution Services for the Life Sciences”, Abstract Book, page 179) in the Tuesday afternoon reception and scientific mixer of the Genomes-to-Life Awardee Workshop.
Please also visit poster 230 (“Standards in Genomic Sciences: Launch of a Standards Compliant Open-Access Journal for the ‘Omics Community”, Abstract Book, page 178) on Monday evening for an update on the recently launched Open Access journal Standards in Genomic Sciences.
Now that the Bacterial Nomenclature database is complete and updated in synchrony with the valid publication of nomenclatural changes, NamesforLife is in the process of linking together Bacterial Nomenclature, technical literature, and the various projects of the Genomes-to-Life program. In N4L, each individual organism is represented by a metadata object (an N4L Exemplar), which is identified by a DOI.
An N4L Exemplar aggregates what is known about an individual organism. The Genomes OnLine Database (GOLD), Standards in Genomic Sciences (SIGS), Genomic Encyclopedia for Bacteria and Archaea (GEBA) and Genomes and Metagenomes Catalogue (GEM) all use unique identifiers that link to each other in some way; via the GCat identifier, GOLD stamp, and GEBA Taxon Identifier. However, there is no single common link to the literature. NamesforLife is closing this gap by tying these disparate sources of information together via N4L Exemplars, which are integrated with the N4L Nomenclature Database and N4L Contextual Index.
The Beta release of the N4L Browser Add-on is officially scheduled to coincide with the Society for General Microbiology conference at the end of March 2010, but it is already available for early testing. Instructions on installation and use can be found at the NamesforLife website. This Firefox Add-on detects and links bacterial names to the N4LDB, providing up-to-date nomenclature, strain and genome information, and a full bibliography.
January 1, 2010
Ann Arbor, Michigan January 20, 2010
On Sunday evening, NamesforLife, LLC joined a host of other Michigan-based startup companies exhibiting at ACE’10: The Annual Collaboration for Entrepreneurship in Ann Arbor, Michigan. The event is the culmination of the year-long activities of the Ann Arbor SPARK economic development group, which brings entrepreneurs and investors together in Southeast Michigan for an evening of networking and showcasing.
Charles Parker, the software architect for NamesforLife, reflected on how the Michigan business environment has changed since ACE’09. “A lot of tech companies like Hewlett-Packard have closed sites in Michigan in the past year. The good news is that the tech incubators - SPARK in Ann Arbor, the Technology Innovation Center in East Lansing where we’re located, and others throughout the region, have turned the surplus of local tech talent into an opportunity to invest in home-grown businesses which have a stake in the state economy. Just look around, almost none of the companies here tonight existed a few years ago, and these are all Michigan-based companies.”
December 28, 2009
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.
May 1, 2009
Philadelphia, Pennsylvania May 17-21, 2009
NamesforLife will be attending the ASM 2009 Meeting. Stop by the Society for General Microbiology booth for a live demonstration of the NamesforLife document annotation and rich content services for publishers.
April 2, 2009
United Nations Convention on Biological Diversity — Seventh Meeting: Ad hoc Open-Ended Working Group on Access and Benefit Sharing
Paris, France April 2-8, 2009
Excerpts from: Studies on the Identification, Tracking and Monitoring of Genetic Resources
After reviewing recent methods of identifying genetic resources directly based on DNA sequences, we have identified methods of tracking and monitoring genetic resources through the use of persistent globally unique identifiers, including practicality, feasibility, costs, and benefits of different options.
Herein, we outline our recommendations for baseline requirements for such a global tracking system to aid users and providers in complying with CBD ABS objectives.
February 8, 2009
Genomics 2009 — GTL Awardee Workshop VII and USDA-DOE Plant Feedstock Genomics for Bioenergy Awardee Workshop
Bethesda, Maryland February 8-11, 2009
Charles Parker will be presenting poster number 135 (“NamesforLife Semantic Resolution Services for the Life Sciences”, Abstract Book, page 182) in the Tuesday afternoon poster session of the Genomes-to-Life Awardee Workshop.
