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User Guide nematode
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Welcome to the Textpresso user guide. This document briefly explains the functionality of the Textpresso website.



1) Home Page

The details of the Textpresso home page are explained in the following figure.


To get help with items on the page, click on the button next to the item if one is available. It opens a pop-up window and shows details.



Keyword search in Textpresso comes with several options:




Category search in Textpresso allows searching for a bag of words that belong to a concept. For example, searching for category 'disease (H. sapiens)' searches for any keyword or phrase that is a human disease. Any item in the cascading menu that does not have a sub-menu (i.e. that does not have a '>' sign at the end) can be selected.

Note that pure category search (without any keywords) can also be performed.




Once the first category is selected, a second category can be selected from the cascading menu again. Simply mouse over the menu again and choose the second category. The search will perform a Boolean AND operation on the two categories i.e. return sentences that contain at least one term from the first category and one term from the second category.




Advanced search options are under a hidden menu.




Advanced search options menu provide options for choosing which sections to search in, search scope, sorting order and filters for other fields.




Advanced filtering with exclusions and inclusions in various fields could be performed once a search is performed.




6) Display Options

Various display options are available for search results:




7) Textpresso Ranking

Textpresso uses simple frequency scores to rank documents. The document that contains the most number of occurrences of keyword(s) and/or categories ranks first and the documents are presented in descending order of scores.

The following figure illustrates the scoring for a search performed for the keyword let-23.





There are currently eleven click-able items aligned horizontally underneath the Textpresso logo. The blue highlighting indicates the current work area of the user.

The following picture explains the other non-obvious items:




8a) To view terms in a category

    To view terms in a category click on the "Categories or Synonyms" link in the Main Menu at the top.




    To check if a keyword of your interest is in any of the Textpresso categories, again use the "Categories or Synonyms" link in the Main Menu at the top.




8b) To find if Textpresso has a document

    To check if Textpresso has a particular document using document ID, use the "Document Finder" link.




    The Textpresso query language is a highly versatile and powerful element of Textpresso. Complicated retrieval tasks can be performed by carefully crafting sets of commands.





    There are three kind of commands: the first kind (set, clear) manipulate parameter settings, the second kind (find) performs keyword, phrase, category and attribute searches, and the third kind (and, or, not, display) manipulates search results, which are kept in an entity called 'variable' here. The syntax for the commands are listed in the explanation box (2).

    The text area (3) accepts commands line by line. The user can either enter one command at a time and then press the 'Submit!' button (4), or enter all commands (line by line) at once and the have it processed by hitting the 'Submit!' button (4).

    The set command sets a parameter to a single or a series of values (example: set literature=elegans, melanogaster). The parameter names are 'literature', 'field', 'exact match', 'case sensitive', 'sentence scope', 'search mode' and 'sorted by'. When entering a parameter name, the name of the parameters needs to be spelled out, however, if a name consists of two words, you can specify either one of them. The value a parameter can be set to depends on the particular implementation of database of Textpresso. It can be obtained from their respective input field (check boxes, popup-menu) in the search interface (accessible through the main menu). A value can be abbreviated by using the first few letters that identify it uniquely (for example, you could use set literature=ele).

    The clear command clears the setting of a parameter (example: clear all). The user can clear all parameter by using the word 'all' or a specific parameter, by naming it, again spelled out completely.

    The find command performs the actual search (example: find keyword egg > 0 -> var_egg). The exact syntax of this command is

find (keyword | category| attribute) (keyword | "phrase" | category | category:attribute:value) (< | == | >) number -> variable-name.

    The second parameter determines what the user wants to search, the choices are 'keyword', 'category' or 'attribute'. The third parameter specifies the data item the user is searching, such as a keyword (for example, mitosis), a phrase (for example, "anchor cell"), a category (for example, association) or attribute (for example, regulation:type:positive). The fourth and fifth parameters determine the numerical constraint with which the data item has to be found in a given search scope (the search scope is set with the set command, see above). Thus, '> 2' means that the item has to be present in the search scope more than two times. The arrow (->) following these two parameter is a fixed character sequence and cannot be changed. It suggestively points to the last parameter, the variable-name, into which the search result is stored. Characters and numbers should be used for this name. If the find command is the last in the text area before the user hits the 'Submit!' button, the search results of this last find command is returned in the result table. The result table is described in detail in the section about the search interface.

    The and, or and not commands concatenate two search results, which have been previously obtained using the find command and stored in two variables. The result of this operation is stored in a third variable, which is specified last (example: and gene-result cell-result -> gene-and-cell). Again, if one of these commands happen to be last in a series of commands in the text area, the result of this operation is returned in the result table.

    Finally, the display command displays a search result that had been previously obtained, but was lost in the course of further operations. The variable name to which the search was assigned to has to be provided as a parameter. Only variables within a session can be retrieved, i.e., once the user leave the query language interface, any search results are lost.

    To give feedback, use the "Feedback" link in the Main Menu at the top.




    Textpresso Sat Sep 23 00:32:41 2017 .