How to use hierarchical texts
INDEX
- Menu Buttons
To quit or to view this on-line help (Java version only).
- Control Buttons
To control handling of hierarchical texts.
- Hierarchical Texts
The hierarchical text data.
- Text Search
Keyword search against hierarchical texts.
- Pathway Map Search
EC number search against pathway maps.
- Genome Map Search
Gene location search against genome maps (Java version only).
1. Menu Buttons (Java version only)
- Help
To view this on-line document.
- Quit
2. Control Buttons
- 1st Level, 2nd Level, etc.
To display the entire hierarchical text data up to the given level (see below).
- Search
- Pathway
When a set of text lines is pre-selected, all the EC numbers appearing in the set are automatically placed in the search window (Java version only; it is necessary to manually copy and paste in the CGI version).
- Genome (Java version only)
When a set of text lines is pre-selected, all the gene IDs in the set are automatically placed in the search window.
3. Hierarchical Texts
The hierarchical text is a collection of lines, each of which is assigned a level in the hierarchy.
The lowest level is the actual body of text data, which is usually a table consisting of the accession number and the definition, for example, the gene accession number and the definition of the gene.
The higher levels are the headers and subheaders hierarchically defining the classification, for example, Riley's classification of E.coli genes or SCOP's classification of protein structures.
When the hierarchical text is called, only the top levels of the hierarchy is displayed at first.
- To unfold a specific branch of the tree, click on the header or subheader line.
- To fold the expanded branch, click again on the same header or subheader line.
- To unfold or fold the entire hierarchical text up to a given level, use the level button shown above.
You may click on the marked items in the lowest level of the hierarchy to retrieve.
For example, the sequence data can be obtained by clicking on the gene ID and the information of enzymes, compounds, and chemical reactions by the EC number.
At this point the user has entered the DBGET integrated database retrieval system where related entries can be obtained from a number of database.
4. Text Search
When the "Search" button is clicked in the main window shown at the top of this document, the following window will appear for the keyword search against hierarchical texts.
Enter any keywords in the search box and hit return or click on "Search".
Then you will receive the search result in the top window used for launching
the hierarchical text.
When multiple keywords are specified, they are taken together with AND operation.
There are three options for the hierarchical text search:
- Accession and definition is the default mode used to search whole texts in the lowest level.
- Accession only is used to search accessions in the lowest level. This is useful when you know beforehand, for example, gene accessions.
- Headers only is used to search whole texts except the lowest level. This is used for identifying, for example, all genes in one functional category.
5. Pathway Map Search
When the "Pathway" button is clicked in the main window shown at the top of this document, the following window will appear for the EC number search against pathway maps.
Enter EC numbers in the search box and click on "Search".
Then you will receive the search result in a different window.
In the Java version only, the user may select beforehand a set of lines by mouse clicking and dragging with the shift key down.
The text selection appears in the following way.
After the selection, click the "Pathway" button.
Then, all the EC numbers appearing in the selected lines will be automatically placed in the search window.
Under the CGI version this process must be performed manually; namely, copy and paste a block of text using the feature provided by the operating system.
6. Genome Map Search (Java version only)
When the "Genome" button is clicked in the main window shown at the top of this document, the genome map window that corresponds to the current gene catalog will appear.
(If the genome map has not been called yet, this will take a while for loading the data.)
Enter gene IDs in the search box and hit return or click on "Show".
Of course, you may pre-select a set of genes by shift-down clicking on the hierarchical texts in order to automatically fetch the gene IDs to be searched.
The result will appear as red spots on the genome map.
Last updated: April 3, 1997