While you’re here please also visit poster 134 (“Release of Taxomatic and Refinement of the SOSCC Algorithm”, Abstract Book, page 180) for updates on the SOSCC algorithm and poster 136 (“Standards in Genomic Sciences: an Open-Access, Standards-Supportive Publication that Rapidly Disseminates Concise Genome and Metagenome Reports in Compliance with MIGS/MIMS Standards”, Abstract Book, page 183) for information on the launch of a new Open Access journal, Standards in Genomic Sciences.
The adoption of DNA sequencing as the preferred method of rapidly characterizing Bacteria and Archaea has tremendously accelerated during the past five years, with the expected consequences. At present, the rate at which “named” sequences are added to the GenBank taxonomy exceeds the rate at which validly published names appear in the taxonomic record by a factor of approximately 35. This confounds the retrieval of related information from various databases and the scientific, technical and medical literature as many of these invalidly named species can not be readily tracked over time, nor can relationships be inferred to those species for which at least one genome sequence is available. This disconnect between the knowledge contained in the literature and the accumulated genomic data is likely to grow as faster and cheaper sequencing methods come into the market place.
The target audience of N4L services is the broad scientific community and others who may need to know the precise meaning of biological names or other terms, in correct temporal context as they are encountered in other digital content (scientific or technical literature, regulatory literature, databases, etc). The dynamic, yet asynchronous nature of biological nomenclature and similar terminology poses a significant burden on information providers, as they must either invest in constantly maintaining their offerings to keep current or shift that burden to their end-users. If the former, the costs can be significant, and, in the absence of a means to synchronize updates across an entire domain of knowledge, end users are still confronted with apparent discrepancies across data sources and content providers. If the burden is shifted to end-users, they must then locate alternative information sources, typically hosted through a web portal, that must be queried separately. This makes utilization of content cumbersome and can lead to considerable ambiguity.
The NamesforLife approach is to semantically enable content in a manner that is transparent to end-users at two points in the value chain: at the source (the data provider or publisher) and at the client side (the end-user). In either case, the end-user experience is the same. At each occurrence of a validly published bacterial or archaeal name, they can have access to precise authoritative information by simply clicking on the name. Tools to enable publishers’ content at the pre-publishing stage that embed persistent N4L identifiers in inline text ensures that their readers will always have access to the correct meaning of the name (as well as additional information), even if the name has changed since publication. Our web-based client supports semantic enablement of other digital content, on-the-fly, providing similar seamless access to NamesforLife content at each point where a validly published name occurs. This provides the reader with direct access to a wealth of information to aid in the interpretation of each enabled article.
January 21, 2009
Ann Arbor, Michigan January 22, 2009
On Thursday evening, NamesforLife, LLC joined several other inaugural tenants of newest tech incubator in Michigan (the East Lansing Technology Innovation Center), in attending ACE’09: The Annual Collaboration for Entrepreneurship in Ann Arbor, Michigan. The ACE event, started in January 2001, brings together several Michigan entrepreneurial groups for an evening of networking and showcasing.
October 5, 2008
East Lansing, Michigan October 5, 2008
NamesforLife, LLC has opened a commercial office at the new Technology Innovation Center (TIC) in downtown East Lansing, Michigan. They are an Inaugural Tenant and the first company to move into the newly renovated space. The recently-launched tech startup is a spin-off from Michigan State University, founded to commercialize patent-pending research on terminology management and classification.
Said George Garrity, co-founder and managing member of the company, “We’ve been looking at office space in downtown East Lansing for several months, and the timing of the launch of this center was perfect. Michigan State University is our research partner in this endeavor, so the location is ideal - they are, quite literally, right across the street. Additionally, the University’s tech-transfer office, MSU Technologies, is in the planning stages of moving into this space as well, which will be very convenient since we are already working with them on technology licensing. There is no question, this is where we need to be.”
The company has recently made its first permanent hires, Charles Parker and Sarah Wigley, both graduates from Michigan State University. Charles, a software architect who left a position at Hewlett-Packard to join the company, said, “I’m really impressed with what the city was able to do with this space - just a few months ago, there was nothing here, but now, even though there’s still some construction going on, we’re up and running as a business. Right now, companies like Hewlett-Packard are scaling back operations in mid-Michigan, but East Lansing has really stepped up to create a great environment for the surplus of local tech talent. The creation of the TIC was a great move by the city and the timing couldn’t be better for us.”
