Robert John Robbins

BRIITE - Biomedical Research Institutions Information Technology Exchange

Helping women make choices to reduce cancer risk and to improve breast health behaviors is important, but the best ways to reach more people with intervention assistance is not known. To test the efficacy of a web-based intervention designed to help women make better breast health choices, we adapted our previously tested, successful breast health...

Background: Efforts to harmonize genomic data standards used by the biodiversity and metagenomic research communities have shown that prokaryotic data cannot be understood or represented in a traditional, classical biological context for conceptual reasons, not technical ones. Results: Biology, like physics, has a fundamental duality—the classical...

We describe the outcomes of three recent workshops aimed at advancing development of the Biological Collections Ontology (BCO), the Population and Community Ontology (PCO), and tools to annotate data using those and other ontologies. The first workshop gathered use cases to help grow the PCO, agreed upon a format for modeling challenging concepts s...

The most fundamental unit of traditional biodiversity - the individual organism (defined as a physically connected, multi-cellular aggregation, with all of the cells clonally derived from one ancestral cell) - has no parallel in the world of prokaryotic biology. Yet recent advances (metagenomics tools, etc) have shown that about half of the world's...

The Genomic Standards Consortium (GSC) is an open-membership community that was founded in 2005 to work towards the development, implementation and harmonization of standards in the field of genomics. Starting with the defined task of establishing a minimal set of descriptions the GSC has evolved into an active standards-setting body that currently...

This position paper, Data Management for LTER: 1980 – 2010, was independently prepared by Dr. Robert J. Robbins, a member of the 30 Year LTER Review Committee. This position paper is not part of the LTER 30 Year Review Report but is provided by the BIO Advisory Committee without comment or endorsement as an independent perspective regarding LTER da...

Public Release: 12/09/2011 Dear Colleagues: The Advisory Committee for the Biological Sciences (BIO AC) has approved the Long Term Ecological Research Program Report of the 30 Year Review Committee for public posting on the Advisory Committee web site. The BIO AC retains its prerogative to comment on the content of the report at a future date. The...

This report summarizes the proceedings of the 14 th workshop of the Genomic Standards Con-sortium (GSC) held at the University of Oxford in September 2012. The primary goal of the workshop was to work towards the launch of the Genomic Observatories (GOs) Network un-der the GSC. For the first time, it brought together potential GOs sites, GSC member...

“If names be not correct, language is not in accordance with the truth of things. If language be not in accordance with the truth of things, affairs cannot be carried on to success.” - Confucius, Analects, Book XIII, Chapter 3, verses 4-7, translated by James Legge Two workshops (hereafter described as “workshops”) were held in 2012, which brough...

The workshop-hackathon was convened by the Global Biodiversity Information Facility (GBIF) at its secretariat in Copenhagen over 22-24 May 2013 with additional support from several projects (RCN4GSC, EAGER, VertNet, BiSciCol, GGBN, and Micro B3). It assembled a team of experts to address the challenge of adapting the Darwin Core standard for a wide...

Following up on efforts from two earlier workshops, a meeting was convened in San Diego to (a) establish working connections between experts in the use of the Darwin Core and the GSC MIxS standards, (b) conduct mutual briefings to promote knowledge exchange and to increase the understanding of the two communities' approaches, constraints, community...

At the GSC11 meeting (4-6 April 2011, Hinxton, England, the GSC's genomic biodiversity working group (GBWG) developed an initial model for a data management testbed at the interface of biodiversity with genomics and metagenomics. With representatives of the Global Biodiversity Information Facility (GBIF) participating, it was agreed that the most u...

Building on the planning efforts of the RCN4GSC project, a workshop was convened in San Diego to bring together experts from genomics and metagenomics, biodiversity, ecology, and bioinformatics with the charge to identify potential for positive interactions and progress, especially building on successes at establishing data standards by the GSC and...

A traditional drawing of the tree of life emphasizes the eukaryota. Classical biology has largely been the study of somatic tissue in multi-cellular eukaryotes. Yet the eukaryotes represent a highly specialized and highly constrained form of life. Attempts to understand biological dark matter -- the invisible prokaryotic realm -- by generalizing fr...

