Structuring strain data for storage and retrieval of information on fungi and yeasts in MINE, the Microbial Information Network Europe

A distributed Microbial Information Network Europe (MINE) is being constructed by a number of major microbial culture collections in countries of the European Community, with the support of the Biotechnology Action Programme (BAP) of the Commission of the European Community. The representatives of the collections participating in MINE have agreed to adopt a general format for the computer storage and retrieval of strain data. This uniform format will facilitate the electronic combination and exchange of data from different collections in order to produce integrated catalogues and the use of identical commands to search the different databases. It is recommended to other collections who may wish to contribute data to the MINE network or between themselves. Three kinds of records can be linked to the leading 'species records': strain records, synonym records, and alternative morphonym records. A minimum data set of 30 fields (similar to the fields used for producing catalogues) is defined that facilitates the exchange of data between the national nodes and serves as a directory to strains available at other nodes. It is suggested that the full strain record comprise 99 fields, grouped in 12 blocks: internal administration--name--strain administration--status--environment and history--biological interactions--sexuality--properties (cytology, biomolecular data)--genotype and genetics--growth conditions--chemistry and enzymes--practical applications. Several fields are divided into subfields of different ranks. Delimiters are used either to separate a range of entries that have to be indexed or to divide an entry from the reference to its source or remarks that should not be indexed. The contents and structure of the fields proposed for filamentous fungi and yeasts are described and in some cases illustrated by examples. Uniformity of input is essential for indexed fields and desirable for non-indexed fields. Seven thesaurus files are envisaged to ensure consistency.     

Does a snapshot show the whole picture? Intrinsic limitations to growth inference of the short lived and fast growing

Individual growth patterns in ecology are often determined from population field data through the use of regression and model selection inference analyses. However, such approaches are typically unable to provide insight into dynamic processes when based upon collections of ‘snapshot’ data that consist of only a single observation for each individual. We caution how model selection inference from size-at-age data may lead to growth models that are mis-specified in the case of species such as squid and fishes that display fast and variable growth and for which, field data of the early part of the lifespan are typically sparse and difficult to obtain.     

Collecting collections: building the library of The New York Botanical Garden

The history of the collections in the Library of The New York Botanical Garden includes the acquisition of previously accumulated collections as well as individual items acquired in the normal course of collection development. Particularly during the first 50 years of the institution, collections of library materials were acquired along with herbaria specimens, and, occasionally, collections of living plants, assembled by an individual as part of his or her personal research interests. While curatorial practice dictates that such an assemblage of research materials be separated when shifted from individual to institutional curatorship, the knowledge of the whole of the collection as received may fill in the background pattern of institutional collection development. A chronological table of these collections is appended, including reference to any extended discussion or listing.     

A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases

Rapid accumulation of large and standardized microarray data collections is opening up novel opportunities for holistic characterization of genome function. The limited scalability of current preprocessing techniques has, however, formed a bottleneck for full utilization of these data resources. Although short oligonucleotide arrays constitute a major source of genome-wide profiling data, scalable probe-level techniques have been available only for few platforms based on pre-calculated probe effects from restricted reference training sets. To overcome these key limitations, we introduce a fully scalable online-learning algorithm for probe-level analysis and pre-processing of large microarray atlases involving tens of thousands of arrays. In contrast to the alternatives, our algorithm scales up linearly with respect to sample size and is applicable to all short oligonucleotide platforms. The model can use the most comprehensive data collections available to date to pinpoint individual probes affected by noise and biases, providing tools to guide array design and quality control. This is the only available algorithm that can learn probe-level parameters based on sequential hyperparameter updates at small consecutive batches of data, thus circumventing the extensive memory requirements of the standard approaches and opening up novel opportunities to take full advantage of contemporary microarray collections.     