July 21, 2008
Michigan State University will continue to be our research partner as we develop commercial applications for the N4L-SRS.
May 28, 2008
Westin Copley, Boston, Massachussetts May 28-30, 2008
George Garrity will be presenting a lecture titled “Say What You Mean: How Semantic Tagging Makes Content More Discoverable, More Useful, and More Valuable” during Seminar 4.
Our next step is to achieve a production-level N4L application (DOI service), which will provide N4L enablement of published STM literature and to investigate other microbiological applications, including a pipeline approach to capture nomenclatural acts and auto-generation of prokaryotic taxonomies. We will also implement a browser plug-in for on-the-fly enablement of web content.
We are actively seeking interested parties to test our tools and concepts.
February 18, 2008
The founder of NamesforLife, George M. Garrity, Sc.D. has been elected among the 2007 Biological Sciences Fellows of the American Association for the Advancement of Science.
AAAS Fellows are elected annually by the AAAS Council for meritorious efforts to advance science or its applications. Fellows have made significant contributions in areas such as research, teaching, technology, services to professional societies, and the communication of science to the public. AAAS congratulates them and thanks them for their service to science and technology.
February 14, 2008
Boston, Massachusetts February 14-18, 2008
George Garrity will be attending the annual meeting of the American Association for the Advancement of Science.
February 10, 2008
Genomics 2008 — GTL Awardee Workshop VI and Metabolic Engineering Working Group Interagency Conference on Metabolic Engineering
Bethesda, Maryland February 10-13, 2008
George Garrity will be presenting poster 142 (“NamesforLife Semantic Resolution Services for the Life Sciences”, Abstract Book, page 136) at the Tuesday evening poster session (5:00pm-8:00pm) in Salon ABCD.
While you are here, please also visit poster 141 (“Further Refinement and Deployment of the SOSCC Algorithm as a Web Service for Automated Classification and Identification of Bacteria and Archaea”, Abstract Book, page 135) during the Monday evening poster session (5:00pm-8:00pm), also in Salon ABCD.
Within the Genomes-to-Life Roadmap, the DOE states that a significant barrier to effective communication in the life sciences is a lack of standardized semantics that accurately describe data objects and persistently express knowledge change over time. As research methods and biological concepts evolve, certainty about correct interpretation of prior data and published results decreases because both become overloaded with synonymous and polysemous terms. Ambiguity in rapidly evolving terminology is a common and chronic problem in science and technology. NamesforLife (N4L) is a novel technology designed to solve this problem.
February 8, 2008
NamesforLife now has a plugin available for the oXygen XML Editor (tentatively named the Scribe). This plugin provides named-entity recognition and annotation over controlled terminologies. When used with the NamesforLife prokaryote nomenclature, the annotation links to Digital Object Identifiers that resolve to monographs representing the complete history of a bacterial or archaeal taxon.
May 27, 2007
The NamesforLife Semantic Resolution Services for the Life Sciences (N4L-SRS) will support the Genomes-to-Life (GtL) roadmap to provide standardized semantics for tracking knowledge over time.
Michigan State University will be our research partner during this project.
NamesforLife, funded by grants from the Department of Energy and the state of Michigan, was founded to resolve the ambiguity between nomenclature and biological objects and concepts. NamesforLife technology, N4L, makes names actionable.
April 21, 2007
East Lansing, Michigan April 25, 2007
George Garrity presents the NamesforLife business model at the Mid-Michigan Entrepreneur’s Day.
NamesforLife, LLC is initially pursuing commercialization in the Scientific, Technical and Medical (STM) publishing sectors, as well as Biological Resource Centers (BRCs) and diagnostic equipment vendors.
In the longer term, we are looking to adapt the NamesforLife model to other terminologies and nomenclatures for economically important eukaryotes, genome annotation and medical/pharmaceutical terminology.
March 6, 2007
The Taxonomic Outline of Bacteria and Archaea (TOBA) 7.7 has been published.
TOBA 7.7 provides coverage of the validly published named species and higher taxa of Bacteria and Archaea through October 1, 2006, including all those names included on Validation Lists through No. 111. In addition, TOBA 7.7 contains a limited number of well known taxa of Cyanobacteria that were included in earlier releases, the myxobacterial taxa described by Reichenbach for which duplicate deposits had not been confirmed at the time of publication), and a number of provisional names of higher taxa that were used as placeholders in previous releases.
