Publications

June 6, 2017

Systems and Methods for Automatically Identifying and Linking Names in Digital Resources

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 23, 2017

Classification of Nucleotide Sequences by Latent Semantic Analysis

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.

December 2, 2014

Semiotic Indexing of Digital Resources

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.

October 11, 2011

Methods for data classification

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

The van Niel International Prize for Studies in Bacterial Systematics, awarded by The University of Queensland Awarded in 2011 to George M. Garrity

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.

June 22, 2011

Intellogist article on NamesforLife

Kristin Whitman from Landon IP has published an article about how NamesforLife adds value to your searches, from the perspective of the patent community.

April 12, 2011

Systems and methods for resolving ambiguity between names and entities

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.

May 20, 2010

DOI News

NamesforLife has a mention in the May 2010 DOI News. See “DOI-based Tool for Taxonomy”.

February 13, 2010

Microbiology Today

NamesforLife has a full page write-up in Microbiology Today.

March 6, 2007

Taxonomic Outline of Bacteria and Archaea 7.7

The Taxonomic Outline of Bacteria and Archaea (TOBA) 7.7 has been published.

April 24, 2006

Computational aspects of systematic biology

Lilburn, Harrison, Cole and Garrity discuss the resources currently available to systematic biologists.

February 24, 2005

Self-organizing and self-correcting classifications of biological data

An algorithm for automated classification based on evolutionary distance data was written in S. The algorithm was tested on a dataset of 1436 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 10, 2004

19th International CODATA Conference —Digital Object Identifiers for scientific data
Berlin, Germany November 10, 2004—November 10, 2004

Norman Paskin has published an article regarding the use of DOIs for scientific data. A description of the NamesforLife system is given on page 7.

January 1, 2003

Future-proofing biological nomenclature

The original white paper behind the NamesforLife concept.

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