This report details the outcome of the 13(th) Meeting of the Genomic Standards Consortium. The three-day conference was held at the Kingkey Palace Hotel, Shenzhen, China, on March 5-7, 2012, and was hosted by the Beijing Genomics Institute. The meeting, titled From Genomes to Interactions to Communities to Models, highlighted the role of data stand...

Microbial ecology has been enhanced greatly by the ongoing 'omics revolution, bringing half the world's biomass and most of its biodiversity into analytical view for the first time; indeed, it feels almost like the invention of the microscope and the discovery of the new world at the same time. With major microbial ecology research efforts accumula...

GBWG (the GSC Biodiversity Working Group, with assistance from RCN4GSC) is reaching out to other communities to engage scientists at the interface of genomics and biodiversity. The NSF RCN4GSC project at UCSD has the mission to: create a research coordination network to promote and integrate standards for genomic and metagenomic data and metadata...

Recent developments in our ability to capture, curate, and analyze data, the field of data-intensive science (DIS), have indeed made these interesting and challenging times for scientific practice as well as policy making in real time. We are confronted with immense datasets that challenge our ability to pool, transfer, analyze, or interpret scient...

Helping women make choices to reduce cancer risk and to improve breast health behaviors is important, but the best ways to reach more people with intervention assistance is not known. To test the efficacy of a Web-based intervention designed to help women make better breast health choices, we adapted our previously tested, successful breast health...

A random, population-based sample of 431 women aged 18–74 in King County, Washington, USA, completed a survey module on Internet use and access. Level of mental health, level of general health perceptions, older age, and higher income predicted women's health-related Internet use. Participants without access reported various barriers to obtaining a...

Data protection is important for all information systems that deal with human-subjects data. Grid-based systems--such as the cancer Biomedical Informatics Grid (caBIG)--seek to develop new mechanisms to facilitate real-time federation of cancer-relevant data sources, including sources protected under a variety of regulatory laws, such as HIPAA and...

Structured interview instruments. This file contains the four interview instruments that were used in the study. The questions for these instruments were developed using a team-based approach as described in the methods section of the paper.

Information explosion and new advances in high throughput experiments have challenged biomedical research, and suggested a future in which inter-institutional and international collaborations will be the norm. The cancer Biomedical Informatics Grid is an ambitious initiative launched by the US National Cancer Institute to develop a network of tools...

Much is written about Internet access, Web access, Web site accessibility, and access to online health information. The term access has, however, a variety of meanings to authors in different contexts when applied to the Internet, the Web, and interactive health communication. We have summarized those varied uses and definitions and consolidated th...

The Internet might transform the way in which health information is communicated to patient and general populations. Understanding differences in usage patterns will be critically important to ensuring the successful distribution of health information. The present study presents early data on the use patterns and predictors of use of a Web-based in...

Bioinformatics, the use of computers to support biological information management, has become an enabling technology, essential for the success of big-science projects in biology. Not yet a true discipline of its own, bioinformatics occupies space between biology and computer science, with interests in library and information science, engineering,...

The original goals of the Human Genome Project (HGP) were: 1) construction of a high-resolution genetic map of the human genome: 2) production of a variety of physical maps of all human chromosomes and of the DNA of selected model organisms; 3) determination of the complete sequence of human DNA and of the DNA of selected model organisms; 4) develo...

Information technology is transforming biology, and the relentless effects of Moore's Law are transforming that transformation. Nowhere are these changes more apparent than in the international collaboration known as the Human Genome Project (HGP). The authors consider the relationship of informatics to genomic research. Topics discussed include: t...

The goals of the Human Genome Project are: (1) construction of a high-resolution genetic map of the human genome, (2) production of a variety of physical maps of all human chromosomes and of the DNA of selected model organisms, (3) determination of the complete sequence of human DNA and of the DNA of selected model organisms, (4) development of cap...

Biology is entering a new era in which data are being generated that cannot be published in the traditional literature. Databases are taking the role of scientific literature in distributing this information to the community. The success of some major biological undertakings, such as the Human Genome Project, will depend upon the development of a s...

This conference was held in St. Petersburg Beach, Florida June 4--7, 1992. The purpose of this conference was to provide a forum for exchange of state-of-the-art information in the field of the human genome. This provided an opportunity to gain firsthand knowledge of the scope, direction, and future prospects of information and computing in complex...