We also include NamesforLife name-ids (N4Lids) to provide direct, persistent links to content provided by that project. N4Lids are suffices of Digital Object Identifiers (DOIs) that resolve to individual NamesforLife Information Objects that contain more detailed information about the nomenclature, taxonomy, and members of higher taxa and additional strain identifiers, sequences, and other information about the type strains and higher taxa. N4Lids preceded by the “DOI:” prefix will resolve to web pages that are part of Release 6.0 of the Taxonomic Outline.
February 7, 2007
Rome, Italy February 14, 2007
George Garrity provides some thoughts on the application of persistent identifiers to Standard Material Transfer Agreements (SMTAs).
NamesforLife provides a method for persistently linking the occurrence of a biological name or other technical term in third party content to managed information about its origins, formal definition, current usage, and related goods and services. This Information Architecture is based on some of the properties of persistent identifiers, and our implementation specifically uses Digital Object Identifiers to link hetereogeneous data and resolve ambiguous names.
January 5, 2007
Hotel Plaza del Bosque, Lima, Peru January 21, 2007
George Garrity presents the lecture “An Overview of Persistent Identifiers” in the afternoon meeting, “New approaches to documentation of genetic resources”.
A persistent identifier (PID) has one or more of the following properties:
- Semantically Opaque (the identifier avoids any embedded meaning)
- Governance (a technical and/or social framework oversees development, implementation and “marketing” of the identifier)
- Persistence (a mechanism guarantees persistence of issued identifiers)
- Registration (a mechanism exists for global registration of identifiers)
- Metadata (minimal requirements exist for metadata associated with each identified object)
- Standardization (the identifier conforms to an accepted standard)
- Globally Unique (the identifier is globally unique)
- Widespread Usage (the identifier is in widespread usage)
- Object/Location Resolution (the identifier actually identifies something)
- Actionable (network services are attached to the identifier)
- Uniqueness (a resolution service checks for uniqueness at the local level)
- Interoperability (the identifiers are readily incorporated into other applications without modification or permission)
- Granularity (the identifiers can be assigned to subcomponents (nesting of entities within entities))
- Business Model (a compelling business need ensures that the identifier infrastructure can be maintained in a self-supporting manner)
The Digital Object Identifier (DOI) exhibits all of these characteristics.
September 7, 2006
Robinson College, Cambridge, United Kingdom September 11-13, 2006
George Garrity discusses NamesforLife and PhenBank at Cambridge. He will also chair Monday’s second session: “Databases and Metadata capture and Exchange efforts”.
Names, taxon concepts and exemplars are independent. Names are fixed in time and are bibliographic events, tied to a particular published description. The taxon concept, however, drifts once it comes into usage, as non-type exemplars are added to the global sample set. There is also a critical need to always tie the data (phenotype and genotype) to the correct source strain.
When one looks at the environmental data, it becomes difficult to accurately interpret results across studies, especially when one is dealing with survey data comprised of a single measurement (e.g., a 16S rRNA sequence). One of the reasons is that investigators use their own identifier to label the data (and strains). More importantly, many of these labels are not unique.
We are in the process of updating our prototype to identify all of the high quality 16S rRNA sequences that have come from type strains held in different Biological Resource Collections (BRCs).
We have been using heatmaps of evolutionary distance matrices to visualize sequence similarity and to uncover annotation errors in the 16S rRNA sequence data set for about five years. Last year, we published the SOSCC algorithm which can undertake this process in an automated manner.
What is particularly useful is that the method allows us to examine 1,000–10,000 sequences simultaneously, thereby revealing the otherwise hidden structure associated with more distant taxonomic relationships.
July 8, 2006
Madrid, Spain July 4-8, 2006
George Garrity presents “Knowledge bleed, PhenBank, and NamesforLife” during Symposium 20 (Biodiversity).
There are different scopes of knowledge. There are those things that we know that we clearly understand. There are also those things that are totally unknown to us. Research helps to increase our fundamental knowledge, pushing back the boundaries of our ignorance and creating a third category of knowledge, those things that we do not yet know, but which we know we do not know them.
