HOW MANY SPECIES OF ALGAE ARE THERE?

Algae have been estimated to include anything from 30,000 to more than 1 million species. An attempt is made here to arrive at a more accurate estimate using species numbers in phyla and classes included in the on‐line taxonomic database AlgaeBase ( http://www.algaebase.org ). Despite uncertainties regarding what organisms should be included as algae and what a species is in the context of the various algal phyla and classes, a conservative approach results in an estimate of 72,500 algal species, names for 44,000 of which have probably been published, and 33,248 names have been processed by AlgaeBase to date (June 2012). Some published estimates of diatom numbers are of over 200,000 species, which would result in four to five diatom species for every other algal species. Concern is expressed at the decline and potential extinction of taxonomists worldwide capable of improving and completing the necessary systematic studies.     

GeneCruiser: a web service for the annotation of microarray data

SUMMARY: GeneCruiser is a web service allowing users to annotate their genomic data by mapping microarray feature identifiers to gene identifiers from databases, such as UniGene, while providing links to web resources, such as the UCSC Genome Browser. It relies on a regularly updated database that retrieves and indexes the mappings between microarray probes and genomic databases. Genes are identified using the Life Sciences Identifier standard. AVAILABILITY: GeneCruiser is freely available in the following forms: Web service and Web application, http://www.genecruiser.org; GenePattern, GeneCruiser access has been integrated into our microarray analysis platform, GenePattern. http://www.genepattern.org.     

Taxonomic and Distributional Databases of Fishes in Taiwan

The fishes of Taiwan comprise total 2450 species in 250 families, about 1/10 of the world's fishes. Curatorial and distributional data of Taiwanese fish have been integrated into a database that can be accessed interactively on the Internet at http://fishdb.sinica.edu.tw. The database includes the following items: basic information and specimen photo of each species, distributional database, bibliographic database, curatorial database, inquiring system for Chinese fish names of the world fishes, and new version of erratum of Fishes of Taiwan. The above regional database of Taiwanese fishes provides hyperlinks to fish data for each species in the global fish data, FishBase, of ICLARM (http://www.fishbase.org). Through the collaboration with FishBase and other global networks for taxonomic purposes, like Species 2000, BioNet, or GBIF (Global Biodiversity Information Facilities), users in the world can also obtain updated data provided by Taiwan. We hope our experience with database establishment can be used as a model to help other countries to develop their own regional fish databases or even to build up databases of other groups of organisms. There should be one good approach for all people in the world for sharing complete and updated biodiversity information via the Internet.     

The EMBL nucleotide sequence database.

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl. html ) constitutes Europe's primary nucleotide sequence resource. DNA and RNA sequences are directly submitted from researchers and genome sequencing groups and collected from the scientific literature and patent applications (Fig. 1). In collaboration with DDBJ and GenBank the database is produced, maintained and distributed at the European Bioinformatics Institute. Database releases are produced quarterly and are distributed on CD-ROM. EBI's network services allow access to the most up-to-date data collection via Internet and World Wide Web interface, providing database searching and sequence similarity facilities plus access to a large number of additional databases.     

MPSS: an integrated database system for surveying a set of proteins

SUMMARY: We design and implement an integrated database system called 'multi-protein survey system' (MPSS), which provides a platform to retrieve information about many proteins at a time. This system integrates several important and widely used databases including SwissProt, TrEMBL, PDB and InterPro, plus useful references such as GO and KEGG to other databases. Users may submit a group of protein IDs, entry names, SwissProt/TrEMBL accession numbers or GenBank GIs through MPSS' web interface, and obtain protein annotation information from public databases and pre-computed molecular properties speedily. MPSS can also supply comprehensive information about query proteins, including 3D structures, domains, pathway, gene ontology and visual presentation of mapping to the GO tree and KEGG pathway, to provide an up-to-date view of available knowledge with regard to the structures and molecular functions of proteins under study. AVAILABILITY: MPSS is freely accessible at http://www.scbit.org/mpss/     

BioQuery: an object framework for building queries to biomedical databases

SUMMARY: BioQuery is an application that helps scientists automate database searches. Users can build and store queries to public biomedical databases, and receive periodic updates on the results of those queries when new data is available. The application is implemented on a portable object framework that can provide database-searching capability to other applications. This framework is easily extensible, allowing users to develop plug-ins that provide access to new databases. BioQuery thus provides end-users with a complete database searching interface and updating service, and gives developers a toolkit to provide database-searching capability to their applications. AVAILABILITY: Free to all users: http://www.bioquery.org.     

Swiss EMBnet node web server

EMBnet is a consortium of collaborating bioinformatics groups located mainly within Europe (http://www.embnet.org). Each member country is represented by a 'node', a group responsible for the maintenance of local services for their users (e.g. education, training, software, database distribution, technical support, helpdesk). Among these services a web portal with links and access to locally developed and maintained software is essential and different for each node. Our web portal targets biomedical scientists in Switzerland and elsewhere, offering them access to a collection of important sequence analysis tools mirrored from other sites or developed locally. We describe here the Swiss EMBnet node web site (http://www.ch.embnet.org), which presents a number of original services not available anywhere else.     

Proteogenomics in the context of the Human Proteome Project (HPP)

Introduction: The technological and scientific progress performed in the Human Proteome Project (HPP) has provided to the scientific community a new set of experimental and bioinformatic methods in the challenging field of shotgun and SRM/MRM-based Proteomics. The requirements for a protein to be considered experimentally validated are now well-established, and the information about the human proteome is available in the neXtProt database, while targeted proteomic assays are stored in SRMAtlas. However, the study of the missing proteins continues being an outstanding issue.

