The parasite Plasmodium falciparum is responsible for hundreds of millions of cases of malaria, and kills more than one million African children annually. Here we report an analysis of the genome sequence of P. falciparum clone 3D7. The 23-megabase nuclear genome consists of 14 chromosomes, encodes about 5,300 genes, and is the most (A + T)-rich genome sequenced to date. Genes involved in antigenic variation are concentrated in the subtelomeric regions of the chromosomes. Compared to the genomes of free-living eukaryotic microbes, the genome of this intracellular parasite encodes fewer enzymes and transporters, but a large proportion of genes are devoted to immune evasion and host–parasite interactions. Many nuclear-encoded proteins are targeted to the apicoplast, an organelle involved in fatty-acid and isoprenoid metabolism. The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria.

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or 'ontologies'. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium is pursuing a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing coordinated reform, and new ontologies are being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality. We describe this OBO Foundry initiative and provide guidelines for those who might wish to become involved.In the search for what is biologically and clinically significant in the swarms of data being generated by today's high-throughput technologies, a common strategy involves the creation and analysis of 'annotations' linking primary data to expressions in controlled, structured vocabularies, thereby making the data available to search and to algorithmic processing 1 . The most successful such endeavor, measured both by numbers of users and by reach across species and granularities, is the Gene Ontology (GO) 2 . There exist over 11 million annotations relating gene products described in the UniProt, Ensembl and other databases to terms in the GO3, of which half a million have been manually verified by specialist curators in different modelorganism communities on the basis of the analysis of experimental results reported in 52,000 scientific journal articles (http://www.ebi.ac.uk/GOA/). Data related to some 180,000 genes have been manually annotated in this way, an endeavor now being refined and systematized within the Reference Genome Project (US National Institutes of Health National Human Genome Research Institute grant 2P41HG002273-07), which will provide comprehensive GO annotations for both the human genome and a representative set of model-organism genomes in support of research on the primary molecular systems affecting human health. From retrospective mapping to prospective standardizationThe domain of molecular biology is marked by the availability of large amounts of well defined data that can be used without restriction as inputs to algorithmic processing. In the clinical domain, by contrast, only limited amounts of data are available for research purposes, and these still consist overwhelmingly of natural language text. Even where more systematic clinical data are available, the use of local coding schemes means that these data do not cumulate in ways useful to research 4 . One approach to solving this problem is the Unified Medical Language System (UMLS) 5 , a compendium of some 100 source vocabularies combined through a process of...

AmiGO is a web application that allows users to query, browse and visualize ontologies and related gene product annotation (association) data. AmiGO can be used online at the Gene Ontology (GO) website to access the data provided by the GO Consortium1; it can also be downloaded and installed to browse local ontologies and annotations.2 AmiGO is free open source software developed and maintained by the GO Consortium.Availability: http://amigo.geneontology.orgDownload: http://sourceforge.net/projects/geneontology/Contact: sjcarbon@berkeleybop.org