It is our opinion that within the knowledge gradient, there exists another type of unknown - representing knowledge that was once known, but has been forgotten or lost over time. We call this the “unknown knowns”. At first glance, this might seem an implausible, but it represents a very real risk, not only in biodiversity studies, but in most fields, with the biosciences being the among the most prone to this problem, because of the extraordinary growth in many of the sub-disciplines, and the accompanying way of reporting results. A principle source of this knowledge loss arises in the very terminology we use to discuss and report our findings. Unless each worker clearly understands the underlying concepts that are used to describe their work in reference to that of others, discovery and retrieval of important findings becomes more difficult, if not impossible. Part of the problem lies in the sheer volume of material that is appearing in “print”. The second involves the rapidly evolving terms that are used to describe biologically relevant concepts at the various levels.
April 24, 2006
Lilburn, Harrison, Cole and Garrity survey the resources currently available to systematic biologists, and outline some steps forward to data integration and interoperability.
The barriers between databases, and between databases and applications need to be reduced. One giant step towards such interoperability will be the institution of methods to tame the nomenclature issues so that biologists can ensure that the names they use are correct or, if not, that they can find the correct name along with the history of labels associated with the organism they are interested in. The automation of identification will also free researchers to apply their intellectual energy to the exploration of new areas in systematics and biodiversity. The discovery of new species and novel, deep-branching lineages equivalent to phyla and the need to discriminate among organisms below the species level are certain to be drivers of future developments in computational systematic biology.
The ability of computational approaches to adapt to new discoveries, present clear depictions of alternative classifications and integrate disparate data types relevant to the classifications, will play a key role in the surveys of the natural world.
February 1, 2006
Taxonomic Databases Working Group GUID-1 Workshop — First International Workshop on Globally Unique Identifiers (GUIDs) for Biodiversity
National Evolutionary Synthesis Center (NESCent), Durham, North Carolina February 1-3, 2006
George Garrity presents unveils a working prototype of the NamesforLife Information Architecture.
In January, we launched a working prototype of an Information Architecture (IA) based on the NamesforLife (N4L) Model. This architecture provides a transparent information layer to deliver Digital Object Identifier (DOI) services to the life science community. The architecture also implements an ontology with a schema that produces metadata consistent with requirements of the International DOI Foundation (IDF). The initial services will conform to DOI Application Profile (AP) 0.
This test case contains 24,176 first-class objects comprising: Name, Taxon, Exemplar, Nomos, Practitioner, Feature, and Nomenclatural Code. This system is based on a nomenclatural taxonomy, but capable of supporting multiple taxonomic views and “time travel”, which will enable us to track changes in concepts over time.
September 7, 2005
Centre for Mathematical Sciences, Cambridge, United Kingdom September 7-9, 2005
George Garrity describes progress on the NamesforLife proof-of-concept and proposes the idea of PhenBank, a phenotypic data repository, at Cambridge.
The currently available taxonomic data sources have an unlimited number of data types, some of which are broadly applicable across all taxa, most of which are not. Some are cumulative, many are comparative. There exist numerous taxon-specific vocabularies, and there are few links to primary literature or original data sets. Existing tools for working with phenotypic data are of variable quality, most are “one-off” and non-interoperable. Fixing these problems has limited public support, since the user bases and data curation varies with economic importance, thus funding is poor to non-existant.
We propose a public repository for phenotypic and taxonomic data that adheres to a common data model and provides a source of interoperable phenotypic data for the Microbiology community.
July 1, 2005
International workshop (IUAP V/23) — Exploring and exploiting microbiological commons: contributions of bio-informatics and intellectual property rights in sharing biological information
University Foundation, Egmontstraat 5, Brussels, Belgium July 7-8, 2005
George Garrity presents the N4L system in “Automating the Quest for Novel Prokaryotic Diversity (revisited)”.
