TRANSPATH® Professional SEARCH ENGINE
 

Search in one table (customizable search)


The search engine should enable you to search and browse the TRANSPATH database. By default, it will also query NetPro™ data (if licensed). This option can be switched off. Choose the table you are interested in, using the menu on the left. This will open the respective search form.


Fig.1 Molecule Search Form

Enter the terms with which you want to query TRANSPATH in the input boxes on the left. The Search Field, in which you want to search, can be selected to the right of the input fields. For a description of the various fields, please see the description for the respective table in the documentation. (The following fields are always conjointly searched: in the MOLECULE table, the "molecule name" field together with the "synonyms" field; and in the GENE table, the "gene name" field together with the "synonyms" field).
You can specify the columns you want to appear in the results list by selecting fields in the list box (Output Fields) on the right. Choose multiple output fields by holding the CTRL (STRG) key while clicking.
After you have made your choice, please use the Submit Query button to start your search.
Example 1 In this example we want to find all reactions in which the G-protein Ras is involved.
We click on REACTION and enter Ras as the search term and choose Name as the "Search Field".
The result will be a long list of entries (This example output list is not operable).
 

The number of hits is indicated at the top of the search result page. Per default, 20 hits are displayed on one page to enhance clarity. The search result can be sorted in alphanumeric order by clicking on a column heading. Clicking on an accession number will result in retrieval of the respective database entry. For each results list entry the PathwayBuilder™ can be started using standard settings to visualize the near vicinity in the TRANSPATH network. Two different output formats can be chosen (gif, svg), the latter requires the installation of a plug-in for your browser.
If you would like to obtain the results list in a pure text format, please click on the link above the results list.

Batch searches: Searches for a list of terms can be accomplished by entering the search terms, separated by line breaks, into the first search box. The function to upload files with lists of molecule/gene identifiers or other search terms is available below the first search term field. You can attach additional information such as expression levels behind a separator (tab or |) in each line. Please note that for the attachment function to work, the three search mode checkboxes must not be ticked.

Combined searches: Searches for different terms in up to three different fields can be combined with the logical operators AND, OR, or NOT.

Search mode: If none of the three check boxes on the left is checked (default setting), wildcards are set automatically in front of and behind every search term, i.e. when searching for "STAT" you will also get "STAT1", "STAT2", but also "somatostatin transactivating factor 1" (IPF1).
Entire words will give only "STAT" (and all entries with adjacent non-word characters such as STAT(h), STAT{pSer}, or Jak1:STAT), but if required wildcards can be added as well. "STAT.*" will also give "STAT1" and "STAT2", but not "somatostatin".
Fuzzy ignores all characters other than letters or numbers, i.e. a search for STAT1, will also give STAT-1.
The different search parameters can also be combined, e.g. Entire words together with Fuzzy. When using Fuzzy the metacharacters (regular expressions) are ignored.

The Browse function will give (in alphabetical order) the content of this Search Field together with a sample list of respective entries.

 

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Save and refine a search


You can save your query and refine it later by combining it with an unlimited number of other queries using logical operators.
Check the option NEW above the topmost Search Term box (it is checked by default). After running the query you can identify it on the web server by entering a name directly on the results list page (option is located above the search result).
To combine a saved query with a new one, open the search form again by clicking on the previously used table in the menu bar (please do not use the back button of your browser). Open the pull-down list Select a previous search you want to process and select your previously saved query.
Select one of the logical operators on the top and enter your new search term and select a search field. The possible combinations are:
NEW Start a new search
AND AND will reduce the result by an additional criterion.
In our example, Ras AND semantic will give us all reaction entries that belong to both categories, e.g. all semantic entries concerning Ras.
NOT NOT will reduce your result set as shown in example 2.
OR OR will increase the result by adding a second category.
A query for Ras OR PI3K will result in all entries with either Ras or PI3K.

In this manner you can save and combine as many queries as you like.
The stored queries can be opened for viewing and working at any time.


Example 2 We run the same query as in example 1, but enter ras_search as the name for the query.
We start another query by again clicking on REACTION.
Now we enter semantic as the search term and Type as the search field.
We then choose the query ras_search instead of last.search and check the checkbox NOT.
If we submit the query, the search engine will perform a "reactions with Ras but NOT semantic" query.
Looking at the result, the semantic reactions are gone.
 

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Wildcards and other metacharacters


In addition to the automatically set wildcards in front of and behind your search term, a number of special characters (which are metacharacters of Perl regular expressions) can be used to confine your search results. (In the Fuzzy mode the metacharacters cannot be used.)
 
Metacharacter Example
. replaces any single character Cdk.(h) as a search term finds all human Cdks (Cdk1(h), Cdk2(h),...).
[...] defines a class of characters that are allowed at this position trans[ac] finds transactivation or transcription, but not transregulation
[^...] defines a class of characters that are not allowed at this position STAT[^3-6] retrieves only STAT1 and STAT2, but not STAT3, STAT4, STAT5, and STAT6
* quantifier, allows none or any number of the preceding character trans.*activator retrieves 'transcriptional activator', 'trans-activator', and 'transcription activator'
^ stands for the beginning of a line ^Smith finds all references with a first author named Smith
\character "masks" character if it is a metacharacter, so that it can be used as a "normal" character in the search term. Cdk1\(h\)
 
 

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Further Query Examples


When you are looking for disease-related molecules and their signaling behavior, use comments as the search field. You will get the best results, if you enter one of the keywords, which cover a broad range of the most common diseases.


Example 3 To find all human molecules with an annotation containing the keyword inflammation,
we can run a query with this keyword as the search term and comments as the search field.
We have to combine this query with a second search (term: human, field: Organism species) using the AND operator.
 
If you are interested in which molecules reside in a certain subcellular compartment, use location positive as the search field. TRANSPATH® uses the same vocabulary for subcellular structures as the ontology cellular compartment from the Gene Ontology™ Consortium (you can find several browsers for this ontology on the website).
 

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