Informatics of some kind will play a role in every aspect of the Human Genome Project (HGP): data acquisition, data analysis, data exchange, data publication and, data visualization. What are the real requirements and challenges? The primary requirement is clear thinking and the main challenge is design. If good design is lacking, the price will be...

Version 5.0 of the Genome Data Base (GDBTM) was released in March 1993. This document describes some of the significant changes to the types of data which are stored within the GDB. In addition to handling a wider scope of data, the GDB 5.0 application software now supports the X-Windows protocol. Although the GDB software still remains the most wi...

The variable white mutation arose spontaneously in 1983 within a laboratory stock of wild-type deer mice (Peromyscus maniculatus). The original mutant animal was born to a wild-type pair that had previously produced several entirely wild-type litters. Other variable white animals were bred from the initial individual. Variable white deer mice exhib...

In 1991 the Genome Data Base at Johns Hopkins University School of Medicine was selected as the central repository for mapping data from the Human Genome Project, and was funded by NIH and DOE under a three year award. GDB has now finished 28 months of Federally funded operation. During this period a great deal of progress and many internal changes...

The purpose and scope of the human genome project are discussed. Basic biological concepts underlying the project are reviewed. The two processes-logic and experimentation-used to understand DNA sequences are compared, and the process of obtaining the sequence is described. Two problem areas in this collaboration between biologists and computer sci...

Mapping and sequencing the entire human genome in a timely fashion requires organization of all available resources to the common goal. Federal funding agencies have established individual genome centers that will focus on one or more chromosomes. Further, chromosome-specific workshops are being organized to permit individual centers, researchers,...

An autosomal recessive mutation affecting hair and eye pigmentation was discovered in the F2 progeny of wild-type deer mice, (Peromyscus maniculatus), trapped near East Lansing, Michigan. When homozygous, the mutation (designated as blonde, bl), reduces both black and yellow pigmentation deposited in the fur, reduces or eliminates pigmentation in t...

Description The book presents test methods on evaluation procedures for chemicals. Devices, and other techniques used to control aquatic and terrestrial vertebrates. The areas of major interest to the reader are methods of reducing potential hazards of pesticides, including insecticides, herbicides, and microbial agents; pesticide hazard to aquatic...

An investigation was made of the occurrence of learned and nonlearned aversions in the acquisition of illness-induced taste aversions in mice of the genusPeromyscus. It was determined: (1) that illness following the ingestion of a novel flavor both produced aversions specific to that flavor and also enhanced neophobia directed toward novel flavors...

An examination of the effect of sex upon taste-aversion learning in deer mice (Peromyscus maniculatus bairdi) found that (a) sex has no apparent effect upon either the acquisition or the extinction of a LiCl-induced aversion to sucrose solution if the animals are tested while fluid deprived, but that (b) if the animals are tested under nondeprived...

Although bait shyness has long been recognized as a problem to be overcome in the control of vertebrate pests, it has recently been suggested that the phenomenon might be turned to an advantage and used as an alternative, non-lethal form of control. Unfortunately, this technique has not proven to be as useful as hoped, as the work which has been do...

An investigation was made of the effects of prior familiarization with sucrose on the acquisition and extinction of LiCl-induced aversions to sucrose by mice of the genus Peromyscus. As in previous studies on other species, it was found that flavor familiarization inhibits the formation of learned taste aversions. However, in contrast to some repor...

A series of experiments tested the ability of mice of the native genus Peromyscus to form learned taste aversions. It was found that (a) the mice acquired a strong aversion after a single flavor/toxicosis pairing, (b) naive mice drinking a LiCl solution apparently began to experience toxic effects within 90 sec after the beginning of consumption, (...

Progress on the project to study the effects of the ELF Communication System on small mammals and nesting birds is detailed for the base period, 1982. Initial population surveys were conducted which showed that the main study species, the Black-capped Chickadee (Parus atricapillus) and the deer-mouse, (Peromyscus gracilis) were present and abundant...

As the Human Genome Project (HGP) moves toward its successful completion, more and more people have become interested in understanding this project and its results. Since the HGP has significant ethical, legal, and social implications for all citizens, the number of individuals who do, or should wish to become familiar with the project is high. In...