Previously, we demonstrated the value of using techniques drawn from the field of Exploratory Data Analysis (EDA) for the analysis and visualization of large sets of sequence data (notably SSU rRNA gene sequences) that are used to construct a comprehensive taxonomy of prokaryotes. While the approach is computationally efficient and quite useful in uncovering a variety of taxonomic and annotation errors, the methods suffered from some practical limitations; notably bottlenecks in the preprocessing of data for our analyses. Work is currently underway to address these limitations that will greatly expedite the preprocessing steps through a pipeline approach. In addition, new methods are under active development that will automatically flag misidentified and potentially novel sequences within a given dataset and automatically place such sequences into close proximity to their nearest neighbors, based on 16S rDNA sequence homology. These methods will also permit linking of EDA plots, derived from such analyses to external data and information resources.
March 29, 2005
The NamesforLife project, “Semantic Resolution Services for the Life Sciences”, has received a $50,000 fast-track grant from the Michigan Universities Commercialization Initiative (MUCI) to develop a working proof-of-concept information portal for semiotic terminology management and resolution for Prokaryotic nomenclature and taxonomy. The project is backed by Intellectual Property of the Michigan State University Board of Trustees.
This web site will serve as a primary means of communicating with end users about the project background, current developments, and information on registration of Names, Taxa, and Nomoi. We expect to provide some services (e.g. look-up and reverse lookup functions and distribution of lookup tables and dictionaries for programmatic embedding of DOIs in text by authors and publishers, and batch insertion into databases. We will also use the website to distribute PDF versions of the new releases of the Outline of Prokaryotic Taxa.
March 14, 2005
Bioinformatics Forum — Names and Objects for Unambiguous Data Access amongst Biodiversity Data Entities
National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan March 14-15, 2005
Catherine Lyons presents “An Introduction to Digital Object Identifiers as background to NamesforLife”.
Systematic taxonomy is a complex network of documents, data, and, concepts. The Digital Object Identifier (DOI) system is built from components that model complexity in other domains. This is an unusual introduction to DOIs, in that it emphasizes those aspects of the DOI system that will be a particular strength in the management of taxonomy and nomenclature. The association of objects with types, and types with type-specific metadata, enable a DOI ‘Application Profile’ (AP). An AP gathers together digital objects that have common metadata properties. For a DOI in a given AP, a service can be implemented that exploits the metadata defined by its AP, and returns, for example, some text, a link, a menu.
Suppose there were a Biological Name AP associated with a ‘Check for Synonyms’ service...this service could be associated with digital objects (Information Objects) in the Name AP (i.e., nomenclatural assertions). By reasoning over Information Objects, we can construct services that can be offered through multiple resolution.
February 24, 2005
An algorithm for automated classification based on evolutionary distance data was written in S. The algorithm was tested on a dataset of 1,436 small subunit ribosomal RNA sequences and was able to classify the sequences according to an extant scheme, use statistical measurements of group membership to detect sequences that were misclassified within this scheme and produce a new classification. In this study, the use of the algorithm to address problems in prokaryotic taxonomy is discussed. The algorithm we have developed provides an intuitive approach to making and viewing classifications; conceivably, persons with no training could generate classifications and, by looking at the heatmaps, see how a classification might be improved. Our algorithm formalizes and automates the means used to achieve such improvements. Errors in data curation, classification and identification (of both sequences and source organisms) can be easily spotted and their effects corrected. Also, the classification itself can be modified so that the information content of the taxonomy is enhanced.
November 16, 2004
Okemos, Michigan November 16, 2004
A new tech startup, NamesforLife, LLC (N4L) has been founded in Okemos, Michigan to commercialize research conducted at Michigan State University. The new company is funded by founder equity and targets terminology management and document classification in the Life Science Publishing space.
NamesforLife is a project, a novel technology, and a University sponsored start-up business (NamesforLife, LLC) that arises from a long-term electronic publishing collaboration between George M. Garrity, ScD. and Catherine Lyons (Explicatrix, LLC, Edinburgh, United Kingdom). NamesforLife models the evolution of biological nomenclature and terminology, resolves instances of synonymy and homonymy, and provides a mapping to the underlying concepts that can be viewed in a temporal context. Through the use of Digital Object Identifiers (DOIs), our technology can make names or terms actionable, can provide a direct path through the literature, and link to a variety of databases and other contextually relevant services. NamesforLife can provide publishers and data providers with a unique opportunity to provide their end-users with a direct path to related content, based on a name or term, even if the name or term has changed over time. Equally important, NamesforLife technology can provide publishers and data providers with opportunities to further exploit the long-tail phenomenon associated with Internet distribution of content and identify new business opportunities outside their normal markets.
