- What is an "entry" in the database?
-
Binding assays: In a gel
shift, for example, it is the data from 1 column on the gel.
DNA transfer experiment: An entry has only 1 construct, but a construct
can be used in more than 1 entry. An entry has only 1 conclusion or result.
An entry is one beta-gal measurement that came from one construct.
- Selection boxes
- For fields with a controlled vocabulary there is a list of terms or
expressions which are used to describe the data in the field. These fields
can be queried on using the scrolling lists and popup menus. Popup menus allow
only 1 item to be selected at a time. Scrolling lists can allow multiple items
to be selected, but not all do. On the query page all the scrolling lists
except the ones under Feature allow multiple selections. See the
FAQ for
more help on Feature section. Multiple selections
within a box are joined with an "OR".
How to select multiple items varys with the computer platforms.
For Netscape and Internet Explorer:
- Windows/PC (Windows 95/98/NT): Hold down the "control" key while clicking the mouse. This key is labeled "Ctrl" on the keyboards for our PCs. If you hold down the "shift" key, all items between the first and second choices will be selected.
To make corrections you must "start over" and click on the first item you wish to select and the rest will automatically be unselected. Then continue to select as before. If you decide to not select any items in this box then select the blank space.
- MacOS/Macintosh: Hold down the "command/apple" key while clicking the mouse. This is the key with the apple on it. If you hold down the "shift" key, all items between the first and second choices will be selected.
To make corrections you must "start over" and click on the first item you wish to select and the rest will automatically be unselected. Then continue to select as before. If you decide to not select any items in this box then select the blank space.
- Unix: Click on as many items as needed each will be added. To remove an item click on it a second time.
Even for the boxes where you select only one, the blank space can be used to unselect a previous choice.
- Text boxes
- The data entered in the fields represented by text boxes are freely typed in
by the data enterer.
The program searches for what is typed in the box within the entry. For example under DNA fragment,
other region name if "neo" is typed it will return entries with names such as "Neo" and
"E. coli neo". It looks for exactly what you type with the exception of letter case which is explained later. It is better to type less instead of more if you are unsure of the exact wording used. To continue with the earlier example if "E coli neo" had been typed
(notice the missing period) neither entry would have been found.
In most of the text boxes you can look for more than one item by typing an AND or OR between the items you are searching for. For example the name could be queried as "coli OR neo".
The case of the words AND and OR does not matter but there must be at least one space before and after the word.
The text boxes for ranges such as the start and stop following
an origin are for numbers only. To search for an exact number enter that number under
both start and stop. To search for all numbers larger than a given number put that number
in the start box. To search for all numbers less than a given number put that number in
the stop box.
- Options next to submit button
- There are some options between the horizontal lines with the submit button which
affect the query and how the data is displayed.
Select the way the data from different boxes will be joined either with an AND or an OR. Letter case of text typed in text boxes can be ignored or search for exact case only.
With the default, ignore case the examples under text boxes above would find all the
entries by searching on "neo". With exact case "Neo or neo" would have to be
used. This doesn't affect what is selected in a selection box. The display format can
be chosen as well.
- Display formats
- The default display format is a Summary table which lists each reference that has
data that meets the criteria of the query. On the summary table there is a button for
each reference to
view all the data (all data format) that is from that reference and meets the query
criteria.
The all data format displays all the fields from the database in an outline
format and if many entries are returned can be a rather large page. These pages are
divided up with 250 entries per page and buttons to view other pages of data. The
detailed display options can be used to limit the fields displayed in this display format.
The last display format is the graphical display. The region to be displayed in the
graph must be entered below where the format is chosen. For each entry that meets the query criteria a link is provided
to the complete data entry (all data format). This link will open a new browser window
so it can viewed at the same time as the graphs. This display has a graph displaying the requested region
and the data from outside that region listed on the left side of the graph. At the top
of the page there is a graph of the region with the landmarks for this region drawn
on it. The boxes for the landmarks are clickable and will bring up the data about that
landmark in the same browser window as the links for the entries.
Also included in the format are qualitative results for the entry and the medline id which is a link to the PubMed entry. Only 100 entries are displayed per page because of
the download time for all the images. If there are more than 100 entries that meet
the query criteria there will be buttons at the bottom to view the other pages of graphs.
- Detailed display options
- These checkboxes and radio buttons allow fields to be removed from
the all data display. If the name of the field is checked it will be
displayed. Clicking on a checked box will remove the checkmark and
prevent that field or fields from being displayed. The radio buttons
allow different categories of some fields to be displayed or skipped.
For example, under References you can select whether to have all the
authors displayed, only the first author or none of the authors.
Clicking on one item in a group of radio buttons will unselect the
previous selection as well as select the one that was clicked.
These options affect the data which is directly viewed in the all data format and
the data that is first viewed in the summary table format and then the all
data format via a reference's button. Viewing all the data data via the button
from the summary page would be an example of a time the reference data is likely not
needed. All the data on the page will belong to the one reference in the
row with the button that was just clicked.
- Origins
- All regions are described with respect to an origin. When an offset
between 2 origins can be calculated the program will search for region
using all the origins that the region can be translated to. Entries
entered using the "humhbb orig" can be searched for and found
with regions using the humhbb, Bulger's humHBB_ORGs_cen, human beta cap,
human Agamma cap, and human Ggamma cap origins.
Origins have direction. In the graphical display the genes and other
indicated regions may not appear in the customary order if the region is
displayed using a reverse origin. Because of this, reverse origins are
indicated in the landmarks graphic by red text saying "reverse complement".