[Simple Retrieval, 593K]
The
Simple Retrieval
search engine is the most basic of the searches Textpresso offers. It is designed to combine a
keyword search with up to four ontology category searches. The output of the search is displayed on a "
Summary Page
",
which summarizes details of the publications which contain matches. The user selects which matches they would like to view and the results
are shown on the "
Results Page
". Additionally, the user can perform an "author search" and a publication "year search"
using the Simple Retrieval tool.
1. Search Buttons
Clicking on the "Search!" button initiates a search with the inputed parameters. There are two additional buttons. The "Load last query!" button
is a useful feature that remembers the last user query and loads it again. The "Undo last changes!" button allows the user to conveniently
undo the last change they did to their search.
2. Text Corpus Selection and Author/Year Search
The user has the option to chose to search any combination of the "Titles", "Abstracts" and "Papers" by selecting the boxes beside
these options. The user also can perform a search for a particular author by selecting the "Author" option and typing the author
name in the search field. Likewise, the user can search for publications from a particular year by selecting the "Year" option
and typing a four digit year in the search field.
3. Search Field
This is where keywords to be searched are entered, for example, "let-60", "dumpy" or "1999". Multiple entries are separated with a
comma, for example, "lin-3, BW136". The wildcard insertion (
*
) is used by default after each word. For example, if you type
"egl" in the search box, the return would include matches with egl, egl-1, egl-2, egl-30 etc. The user can select the exact match
box to turn off the wild card insertion. Note: the keyword search is
not
case sensitive.
4. Ontology Category Menu
Above the search field box are drop down menu's where the user can specify up to four different Textpresso Ontology
categories with which to
search. Note: each ontology category will only be searched for once, even if the user selects the same ontology category
more than once.
5. Sentence Search vs Publication Search
The user has the option to search the input parameters within individual sentences or entire publications. Note: this only applies when
"Abstracts" and/or "Papers" are selected to search against.
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1. Matches Information
This is where the number of matches of the search parameters is displayed. If the system is searching either sentences or publications,
the total number of sentences
containing the search parameters is displayed. Also shown is the total number of publications that contain one or more hits.
2. Summary Display Controls
The summary page is returned with ten summaries displayed per page (this is the default, the number of results summaries displayed
per page can be customized in the "
Customization
" page). The
summary display controls allow the user to display any page by selecting the page from the drop down menu and pressing the "Display" button.
Alternatively, the user can navigate the summary page using the "Previous" and "Next" buttons.
3. Email Settings
The user can opt to have the summary page sent to them via email. To do this the user must enter their email address in the text box and
press the "E-mail" button. By selecting the include matches option, the email will also contain the resulting matches from the search.
Beware, this can result in very large emails!
4. "View all matches" Button
Clicking this button brings the user to a results page containing all the results for a given search.
5. "Abstract Expansion" Buttons
By default (and for the sake of clarity) only the first two sentences of an abstract are displayed in the "Abstract" column. Pressing the
"Expand abstract" button will display the full abstract in the column. This full abstracts can be collapsed again by pressing the
"Collapse abstract" button.
6. "View matches" Button
Clicking this button brings the user to a results page containing the results for a that particular publication.
7. "PDF" Button
Clicking
on the PDF button displays the pdf version of that publication
(only available to Caltech users)
.
8. "Related articles" Button
This button outlinks to the PubMed web-site page of citations that are related to that particular publication.
9. "Results in PDF" Button
Clicking on the Results in PDF button brings the user to a web page where they can opt to download all the resulting
hits for their query in PDF format.
(This may take a few minutes, depending on the number of resulting hits)
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1. Query Display
At the top of the results page the search query is displayed. Note that the different search parameters are displayed with different
color as a visual aid.
2. Results Display
The result display is returned with ten matches displayed per page (this is the default, the number of matches displayed
per page can be customized in the "
Customization
" page). The
summary display controls allow the user to display any page by selecting the page from the drop down menu and pressing the "Display" button.
Alternatively, the user can navigate the summary page using the "Previous" and "Next" buttons.
3. Publication Identifier
The "File ID" identifies the publication from which the match comes according to
WormBase
abstract nomenclature. The type of publication is displayed in parenthesis after the File ID, i.e. Abstract.
4. Sentence Identifier
The "Sentence ID" specifies the sentence number of the match in the publication.
5. Search Matches
The matching sentences are displayed in boldface font. For the sake of context, the sentences that surround the match in the publication
may also be displayed (the default number is ten, the number of surrounding sentences displayed per match can be customized in the
"
Customization
" page).
6. Links to Wormbase
Some words and terms in the matching sentences will link to their corresponding report pages in
Wormbase, a database repository for the biology and genome of C. elegans.
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Below is an example of a text search using the Simple Retrieval tool in Textpresso. Please see the
"
Examples
" section for many more examples of Textpresso
searches.
The user first selects whether they would like to search for the terms in entire publications or the individual sentences of the publications.
In this instance, the "publications" option was selected. The user then enters the parameters for the text search. In this case, the user
has chosen one ontology class, "regulation", and entered the keyword "tra-3". The user must then decide whether they wish to search for these
parameters in publication titles, abstracts or papers (where more than one of these options can be selected). In this case the user has opted
to search papers. The user can modify the search parameters with the "Load last query" and/or the "Undo last change" buttons. When the user
is satisfied with the search parameters, the "Search" button is pressed to initiate the search.
If the search is successful, it returns a summary page from which the user can select the matches to be displayed. The summary pages are
navigated and the user can choose to display matches for any publication with the "View matches" button. All matches
are shown in another window by pressing the "View all matches" link. Alternatively, the selected summaries and their corresponding
matches can be sent to the user in plain text format via email.
The sentences that match the search parameters and were selected by the user for display are then shown on the results page. In this case,
any sentence in a publication that contains either a member of the "allele" ontology class or the keyword "tra-3" is displayed.
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Below is an example of an author search using the Simple Retrieval tool in Textpresso. Please see the
"
Examples
" section for many more examples of Textpresso
searches.
The sentence or publication and the ontology class parameters are not used in this search.
The user enters an author name
in the text box, entering the lastname and then, optionally, the firstname initial (for example "Sternberg" or "Sternberg, p"). "Author"
is selected to search against (make sure to unselect the other options). The "Search" button is then pressed to initiate the search.
An index of all the author names in Textpresso is searched and if the search is successful, a page is returned which gives details of all abstracts
and papers in Textpresso where the author name is matched.
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Below is an example of a text search using the Simple Retrieval tool in Textpresso. Please see the
"
Examples
" section for many more examples of Textpresso
searches.
The sentence or publication and the ontology class parameters are not used in this search.
The user enters a year in
the text box, in the format
yyyy
(for example "2000" or "1986"). "Year"
is selected to search against (make sure to unselect the other options). The "Search" button is then pressed to initiate the search.
An index of all publication dates of all the abstracts and papers in Textpresso is searched and if the search is successful,
a page is returned which gives details of all abstracts and papers published that year.
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