November 15, 2004
Okemos, Michigan November 15, 2004
November 10, 2004
Berlin, Germany November 10, 2004
Norman Paskin has published an article regarding the use of Digital Object Identifiers (DOIs) for scientific data. A description of the NamesforLife system is given on page 7.
The aim of this project is “future-proofing biological nomenclature”; it proposes DOIs as persistent identifiers of taxonomic definitions. A name ascribed to a given group in a biological taxonomy is fixed in both time and scope and may or may not be revised when new information is available.
The NamesforLife project is developing a model for assigning DOIs to prokaryotic taxa as a test case. Though the definition of a taxon may be refined and its nomenclature redefined, the DOI will persist, leaving a forward-pointing trail that can be used to reliably locate digital and physical resources, even when a name may be deemed obsolete. Forward linking from a synonym to a record of the publication that asserts synonymy is especially important, as there is currently no mandatory mechanism for asserting and resolving names that become ambiguous.
The model seeks to strengthen the association of names with taxa by using DOIs to track the taxonomic definition of a name over time. It is extensible to the level of individual genes within a given species. However, the real power of this method lies in the ability of DOIs to become embedded in the information environment, providing a direct and persistent link to the full record of taxonomic and nomenclatural revision and ensuring consistency and accuracy throughout online scientific resources. A DOI-based infrastructure for formally associating nomenclature with taxonomy enables a name to be used unambiguously and persistently, only one mouse-click away from a record of its current definition and historical development.
June 22, 2004
Annual International DOI Foundation Members Meeting — Session 4: Uses of identifiers - Identifiers for data
London, United Kingdom June 22, 2004
Catherine Lyons presents the NamesforLife concept at the IDF Members Meeting.
The Alteromonadales represent an interesting test case for demonstrating how one could apply Digital Object Identifiers (DOIs) to solve the problems associated with changes in nomenclature and taxonomy of a particular group. The family was effectively defined by Garrity et al. in version 1.0 of the Taxonomic Outline and independently by Ivanova and Mikhailov in 2001 and is formed on the genus Alteromonas, which serves as the type genus for the family and class. Alteromonas was initially circumscribed by Bauman et al. in 1972 and subsequently emended (although not formally in all cases) on more than 15 occasions through the addition 20 species. Nineteen of these species were subsequently moved to four other genera, two of which are also members of the Alteromonas (sensu Garrity et al.) and two genera are members of the family “Oceanospirillacea”, class “Oceanospirillales”. Some of the later proposals also yield three heterotypic synonyms, two homotypic synonyms, the subdivision of one species into two subspecies which were subsequently rejoined following a move to another genus, the subsequent subdivision of one reassigned species into five distinct species in that genus, and one orthographic correction that was required to correct an error when latinizing a species name. Thus, the original 20 species of Alteromonas have appeared under a total of 64 different names in five genera, two families and two classes.
If we apply an Information Model based on the separation of the Names (labels), Taxa (concepts), and Exemplars (strains/objects), we are able to track changes in nomenclature and taxonomic opinion separately, without losing track of the underlying organism (the Exemplar). This enables a means of separating competing taxonomic views, thereby effectively disambiguating any synonymous names and competing taxonomies applied to an exemplar.
Further, if we assign a DOI to each Name, Taxon, and Exemplar, we essentially create a set of Information Objects - persistent, online, public documents - which serve to instantiate nomenclatural events, taxonomic opinions, and exemplars. These Information Objects provide metadata and form a navigable graph when linked with other Information Objects and to online information outside of NamesforLife. They are easy to link to from online journals, databases, and similar resources, and are guaranteed to be persistent.
To achieve a working prototype based on this Information Architecture, we plan to perform some exploratory work with publishers, biodata curators and genomics researchers to find a path toward obtaining funding for this project and developing standards for clean nomenclatural and taxonomic data.
May 23, 2004
New Orleans, Louisiana May 23-27, 2004
Dr. Garrity will be presenting a taxonomy browser backed by a novel algorithm for building self-organizing and self-correcting classifications.