Areas covered: This review is focused on the implementation of proteogenomic methods designed to improve the detection and validation of the missing proteins. The evolution of the methodological strategies based on the combination of different omic technologies and the use of huge publicly available datasets is shown taking the Chromosome 16 Consortium as reference.

Expert commentary: Proteogenomics and other strategies of data analysis implemented within the C-HPP initiative could be used as guidance to complete in a near future the catalog of the human proteins. Besides, in the next years, we will probably witness their use in the B/D-HPP initiative to go a step forward on the implications of the proteins in the human biology and disease.     

Larval host records of butterflies in Japan

Using Japanese literature, we created a consolidated list of host records of butterflies in Japan. The list used the host records described in eight major illustrated reference books, two checklists, and 14 other pieces of literature. The presence of larvae on plants, the observation of larvae eating plants or insects in the field were considered as host records. We collected all species recorded in Japan. Scientific, family, and Japanese names of butterflies were consolidated using the BINRAN database (http://binran.lepimages.jp/). Scientific and Japanese names of host plants were based on the YList database (http://ylist.info/). If scientific names of host plants were not found in YList, we used scientific names based on The Plant List (http://www.theplantlist.org/). Family names of host plants were based on the Catalogue of Life database (http://www.catalogueoflife.org/). Scientific, family, and Japanese names of host insects were based on the MOKUROKU database (http://konchudb.agr.agr.kyushu-u.ac.jp/mokuroku/) for Hymenoptera and the catalogue of the Paraneoptera of Japan published by the Entomological Society of Japan for Hemiptera. We also provided the references of each host record and the original names described in the referred literature. Two datasets, HostDB and ReferenceDB, were created to include 3600 records of butterfly larval hosts in Japan, along with scientific and Japanese names of each species and a literature list. These datasets will be useful for basic and applied biological studies of butterflies. Data files are stored in the Ecological Research Data Archives (http://db.cger.nies.go.jp/JaLTER/ER_DataPapers/) and available from http://hostbj.lepumus.net/. These datasets are published under the Creative Commons License Attribution-ShareAlike 4.0 (CC BY-SA, https://creativecommons.org/licenses/by-sa/4.0/).     

PartiGene--constructing partial genomes

Expressed sequence tags (ESTs) offer a low-cost approach to gene discovery and are being used by an increasing number of laboratories to obtain sequence information for a wide variety of organisms. The challenge lies in processing and organizing this data within a genomic context to facilitate large scale analyses. Here we present PartiGene, an integrated sequence analysis suite that uses freely available public domain software to (1) process raw trace chromatograms into sequence objects suitable for submission to dbEST; (2) place these sequences within a genomic context; (3) perform customizable first-pass annotation of the data; and (4) present the data as HTML tables and an SQL database resource. PartiGene has been used to create a number of non-model organism database resources including NEMBASE (http://www.nematodes.org) and LumbriBase (http://www.earthworms.org/). The packages are readily portable, freely available and can be run on simple Linux-based workstations. AVAILABILITY: PartiGene is available from http://www.nematodes.org/PartiGene and also forms part of the EST analysis software, associated with the Natural Environmental Research Council (UK) Bio-Linux project (http://envgen.nox.ac.uk/biolinux.html).     

PSPDB: Plant Stress Protein Database

Plants produce various proteins to overcome biotic and abiotic stresses. Current plant stress databases report plant genes without protein annotations specific to these stresses. To date, according to our findings, a unique plant stress protein database for both biotic and abiotic stresses is not available explicitly for plant biologists that describe linking out to other related databases. This need initiated us to formulate a distinctive database that includes important resources for stress-based factors. We developed the Plant Stress Protein Database (PSPDB), a web-accessible resource that covers 2,064 manually curated plant stress proteins from a wide array of 134 plant species with 30 different types of biotic and abiotic stresses. Functional and experimental validation of proteins associated with biotic and abiotic stresses has been employed as the sole criterion for inclusion in the database. The database is available at http://www.bioclues.org/pspdb/.     

The EMBL Nucleotide Sequence Database: major new developments

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) incorporates, organizes and distributes nucleotide sequences from all available public sources. The database is located and maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK. In an international collaboration with DDBJ (Japan) and GenBank (USA), data are exchanged amongst the collaborating databases on a daily basis to achieve optimal synchronization. Webin is the preferred web-based submission system for individual submitters, while automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via FTP, Email and World Wide Web interfaces. EBI's Sequence Retrieval System (SRS) integrates and links the main nucleotide and protein databases plus many other specialized molecular biology databases. For sequence similarity searching, a variety of tools (e.g. Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. All resources can be accessed via the EBI home page at http://www.ebi.ac.uk.     

Online Mendelian Inheritance in Animals (OMIA): a comparative knowledgebase of genetic disorders and other familial traits in non-laboratory animals

Online Mendelian Inheritance in Animals (OMIA) provides up-to-date information on inherited disorders and other familial traits in non-laboratory animals. It is freely available online at http://www.angis.org.au/omia. With a strong emphasis on comparative biology, OMIA is modelled on, and reciprocally hyperlinked with, Online Mendelian Inheritance in Man (OMIM). It provides a comprehensive catalog of animal models of human inherited disorders, and also provides comprehensive access to information on potential human homologues of inherited disorders and traits in animals. Because its whole structure is based on comparative biology, it provides phenotypic information in a format that is complementary to all the relevant mapping and sequence databases now existing or being created across the animal kingdom.