Recent trends in US patent grants and issues to be considered

The life sciences have changed radically since the Convention on Biological Diversity first opened for signatures in 1992. Traditional organism-based approaches to discovery and use of genetic resources have been supplanted by molecular approaches. Biodiversity prospecting is more likely to be a programmatic bioinformatics activity rather than an activity conducted by field scientists. Access to genetic resources is no longer centered on a hunt for novel species. Rather, the hunt is for novel genes and metabolic pathways that can be cloned into well-understood expression systems and readily scaled-up for industrial production. Information about contemporary research, development, and manufacturing practices needs to be addressed, especially when those genes do not need to be associated with their native host at the time of discovery. Information about the research organizations participating in all phases of the discovery and development process also needs to be considered, especially when it involves partnerships between academic and industrial organizations. 

We present a high-level view of recent trends in the issuance of US patent grants to commercial and non-commercial research organizations, and introduce a technology that is already in place which can be applied to monitoring the use of genetic materials by various stakeholders in an open and transparent manner, as intended under the International Regime for Access and Benefit Sharing (ABS).
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Genome sequences published outside of Standards in Genomic Sciences, January – June 2011

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to this subsequent versions of this list are invited to provide the bibliometric data for such references to the SIGS editorial office

Genome sequences published outside of Standards in Genomic Sciences, January-March 2012

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office

Final Report PIPELINING RDP DATA TO THE "TAXOMATIC"

This project builds on the results of previously funded research by integrating data and software that had been previously used in building resources used in the preparation of Bergey?s Manual of Systematic Bacteriology, 2nd Edition (Volumes 1 & 2A-C) and the Ribosomal Database Project-II (RDP-II) so as to both enhance the value of the data and create a pipeline approach to keeping the data current. Earlier, we demonstrated the value of using exploratory data analysis (EDA) to visualize large sets of sequence data (notably SSU rRNA gene sequences used in constructing a comprehensive phylogeny of prokaryotes. While the Self- Organizing Self-Correcting Classification (SOSCC) algorithms we developed were computationally efficient and useful for unraveling problems within the underlying data (e.g., identification of annotation errors, detection of unresolved synonymies, taxonomic and nomenclatural errors), bottlenecks at the preprocessing stage limited deployment of our applications as tools for end-users. To overcome the bottlenecks (which included hand alignment and computation of large matrices of pair-wise evolutionary distances), we proposed building a data pipeline between the ?Taxomatic? application and RDP-II. The objectives were to accelerate the production and distribution of the updated versions of the prokaryotic taxonomy in lock-step with publication of new taxa and rearrangement of existing taxa, and to distribute these data more readily with the RDP-II and and other stakeholders in the community. A related goal of the current project is to deploy our visualization techniques as an interactive web application by which end-users can view manipulate, and select datasets of particular interest based upon phylogenetic and genomic information, access sequence data, and ultimately the scientific literature where the original observations were made and those that build on the original observations. The Taxomatic is a web-based tool to visualize distance matrices. The tool accepts raw distance matrices or aligned sequence information as data sources. When sequence information is provided the distance matrix is computed using the uncorrected distance model. Users can upload files to the Taxomatic website or sequences can be submitted by a SOAP service. This SOAP service is used by RDP to streamline Taxomatic use with RDP data. In addition to supplying source information, users can either supply their own taxonomic information by uploading it in XML, retrieve data taxonomic information from the RDP using either RDP or Genbank identifiers as source data, with or without classification by the RDP Classifier web service, or completely omit taxonomic data. In the latter case, the input distance matrix can be viewed in the order in which it was loaded

NamesforLife Semantic Resolution Services for the Life Sciences

A major challenge in bioinformatics, life sciences, and medicine is using correct and informative names. While this sounds simple enough, many different naming conventions exist in the life sciences and medicine that may be either complementary or competitive with other naming conventions. For a variety of reasons, proper names are not always used, leading to an accumulated semantic ambiguity that readers of the literature and end users of databases are left to resolve on their own. This ambiguity is a growing problem and the biocuration community is aware of its consequences. 

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. 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