Pandanus from Ok Tedi region,Papua New Guinea,collected by Debra Donoghue

In the course of ethnobotanical and ethnoarchaeological studies in the Ok Tedi region, Kiunga subprovince, Western Province, Papua New Guinea, Debra Donoghue collected several botanical specimens as vouchers for her studies into the prehistory of edible-nut pandans in the New Guinea Highlands and for David Hyndman’s study of the use and names of pandans in the region. These specimens were submitted to me through Dr. Hyndman for identification, and one set of duplicates has been deposited in the Lae Herbarium (PNG) and another in the University of Malaya Herbarium (KLU). Some of the collections are of considerable botanical interest, representing hitherto little-known species. One collection represents a new edible-nut species. The following list contains the botanical identifications, collection data, and some taxonomic comments. All the collections were made in June 1981. The Ok Tedi region is located around 5°12’S, 141°17’E.     

植物标本标签的计算机印制数据系统

本文讨论了主要用以印制标本采集记录标签的数据系统及其数据库建库方案与编程原理。该系统可在ＩＢＭ及其兼容系列个人计算机上使用,适合用于个人或科研与教学机构中小型标本采集信息管理;可用以数据的检索、标本标签的印制和植物名录的打印;也可用以地区性的植物区系与生态学研究。     

High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching

Cryo-electron tomography allows the visualization of macromolecular complexes in their cellular environments in close-to-live conditions. The nominal resolution of subtomograms can be significantly increased when individual subtomograms of the same kind are aligned and averaged. A vital step for such a procedure are algorithms that speedup subtomogram alignment and improve its accuracy to allow reference-free subtomogram classifications. Such methods will facilitate automation of tomography analysis and overall high throughput in the data processing. Building on previous work, here we propose a fast rotational alignment method that uses the Fourier equivalent form of a popular constrained correlation measure that considers missing wedge corrections and density variances in the subtomograms. The fast rotational search is based on 3D volumetric matching, which improves the rotational alignment accuracy in particular for highly distorted subtomograms with low SNR and tilt angle ranges in comparison to fast rotational matching of projected 2D spherical images. We further integrate our fast rotational alignment method in a reference-free iterative subtomogram classification scheme, and propose a local feature enhancement strategy in the classification process. As a proof of principle, we can demonstrate that the automatic method can successfully classify a large number of experimental subtomograms without the need of a reference structure.     

Text similarity: an alternative way to search MEDLINE

MOTIVATION: The most widely used literature search techniques, such as those offered by NCBI's PubMed system, require significant effort on the part of the searcher, and inexperienced searchers do not use these systems as effectively as experienced users. Improved literature search engines can save researchers time and effort by making it easier to locate the most important and relevant literature. RESULTS: We have created and optimized a new, hybrid search system for Medline that takes natural text as input and then delivers results with high precision and recall. The combination of a fast, low-sensitivity weighted keyword-based first pass algorithm to cast a wide net to gather an initial set of literature, followed by a unique sentence-alignment based similarity algorithm to rank order those results was developed that is sensitive, fast and easy to use. Several text similarity search algorithms, both standard and novel, were implemented and tested in order to determine which obtained the best results in information retrieval exercises. AVAILABILITY: Literature searching algorithms are implemented in a system called eTBLAST, freely accessible over the web at http://invention.swmed.edu. A variety of other derivative systems and visualization tools provides the user with an enhanced experience and additional capabilities. CONTACT: Harold.Garner@UTSouthwestern.edu.     

Towards a virtual reality for plant-associated fungi in the United States and Canada

At present knowledge of fungal biodiversity in North America is scattered in diverse sources ranging from well-reviewed, comprehensive databases to unedited databases of reports from the literature, information on file cards, and uncomputerized reference collections. Resources available electronically were used to determine their relative importance in evaluating the plant-associated fungi known from the United States and to a lesser extent Canada. The results demonstrate that the literature provides the greatest information but that reference collections in the US National Fungus Collections contribute between 22–31% additional data. Little overlap exists between fungi isolated as endophytes and those reported in the literature or as reference collections. Eighty to 100% of the plant-associated fungi reported from Canada are accounted for in comprehensive resources for the United States. A comprehensive database of plant-associated fungi in Canada, the United States, and eventually Mexico would serve as a valuable resource for those making plant quarantine decisions.     

