Mapping cellular signaling.

Cellular signaling is an area of extensive and active research. It is also a complex topic, with information from many different cell types and organisms all contributing to the plethora of data available in this multidisciplinary field. In this issue, "Mapping Cellular Signaling," Science ( ) and STKE bring you a series of roadmaps to some signaling processes important in many cell types, signaling specific to immune cells, signaling in development and neural differentiation, and signaling in plants. The Viewpoints in Science provide both a broad overview of exciting developments in the field and new insights into the biological relevance, whereas the associated Connections Maps provide details about the molecular components involved in these pathways. The Connections Map database is intended to provide a mechanism by which potentially overwhelming amounts of information on signal transduction can be organized by experts in the field in way that is accessible to a broad audience of both experts and novices. [The Connections Maps][1] are dynamic interactive entry points for the information that is contained in the underlying database. This information represents a compendium of expert knowledge about the components involved in receiving, processing, and transmitting cellular signaling events and the relations between these components. The components are organized into pathways, allowing the interactions between components to be illustrated and allowing a convenient visual tool for beginning to understand the complexity of cellular signaling systems. The pathways are more simplified than what actually occurs within any given cell, but they help to place components into a context for understanding cellular functions. Experts in the field, whom we call Pathway Authorities, supply the data about the components, their relations, and the pathways in which they occur. This information is updated as often as is deemed necessary by the authority. New information in the database is immediately available through the Connections Maps because of the dynamic interface between the database and the Connections Maps as viewed at STKE. In order to understand the presentation of the information through the Connections Maps, it is helpful to understand the underlying structure for the information in the database. The information in the Connections Maps is organized into categories we call "canonical" and "specific." Canonical information is based on consensus knowledge from many cell types in many organisms. Specific information represents the details about a specific component as it exists in a particular cell at a particular developmental stage in a particular organism. The basic element in the Connections Map database is a component, which can be either canonical or specific, and which represents the basic attributes of that signaling entity. Components are pathway-independent in that they are found in nature (and in the Connections Maps) incorporated into multiple pathways. Once a component is incorporated into a pathway by an authority, we create a new data record to store information that is relevant to the function of that component in the context of the particular pathway. Thus, the component now has two associated records: (i) the general or pathway-independent information and (ii) pathway-dependent information that pertains to its occurrence in a particular pathway, but may not be generalizable to that component's roles in other pathways. In addition to information about the components, the database contains information about the interactions among components. The information about the components and the relations between components is elucidated with a combination of natural language descriptions, attributes defined by terms in controlled vocabularies, selected references, and links to external databases, such as the Entrez database of gene and protein sequences and FlyBase. The pathways presently in the Connections Maps represent a small fraction of the total we expect to amass. These pathways were started by scientists willing to be pioneers in this novel method for systematizing information and in this new form of authorship. Authorities are at work on many more pathways, including mitogen-activated protein kinase pathways, specific G protein-coupled receptor pathways, intrinsic apoptosis pathways, and many others. The editors and Authorities invite you to explore the pathways. Although each of the pathways highlighted in this week's focus issue has been reviewed by scientists in the field, the community is encouraged to send in feedback that will help validate and authenticate the information in the database, and thus to join us in the process of building what promises to be an incredible resource for scientists, educators, students, or anyone interested in cellular regulation. [1]: http://stke.sciencemag.org/cm/