About Textpresso Copyright Feedback Search User Guide

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

Main Menu

    There are currently 5 click-able items aligned horizontally underneath the logo (above). The highlighting indicates the current work area of the user. The menu items are:

    About Textpresso & Copyright: Information about Textpresso and copyright issues can be found here.

    Feedback: This interface presents a form to leave feedback, questions and suggestions for the CGD team.

    Search: Most common search tasks can be performed using this option. It is the most frequented page of the system.

    User Guide: This document.


This form allows the user to send a message to the CGD team. Fill out all the information in the given text field and hit the Submit button. If some fields are left empty, the form will be returned to the user, and the message will not be accepted for submission.


    The search page is probably the interface the user will frequent most. The user can enter a keywords or phrase in a text field, and multiple keywords and/or phrases can be concatenated with the usual operators 'AND', 'OR', and 'NOT' in the same text field, using the syntax described below the text field. Exact matches and case sensitivity can be requested by clicking on the corresponding boxes. The search can be confined to particular sections of the publication called fields. Search scope, search mode and sort option can be modified with popup menus. The search scope determines where keywords and categories requirements have to be met, either on a sentence level, on a field level (abstract, author, body, title, year) or on a document level (anywhere in the document). The search mode determines how the score is calculated. 'Boolean' just adds up occurrences of matched entities in an integer fashion. 'tf·idf' (term frequency times inverse document frequency) overweights rare terms. 'Latent themes' emphasizes matches that have similar semantic contexts as the query, but is not implemented yet. The search return can be sorted according to certain output fields, such as year of publication, author, title etc. It also can be sorted according to score. Finally, to submit the search, hit the 'Search!' button. An example result page is shown:

    The result table of a search return has several features: the user can flip through all pages of the search return by using the page selector (1). The output of the result table is edited by the display options panel (2). You can switch on or off the display of abstract, accession, author, citation, journal, title, type or year information by clicking on the respective links. You can further toggle the supplemental links and files as well as the presence of links in text ('textlinks'). Highlighting of search terms that are matched in the text can be switched on or off. The 'matching-sentences' menu allows the user to choose how many sentences around a match should be displayed. The option 'none' does not display the matching sentences at all, while '1' just displayed the matching sentence. Finally, the entries/page menu determines how many publications are displayed per page. For speedy returns, choose a low number for both the 'matching-sentences' option as well as the 'entries/page' option.

    The search summary (3) tells the user how many matches have been found in how many documents, and indicates the search time. The search time does not include the time to produce the webpage. Following the search summary, links that concern all entries of a search return are presented (4): The first link produces an Endnote file for all result entries, the second link produces a printer-friendly version of the result table. The production of this table might take quite a while when the search return is huge. The publication display (5) shows detailed bibliographical information about each publication which can be customized in the display options panel. The publication display might contain textlinks to other databases (such as gene or cell report pages). Search terms that match are highlighted if the option is turned on. In case of phrases, not only the phrase, but also the phrase is highlighted, but also its constituents. The score of each entry is displayed in the upper right corner (6). Finally, at the bottom of each entry, there are several links to supplemental files and other web pages pertaining to that particular entry. The first links produces an Endnote file for the publication, the second links to the on-line text of the publication. At last, the third link lead to PubMed displaying related articles.

Not all of the features of the Textpresso software have been implemented at CGD.

Please contact the CGD curators with any questions, comments, or suggestions.
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Textpresso Wed Mar 22 19:13:18 2017 .
CGD Copyright 2004-2009 The Board of Trustees, Leland Stanford Junior University. Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided AS-IS without any warranty, expressed or implied.