Awareness and use of biodiversity collections by fish biologists

A survey of 280 fish biologists from a diverse pool of disciplines was conducted in order to assess the use made of biodiversity collections and how collections can better collect, curate and share the data they have. From the responses, data for how fish biologists use collections, what data they find the most useful, what factors influence the decisions to use collections, how they access the data and explore why some fish biologists make the decision to not use biodiversity collections is collated and reported. The results of which could be used to formulate sustainability plans for collections administrators and staff who curate fish biodiversity collections, while also highlighting the diversity of data and uses to researchers.     

The Montana collections of Francis Duncan Kelsey

Francis Duncan Kelsey amassed one of the important early herbaria of Montana plants from 1885 to 1893. His Montana collections contain over 1200 specimens of algae, bryophytes, ferns, angiosperms, and fungi and include at least 41 that serve as types. Originally donated to the Oberlin College Herbarium (OC), the Montana collections, records, and later correspondence of Kelsey are now housed at the Miami University Herbarium (MU). The mycological collections of Kelsey are numbered, dated, and include site information; his other collections are unnumbered and often lack precise dates and/or localities. Kelsey's Montana fieldwork itineraries and sources of exchange are presented. All valid and legitimate names based on Kelsey's Montana collections are listed with pertinent information from his collection notebooks.     

Nonparametric mixed effects models for unequally sampled noisy curves

We propose a method of analyzing collections of related curves in which the individual curves are modeled as spline functions with random coefficients. The method is applicable when the individual curves are sampled at variable and irregularly spaced points. This produces a low-rank, low-frequency approximation to the covariance structure, which can be estimated naturally by the EM algorithm. Smooth curves for individual trajectories are constructed as best linear unbiased predictor (BLUP) estimates, combining data from that individual and the entire collection. This framework leads naturally to methods for examining the effects of covariates on the shapes of the curves. We use model selection techniques--Akaike information criterion (AIC), Bayesian information criterion (BIC), and cross-validation--to select the number of breakpoints for the spline approximation. We believe that the methodology we propose provides a simple, flexible, and computationally efficient means of functional data analysis.     

A web-based GIS tool for exploring the world's biodiversity: The Global Biodiversity Information Facility Mapping and Analysis Portal Application (GBIF-MAPA)

Legacy biodiversity data from natural history and survey collections are rapidly becoming available in a common format over the Internet. Over 110 million records are already being served from the Global Biodiversity Information Facility (GBIF). However, our ability to use this information effectively for ecological research, management and conservation lags behind. A solution is a web-based Geographic Information System for enabling visualization and analysis of this rapidly expanding data resource. In this paper we detail a case study system, GBIF Mapping and Analysis Portal Application (MAPA), developed for deployment at distributed database portals. Building such a system requires overcoming a series of technical and research challenges. These challenges include: assuring fast speed of access to the vast amounts of data available through these distributed biodiversity databases; developing open standards based access to suitable environmental data layers for analyzing biodiversity distribution; building suitably flexible and intuitive map interfaces for refining the scope and criteria of an analysis; and building appropriate web-services based analysis tools that are of primary importance to the ecological community and make manifest the value of online biodiversity GBIF data. After discussing how we overcome these challenges, we provide case studies showing two examples of the use of GBIF-MAPA analysis tools.     

A new approach for efficient genotype imputation using information from relatives

Background

Genotype imputation can help reduce genotyping costs particularly for implementation of genomic selection. In applications entailing large populations, recovering the genotypes of untyped loci using information from reference individuals that were genotyped with a higher density panel is computationally challenging. Popular imputation methods are based upon the Hidden Markov model and have computational constraints due to an intensive sampling process. A fast, deterministic approach, which makes use of both family and population information, is presented here. All individuals are related and, therefore, share haplotypes which may differ in length and frequency based on their relationships. The method starts with family imputation if pedigree information is available, and then exploits close relationships by searching for long haplotype matches in the reference group using overlapping sliding windows. The search continues as the window size is shrunk in each chromosome sweep in order to capture more distant relationships.

