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...

A simple technique is described for the preparation of collagen substrata containing 0 1% of collagen by weight, in the form of native bundles with a 640 A period, the substrata are similar in these respects to soft-tissue matrices These substrata are hydrated collagen lattices (HCLs) in which the watery milieu is held within a fibrous collagen net mainly by capillary forces. HCLs have been characterized in terms of the course of coltagen precipitation and aggregation, ultrastructure, and their stability under various conditions. The ways in which HCLs can be employed as both two-and three-dimensional substrata in cell behavioral studies are illustrated with some preliminary observations on the form, motility, adhesion, and growth of human diploid ceils and two lines of malignant ceils.

Wilms' tumour is an embryonic kidney tumour thought to arise through aberrant mesenchymal stem cell differentiation and to result from loss of function of a 'tumour suppressor' gene(s). Both sporadic and syndrome-associated Wilms' tumours are accompanied by an increased frequency of abnormalities of the urinary tract and genitalia. Deletional analysis of individuals with the WAGR syndrome (for, Wilms' tumour, aniridia, genitourinary abnormalities and mental retardation) showed that a Wilms' tumour gene lies at chromosomal position 11p13. This led to the isolation of a candidate Wilms' tumour gene, encoding a zinc-finger protein which is likely to be a transcription factor. To gain insight into the role of this candidate gene in normal development and tumorigenesis, we have now performed in situ messenger RNA hybridization on sections of human embryos and Wilms' tumours. The candidate Wilms' tumour gene is expressed specifically in the condensed mesenchyme, renal vesicle and glomerular epithelium of the developing kidney, in the related mesonephric glomeruli and in cells approximating these structures in tumours. The other main sites of expression are the genital ridge, fetal gonad and mesothelium. These data suggest that (1) this candidate is indeed a Wilms' tumour gene, (2) the associated genital abnormalities are pleiotropic effects of mutation in the Wilms' tumour gene itself, in support of recent genetic analysis, and (3) this gene has a specific role in kidney development and a wider role in mesenchymal-epithelial transitions.

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An ontology for cell types

We describe an ontology for cell types that covers the prokaryotic, fungal, animal and plant worlds. It includes over 680 cell types. These cell types are classified under several generic categories and are organized as a directed acyclic graph. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases. The ontology is freely available at http://obo.sourceforge.net/ and can be viewed using standard ontology visualization tools such as OBO-Edit and COBrA.

The early chick cornea is composed of an acellular collagenous stroma lined with an anterior epithelium and a posterior endothelium. At stage 2?-28 of development (51/2 days), this stroma swells so that the cornea is 75 120 #m thick. At the same time, fibroblasts that originate from the neural crest begin to invade this stroma. Using Nomarski light microscopy, we have compared the behavior of moving cells in isolated corneas with the migratory activities of the same cells in artificial collagen lattices and on glass. In situ, fibroblasts have cyclindrical bodies from which extend several thick pseudopodia and/or finer filopodia. Movement is accompanied by activity in these cytoplasmic processes. The flat ruffling lamellipodia that characterize these cells on glass are not seen in situ, but the general mechanism of cell movement seems to be the same as that observed in vitro: either gross contraction or recoil of the cell body (now pear shaped) into the forward cell process, or more subtle "flowing" of cytoplasm into the forward cell process without immediate loss of the trailing cell process. We filmed collisions between cells in situ and in three-dimensional collagen lattices. These fibroblasts show, in their pair-wise collisions, the classical contact inhibition of movement (CIM) exhibited in vitro even though they lack ruffled borders. On glass these cells multilayer, showing that, while CIM affects cell movement, fibroblasts can use one another as a substratum. Postmitotic cells show CIM in moving away from each other. Interestingly, dividing cells in situ do not exhibit surface blebbing, but do extend filopodia at telophase. The role of CIM in controlling cell movement in vivo and in vitro is stressed in the discussion.

The Edinburgh MouseAtlas Project (EMAP) is a time-series of mouse-embryo volumetric models. The models provide a context-free spatial framework onto which structural interpretations and experimental data can be mapped. This enables collation, comparison, and query of complex spatial patterns with respect to each other and with respect to known or hypothesized structure. The atlas also includes a time-dependent anatomical ontology and mapping between the ontology and the spatial models in the form of delineated anatomical regions or tissues. The models provide a natural, graphical context for browsing and visualizing complex data. The Edinburgh Mouse Atlas Gene-Expression Database (EMAGE) is one of the first applications of the EMAP framework and provides a spatially mapped gene-expression database with associated tools for data mapping, submission, and query. In this article, we describe the underlying principles of the Atlas and the gene-expression database, and provide a practical introduction to the use of the EMAP and EMAGE tools, including use of new techniques for whole body gene-expression data capture and mapping.