Recently, we developed an algorithm that builds self-organizing and self-correcting classifications. We have applied this algorithm to the problems arising from sequence annotation errors on prokaryotic classification. The comparison of the optimized classifications developed with our algorithm with other taxonomic proposals has allowed us to resolve outstanding problems in prokaryotic classification and taxonomy.
To make such comparisons available to the research community, we have built a website that allows users to compare the current Bergey’s Taxonomic Outline with an optimized classification. The website serves as user interface to a dedicated analytic server, built using StatServer (Insightful). The application allows users to select the taxonomic group they are interested in, choose how they want the results to be organized (that is, at the species, genus or family level) and display the comparison. The organization of the compared classifications is visualized in the form of shaded evolutionary distance matrices. The colors of the matrix indicate the distances between the pairs of sequences in the matrix. The grouping of the colors in the matrix reflects the higher level groupings of the sequences (and, by extension, of the parent organisms). One matrix is arranged according to the hierarchy of the Outline and the other matrix is arranged according to the groupings generated by the classifier. Users can drill down in the display to see the comparisons at lower taxonomic levels or move up the hierarchy. The side-by-side comparison illuminates possible solutions to evident problems in the current classification. We illustrate how the taxonomy browser works by looking at the classification and taxonomy of the Archaea.
October 27, 2003
Hotel Metropole, Brussels, Belgium October 27-28, 2003
George Garrity presents “Biological nomenclature in the postgenomic era: Biological and computational issues”.
Within biology, the fundamental taxonomic unit is the species. However, species can be further subdivided into subspecies, varieties and other categories that are specific to the disciplines of botany, zoology, prokaryotic biology and virology. In the preferred example, the species are within the domains Bacteria and Archaea, which are collectively referred to as prokaryotes.
The N4L/Bergamot model and Information Objects provide a transparent middle layer that permanently links together Names and Taxa (at all levels of the hierarchy) with their occurrences in the literature and data repositories. Through the use of DOIs and multiple resolution technology, Names can serve as future-proof links to the complete taxonomic record of a given taxon (including relevant information regarding synonymies, orthographic errors, priority, etc.) and to a variety of third-party services specific to a given taxon without the intervention of search engines or other methods. End-users simply need to click on a name or other similar graphic device to gain access to the desired information.
February 9, 2003
Genomes to Life Contractor-Grantee Workshop I — Workshop Breakout Session - Comparative Genomics: New Approaches & Insights
Arlington, Virginia February 9-12, 2003
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.
February 2, 2003
Lister Hill Center, NLM, NIH Campus, Bethesda, Maryland February 2-3, 2003
George Garrity will be present to discuss the white paper, “Future-proofing biological nomenclature”.
The disjunction of nomenclature and taxonomy results in an accumulation of names of dubious value in the literature and databases. While systematic biologists may be adept at recognizing such problems, most others (including the curators of some databases) are not.
It is becoming 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 new data become available, the inferred relationships among the named entities may change: a taxon may be promoted or demoted, new taxa may be interposed between formerly contiguous taxa. As a result, the association of names with taxonomic concepts tends to weaken as the rate at which gene sequencing accelerates. Failure to address this problem will result in increasingly unpredictable responses when biological names are used to query either the literature or databases. What is required is a resolution system that can handle the complex relationships between biological names and the entities they denote and provide links to both the historical and current definition of each named taxon.
We believe that an implementation of the Digital Object Identifier (DOI) may provide the most robust and future-proof solution to this problem. A DOI is a unique, persistent identifier of an information resource that is registered together with a URL. Its purpose is the management and retrieval of that resource in the networked environment. In practice, most current DOIs identify journal articles, but DOIs are now being applied to trade publications, stock photography, and physicochemical data sets.
January 1, 2003
The original white paper behind the NamesforLife concept.
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. We believe that an implementation of the Digital Object Identifier (DOI) may provide the most robust and future-proof solution to this problem.
We are developing a model for assigning DOIs to prokaryotic taxa as a test case. The real power of this method lies in the ability of DOIs to become embedded in the information environment, providing a direct and persistent link to the full record of taxonomic and nomenclatural revision and ensuring consistency and accuracy throughout online scientific resources.