Introduction

Purpose
Our aim is to build a generally accepted nomenclature for the components of the mouse embryo, at successive stages from fertilization to birth. The purpose is to provide a standardized vocabulary that will be a framework for describing patterns of gene expression and other processes occurring during normal and abberant development.

Process
We will do this in three phases.

• Production of the basic version, which will establish the principal names and organization.
• Refinement, which will add further names, alternative ways of organizing the hierarchy, and information on lineage and tissue derivation.
• Editing, which will implement changes and improvements in the light of feedback and experience.

Organization of the data

The list of components was made by Matt Kaufman, Jonathan Bard, Renske Brune, Jane Quinn and Duncan Davidson. We have also received helpful comments and suggestions from Mary Mangan and Martin Ringwald at the Jackson Laboratory who are preparing a database of adult mouse anatomy nomenclature. The two groups are working closely to ensure that the embryonic and adult databases are consistent. We used names from "The Atlas of Mouse Development" (Kaufman, 1992), with additional names as required. Our aim was to assign a name to every part of the embryo with a reasonably consistent level of resolution, similar to that of the whole-embryo sections in "The Atlas of Mouse Development", M.H. Kaufman, Academic Press, London, 1992. To enable gene-expression domains to be assigned uniquely, the named subdivisions of an anatomical component do not overlap.

Please note that in some cases not all subregions of a tissue have been given specific names; for example, the surface epithelium comprises named subcomponents plus regions that are as yet unnamed. When the database is used ito describe gene expression domains etc., unnamed regions will be provided in order to explicitly assign gene expression domains pending further naming of regions within such a component. For the present, however, unnamed regions do not appear explicitly and are simply subsumed under the name of the parent component.

Naming
Singular names are used throughout, to facilitate text strings searches. Where there is obvious right/left duplication (limbs, either side of the neural tube, the somites, ganglia, etc.) only a single name is given for the two.

Associated with some of the tissue names (to be extended as required) are common synonyms. These names will be usable as alternative terms for querying and submitting data. The current list of synonyms can be seen on the automatically generated list.

Temporal organization and grouping
In the database, anatomical components are listed for each Theiler Stage. The list includes all those components that are present during that stage, for example, both the otic placode and otic pit will be included if the placode develops into the pit during this stage. If components are found only at particular parts of a stage this is noted in the database with one of two values: early and late. Similarly, where different phases of development of a component are represented in space (for example, along the A-P axis) the names representing these different phases are listed under the same Theiler stage. Many structures differentiate or sufficiently change their character during development to justify a change of name. Most of these changes are obvious. However, there are instances where the change in character is too gradual to justify an abrupt change of name: we have tried to rename a component when there is a sound biological justification to do so. In several such cases the times at which names should be changed are debatable: examples are the mesoderm (changes to mesenchyme, mesothelium, etc.) and ectoderm (changes to epithelium, etc.). In later versions these changes will be marked by lineage links. (Note: there is some debate about the usefulness of the terms ectoderm, mesoderm, and endoderm. We have kept them because they are in common use.) Each component is listed from the earliest stage when it can be reasonably identified morphologically, even in cases where the definitive morphology becomes clear at a later stage. A few structures, for example, in the brain, have been named according to their future identity in order to facilitate regional descriptions without intending to imply precise demarcation.

Spatial organization and grouping
The list is currently organised as a spatial hierarchy, with the proviso that some components are grouped under "organ systems" in order to provide a more convenient view of the data. The hierarchy starts with the embryo vs. extra-embryonic tissue and ends with individual tissues. It is not a lineage hierarchy, though some of the terms have lineage implications, for example, ectoderm, mesoderm, etc. (see above note). Within each "branch" of the tree, components at the same level of the hierarchy are organized alpha-numerically. Though this leads to obvious difficulties in presenting the order of components in space (e.g. foregut, hindgut, midgut is alphabetical rather than spatial), similar problems arise with any ordering system. The advantage of the alpha-numeric system is that any user can find a component according to a simple rule. We intend to create alternative views of the list (i.e. different ways of grouping the components - for example, by tissue type or organ systems) and to provide the user with the means to create their own views. These new groupings will include information on the derivation of one component from another and will enable the user to follow the "lineage" of components to the extent that reliable information is available.

Specific points

We have excluded extraembryonic membranes after Stage 12. The "painted"domains of the 3D anatomical atlas of mouse development correspond to the anatomy names. However, some of the components listed will not be painted on the atlas because they are too small or have a stochastic "pepper and salt" distribution (for example, neural crest-derived cells mixed with mesodermally-derived mesenchyme in the 1st branchial arch). In these cases, they will be included as part of a larger painted domain (for example, 1st arch mesenchyme).

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