Example Searches in Textpresso




[Contents] [Advanced Retrieval Examples]


Examples




[Contents] [Advanced Retrieval Examples]


If you have any comments or would like to see examples of more searches please email Textpresso to let us know!

Examples of Simple Retrieval Searches

1. Performing a keyword search

Note: the keyword search is not case sensitive.

The keyword search allows user to search for any word(s) or string in the Textpresso corpus. To do a keyword search, simply enter that word or string into the text field box on the Simple Retrieval search page (e.g. "gene", "ANC-1", "reacts", "briggsae"). The user has the option to choose to search any combination of the "Titles", "Abstracts" and "Papers" by selecting the boxes beside these options. If more than one keyword is entered (see below) the user can decide if they would like to be shown cases where the keywords appear together in a sentence or whether the just occur in the same publication, by selection the sentence or publication radio buttons respectively.

Using the wild card

The wildcard insertion ( * ) is used by default after each word. In other words, Textpresso searches for matches that start with the keyword entered by the user, where the hit matches that keyword exactly and also as part of a word.

What publications mention anything that starts with let-6?

For example, the figure shows that when "let-6" is entered as a keyword to be searched for in titles, 59 matches are shown on the summary page. These matches not only include "let-6" , but also "let-60" , "let-653" and "let-601" .



Performing an exact search

Sometimes the user whats to search for only what the keyword matches exactly.

What publications mention let-6 exactly?

For example, look what happens to the same " let-6 " keyword search when the user selects the "Exact match" option! Now only 2 matches are shown on the summary page, where each of the titles contains only the keyword " let-6 ". Also, when the "Exact match" option is turned on it will apply to all keywords entered in the text field!!



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Searching multiple terms

Textpresso also allows the user to enter more than one keyword to search against, where each keyword is separated by a comma. An example search is shown here ...

Does let-7 regulate development?

In this search the multiple keywords "let-7", "regulat" and "develop" were used as search parameters to identify sentences from papers. Advantage was taken of the automatic wild card insertion so that "regulate(s)", "regulating", "regulation" and "regulated" and also "develop(s)", "developed", "development", "developing" and "developmental" may be matched. The diagram below shows the results page for this search. Here we see that even a simple keyword search is powerful enough to pin-point sentences discussing a fact of interest from a corpus of papers!




Another example uses multiple terms in a keyword search to ask a vague question like ....

Is there a correlation between "caloric restriction" and "aging" in the worm literature?

If there is correlation between these two phenomena in the literature, one might expect them both to occur in the same sentence in a publication, therefore, the search is once again delimited by sentence. Again, advantage is taken of the wild card insertion so that "age(s)", "aging", "aged", "restrict(s)", "restriction", "restricted" and "restricting" can be matched. By checking the box beside both papers and abstracts, the user can search in the ~2,000 (over 1/3 of all known C. elegans papers) and ~10,000 abstracts in the Textpresso system.



The a sample result of the above search is shown below. It is clear from this result that there is a correlation between caloric restriction and aging in worms. Further, from this simple 15 second search, the user can learn of the effects of caloric restriction in aging, "Caloric restriction attenuated the aging responses...." and "Gene expression profile of aging and it's retardation by caloric restriction" and also which genes are involved, "... induced in weak daf-1 and age-1 mutants".



2. Performing a search using ontology classes

While the keyword search allows the user to identify specific words in the Textpresso corpus, performing a search using the Textpresso ontology classes offers a alternative fuzzier type of search. If applied properly, the ontology class query can facilitate semi-semantic searches of the literature. To use ontology classes to perform a search, simply select from the the drop-down menus of ontology classes on the Simple Retrieval search page. The user has the option to chose to search any combination of the "Titles", "Abstracts" and "Papers" to search against by selecting the boxes beside these options. If more than one ontology class is entered (see below) the user can decide if they would like to be shown cases where the ontology classes appear together in a sentence or whether the just occur in the same publication, by selection the sentence or publication radio buttons respectively.

So what are these ontology classes and how can they be used for searching text?

To locate types of abstracts by querying their title.

Which abstracts mention an allele and a biological process in the title?

One might use the ontology classes to find, as in the first example, all publications that have any C. elegans allele and a biological process mentioned in title. To do this, choose "allele" from one ontology class menu and "biological process" from another and select the box beside the "title" option.



The diagram below is a snapshot of the summary page for this query. It shows the various different allele and biological processes co-occurring in publication titles.



To locate publications containing particular facts

What publications talk about genetic regulation in cells?

The ontology classes in Textpresso may also be used to identify groups of papers that discuss particular facts, for example, if you want to know which papers discuss genetic regulation of cells. In this case choose "gene", "regulation" and "cell or cell group" each from an ontology class menu and select both abstracts and papers to search in. Also ensure that sentences is selected as a delimiter.



In this example 2616 publications were found where a gene, regulation and cell term were matched in at least one sentence. The number of matches shown on the summary page can be used as an indicator how likely it is that the publication is about genetic regulation of cells.

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3. Combining ontology classes and keywords in a search

By combining both the keyword and ontology class search, users can construct an near semantic query to search text with.

Example one

What genes does daf-16 associate with?



Using the sentence delimiter, the results page shows sentences that describe the association of the daf-16 gene to various other genes.



Example two

Which proteins localize in AB cells?



Using the sentence delimiter, the results page shows sentences that describe the localization of various proteins in AB cells.





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[Contents] [Advanced Retrieval Examples]