Results

The proposed method gave higher or similar imputation accuracy than Beagle and Impute2 in cattle data sets when all available information was used. When close relatives of target individuals were present in the reference group, the method resulted in higher accuracy compared to the other two methods even when the pedigree was not used. Rare variants were also imputed with higher accuracy. Finally, computing requirements were considerably lower than those of Beagle and Impute2. The presented method took 28 minutes to impute from 6 k to 50 k genotypes for 2,000 individuals with a reference size of 64,429 individuals.

Conclusions

The proposed method efficiently makes use of information from close and distant relatives for accurate genotype imputation. In addition to its high imputation accuracy, the method is fast, owing to its deterministic nature and, therefore, it can easily be used in large data sets where the use of other methods is impractical.     

Methods of developing a core collection of annual Medicago species

A core collection is a subset of a large germplasm collection that contains accessions chosen to represent the genetic variability of the germplasm collection. The purpose of the core collection is to improve management and use of a germplasm collection. Core collections are usually assembled by grouping accessions and selecting from within these groups. The objective of this study was to compare 11 methods of assembling a core collection of the U.S. National collection of annual Medicago species. These methods differed in their use of passport and evaluation data as well as their selection strategy. Another objective was to compare core collections with sample sizes of 5%, 10% and 17% of the germplasm collection. Core collections assembled with evaluation data and cluster analysis better represented the germplasm collection than core collections assembled based solely on passport data and random selection of accessions, The Relative Diversity and the logarithm methods generated better core collections than the proportional method. The 5% and 10% sample size core collection were judged insufficient to represent the germplasm collection.     

The Genome Sequence DataBase: towards an integrated functional genomics resource.

During 1998 the primary focus of the Genome Sequence DataBase (GSDB; http://www.ncgr.org/gsdb ) located at the National Center for Genome Resources (NCGR) has been to improve data quality, improve data collections, and provide new methods and tools to access and analyze data. Data quality has been improved by extensive curation of certain data fields necessary for maintaining data collections and for using certain tools. Data quality has also been increased by improvements to the suite of programs that import data from the International Nucleotide Sequence Database Collaboration (IC). The Sequence Tag Alignment and Consensus Knowledgebase (STACK), a database of human expressed gene sequences developed by the South African National Bioinformatics Institute (SANBI), became available within the last year, allowing public access to this valuable resource of expressed sequences. Data access was improved by the addition of the Sequence Viewer, a platform-independent graphical viewer for GSDB sequence data. This tool has also been integrated with other searching and data retrieval tools. A BLAST homology search service was also made available, allowing researchers to search all of the data, including the unique data, that are available from GSDB. These improvements are designed to make GSDB more accessible to users, extend the rich searching capability already present in GSDB, and to facilitate the transition to an integrated system containing many different types of biological data.     

MEMOR: A database of archeological human remains collections from Flanders,Belgium

The aim of this article is to describe a newly created open access database of archeological human remains collections from Flanders, Belgium. The MEMOR database ( www.memor.be ) was created to provide an overview of the current practices of loans, reburial, and the research potential of human skeletons from archeological sites currently stored in Flanders. In addition, the project aimed to provide a legal and ethical framework for the handling of human remains and was created around stakeholder involvement from anthropologists, geneticists, contract archeologists, the local, regional and national government agencies, local and national government, universities, and representatives of the major religions. The project has resulted in the creation of a rich database with many collections available for study. The database was created using the open-source Arches data management platform that is freely available for organizations worldwide to configure in accordance with their individual needs and without restrictions on its use. Each collection is linked to information about the excavation and the site the remains originate from, its size and time period. In addition, a research potential tab reveals whether any analyses were performed, and whether excavation notes are available with the assemblage. The database currently contains 742 collections, ranging in size from 1 to over 1000 individuals. New collections will continue to be added when new assemblages are excavated and studied. The database can also be expanded to include human remains collections from other regions and other material categories, such as archaeozoological collections.