Textpresso User Guide

[Advanced Retrieval, 680K]

• Advanced Retrieval
  • Advanced Retrieval Search Features
    • Search Buttons
    • Text Corpus Selection and Author/Year Search
    • Sentence Search vs Publication Search
    • Setting the Number of Rows
    • The Query Table Features
      • Boolean Operator
      • Category or Keyword
      • Category or Match Attributes
      • Specification
      • Numerical Comparison of Matches and Number of Matches
  • Search Summary Page Features
    • Matches Information
    • Summary Display Controls
    • Email Settings
    • "View all matches" Button
    • "Abstract Expansion" Button
    • "View matches" Button
    • "PDF" Button
    • "Related articles" Button
    • "Results in PDF" Button
  • Result Page Features
    • Query Display
    • Results Display
    • Publication Identifier
    • Sentence Identifier
    • Search Matches
    • Links to Wormbase
  • Performing a Text Search

Advanced Retrieval

The Advanced Retrieval search engine is a very powerful tool offered by Textpresso for real-time information retrieval from C. elegans literature. Like the Simple Retrieval , the Advanced Retrieval tool is designed to combine keywords with ontology categories in performing searches. However, the Advanced Retrieval tool allows the user to specify boolean terms, ontology category subgroups and number of occurrences of an ontology category or keyword in the search. If used properly, the Advanced Retrieval facilitates the formulation of queries that are closer to semantic questions than any other search engine for biological literature . A well designed Advanced Retrieval query allows the user to ask questions such as, " What genetic expression affects Ras signaling? ". In order to make optimal use of the Advanced Retrieval tool, the user must have a good understanding of sense meaning of each ontology category and its subgroups.

A few notes before we start:

1. The first row in the query table must be filled out, otherwise no matches will be returned (this prohibits the user from performing just a keyword search with the Advanced Retrieval tool). Any other lines left empty will not affect the query.
2. The Advanced Retrieval search engine processes rows from top to bottom. In other words, the matches of the first row are found first, the system then applies the boolean operator of the next filled row (if it is present) and matches the next row against the return of the first and so on ....
3. It is possible to generate some pretty big returns with the Advanced Retrieval tool. The goldturtle server is set to time out after 5min.s, so, until we get a better server, try big return queries at times of low traffic for best results (i.e. at night).

Advanced Retrieval search features

1. Search Buttons

Clicking on the "Search!" button initiates a search with the inputed parameters. There are three other buttons. The "Load last query!" button is a useful feature that remembers the last user query and loads it again. The "Clear last query" sets the query table back to the default values. The "Undo current changes!" button allows the user to conveniently undo the last change they did to their search.

• Boolean Operator
  
  The user may choose to specify one of three boolean operators (AND, OR, NOT) between any two keywords or ontology categories. The default boolean term is AND.
  
  
• Category or Keyword
  
  Keywords and/or ontology classes are selected in this column. In the top portion of the query table, the user may choose from a drop down menu of ontology classes. Keywords to be searched are entered in these search fields at the bottom portion of the query table, for example, "let-60", "dumpy" or "1999". The wildcard insertion ( * ) is used by default after each word. For example, if you type "egl" in the , 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 (see Category or Match Attributes below). Note: the keyword search is not case sensitive. There are three ontology class menus and three keyword search fields in the query table by default. The number of text boxes and ontology class menus that appear on the Advanced Retrieval search page man be altered for a particular search (see "Setting the number of category and keyword rows in the query table" below) or the default number that appear may be set on the customization page .
  
  
• Category or Match Attributes
  
  Attribute values of a corresponding ontology class and/or whether or not a keyword should be matched exactly is selected in this column. The attribute values of the ontology classes are listed in alphabetical order in a scrollable list window in the ontology class rows. The category that a particular attribute is associated with is in parenthesis after the attribute value name in the format:
  
  < ontology_class > < attribute_type >: < attribute_value >
  
  For example, the ontology class "involvement" has an attribute, "requirement", with two values, "yes" and "no", which appear in the attribute list as "involvement requirement: yes" and "involvement requirement: no" respectively. The user may select multiple attributes for particular ontology class, if that class has more than one attribute type. For example, the ontology class "biological process" has three attributes, "source", "biosynthesis" and "type" and the user may choose values for any or all of these attributes. For more information about the ontology classes and their associated attributes, check out our Ontology page . Selecting the box beside "Exact match" on a keyword row, determines whether the keyword is matched exactly or may also appear as the start of a word.
  
  
• Specification
  
  Some ontology classes have a special attribute that determines whether they are referred to directly or indirectly. For example , in the case of genes (the "gene" ontology class) a gene may be mentioned directly by name, "eat-4" or indirectly as "the gene". Here, the user may specify whether the want to match something that is only directly named (the "named" option), only indirectly named (the "unnamed" option) or both (the "all" option, which is the default). The following ontology classes can be referred to directly or indirectly: "allele", "cell", "drugs", "entity_feature", "molecular function", "gene", "life stage", "mutants", "nucleic acid", "organism", "sex", "strain".
  
  
• Numerical Comparison of Matches and Number of Matches
  
  The "numerical comparison of matches" and "number of matches" values allow the user to determine the amount of times they wish to match the ontology class or keyword they have set on the same row in the text. By combining these two values provides the user with great flexibility for matching frequency of occurrences. From the drop down menu in the "number of matches" column the user can select a number and then, by choosing one of the options in the "numerical comparison of matches" menu, decide if the would like to see, that exact number ("equal to") of occurrences, or a greater ("greater than") or lesser ("less than") number.
  
  

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[Simple Retrieval]

[Contents]

[Fact Extraction]

Search Summary Page Features

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[Simple Retrieval]

[Contents]

[Fact Extraction]

Result Page Features

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[Simple Retrieval]

[Contents]

[Fact Extraction]

Performing a Text Search

Below is an example of a text search using the Advanced Retrieval tool in Textpresso. Please see the " Examples " section for many more examples of Textpresso searches.

What genetic expression affects Ras signaling?

A number of ontology classes are employed to formulate a query that asks, "what genetic expression affects Ras signaling?". In the Textpresso Ontology, terms that indicate expression are contained in the Biological Process ontology class and have the attribute value, "expression". Therefore in the first row, where the ontology class "Biological Process" is chosen, an attribute, "biosynthesis" with the value, "expression" is assigned to the ontology class. The next row determines that the match must also contain (by specifying the AND operator) one or more ("greater than 0") directly named genes. The selection of the ontology class "Effect" in the third ontology row influences the relationship between the two entities, the named gene and "Ras", which is entered as a keyword in the fifth row to be matched exactly. The inclusion of one or more occurrences of a "Pathway" class term in the fourth row serves to refine the search to Ras signaling. The substitution of a different "relationship" ontology class here, such as "involvement" or "purpose", could be used to determine subtlety different queries, "how is genetic expression involved in Ras signaling?" and "what role does genetic expression play in Ras signaling?" respectively. The differing result from each of these three subtle variations are shown below:

What genetic expression affects Ras signaling?

How is genetic expression involved in Ras signaling?

What role does genetic expression play in Ras signaling?

to the top

[Simple Retrieval]

[Contents]

[Fact Extraction]