The database can be thought of as recursive sets subdividing the embryo into anatomical components at each Carnegie Stage. Of course, this is not a good representation of reality, because it obscures the tissue continuity through the stages it appears in, and some tissues appear more than once for ease of navigation. (E.g. do you define the subsets in a geographical, functional, morphological or other manner.) The important issues of philosophically correct taxonomic approach versus correct database practice of one entity, one object, have frequently been ignored in this database in deference to the priorities of ease of use and financial reality. Anybody who is interested in pursuing these issues may wish to contact the Mouse Atlas Project, where many of them are being actively tackled.
To illustrate the recursive set hierarchy, I will take an example from CS07 (Carnegie Stage 7). At this point the top level divisions are:
cavitiesIf we recurse one level down the hierarchy of cavities, we find that cavities contains:
embryo
extraembryonic tissue
amnioticetc, etc. Go to the hierarchical search form and click on CS07 box, then the submit box, and you will see the full stage displayed.
secondary yolk sac
Whilst a bare listing of the tissue hierarchies may be useful, it was felt that there were frequently issues that required brief notes on the underlying processes, so if a component is underlined, it means that clicking on it will access a note specific to that point in development. The notes will often contain links to other notes and also to the references list.
The number of options on the advanced query form is intimidating at first glance, but although the default options are probably what is most often required, being able to customise a seach to produce only the data required is very valuable.
At the top of the form is the Carnegie Stage chooser:
The default option is to choose one of more stages from the ones listed. Notice that Choose and All have a slightly different look to them than the CSXX stage boxes, and that the Choose box has been selected. This is because they are meta controls, and Choose has been chosen by default. If All is selected then it doesn't matter which of the Carnegie Stages are selected. To go back to selecting just a few stages click on the Choose button again. Note that if you have selected a CSXX box you can deselect it by clicking on it again.
Next comes a choice of showing or hiding the links to notes and the option to limit the search to a number of levels.
The first of these is fairly obvious, but the second requires a bit more explanation. Once one reaches the later stages, perhaps all that is required is an overview before doing a more detailed search on a more specific area. The default is to search out all components, however deeply nested the substructures, but if you want only to see things to a few levels try selecting a number of levels of subset nesting you require to see in the hierarchy.
Next comes sub-component selection.
Sorry, this is not yet implemented.
If you want to select only certain areas to view - perhaps through several stages to see how they change, you can type in a subcomponent definition, and only that part of the hierarchy will be displayed.
You can discover exactly what the components are called by doing a depth limited search, and then typing the component into the box e.g.
in the case of the earlier example at CS07.
Finally the fairly self explanatory Reset, Search and Help buttons.
Reset will return all the fields in the form to their default state. Search will submit your query to the database (some browsers may require you to confirm it depending on how their security preferences are set). Help should get you this page.
This is intended for finding a component when you don't really know where to start. If you want to know where to start looking liver as an example you can just type in liver and submit the query. What will be returned is the Carnegie Stage at which liver appears at some point in the name of one or more tissues. You could equally well use this for examples such as somite 13. Note how important the 13 might be!
There is a list of synonyms supplied to help this process.
This is by no means a comprehensive list, but will show some useful techniques to better use your browser.