Examples
If you have any comments or would like to see examples of more searches please email
Textpresso
to let us know!
The
Textpresso
Advanced Retrieval search engine is a very powerful tool for finding facts from
C. elegans
literature. With its user-friendly interface one can utilize the full depth of the
Textpresso
ontologies and
also refine queries with added boolean operators, frequency of term or keyword occurrences and keywords.
It may take a little practice to
to use this feature optimally. Referring to the
Textpresso
ontology category definitions
is often helpful. The examples below demonstrate the real
power of the system. We hope you have fun trying out queries. These examples and the corresponding
User Guide
section should provide a solid introduction to this tool. The
Textpresso
team are also at hand to answer any questions you might have along the way. Finally, if you feel you have constructed a particularly useful query that
we have not included on the examples page, please let us know so that we can add it!! Thanks.
Some quick pointers:
- The first row of the Advanced Retrieval table
must
be complete to run an Advanced query!
- Javascript
must
be enabled in your browser to run the Advanced Retrieval interface.
- If an ontology category has subgroups (e.g. category "sex", subgroups "male, female or hermaphrodite"), these will appear in the "category or
match subgroup" column when the ontology
category is selected. One of each type of subgroup may be optionally select to refine a search.
- For some ontology categories there will appear options in the "Specification" column.
In the case of the "allele" category, for
example,
one can choose a specifically "named" allele, e.g. ad819, or a reference to an allele, "unnamed",
e.g. the word "allele". The default is "all"
which includes both these categories.
-
The keyword search is
not
case sensitive.
Now for some examples!!
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Example:
eat-4
This search utilizes two ontology categories and a keyword.
The ontology category "biological process" is selected in the first row.
A subgroup of the biological process ontology category, TYPE: "biosynthesis", VALUE: "expression",
is selected from the subgroup menu. This subgroup of the biological process ontology contains only terms
that indicate genetic expression ("over-express", "encodes" etc.) .
The ontology category "molecular function" is selected in the second row.
A subgroup of the "molecular function" category, TYPE: "protein", VALUE: "yes" is selected from the subgroup menu.
This subgroup contains terms that are protein names
. Further, a specification value of "all" is selected so that specifically named proteins ("UNC-60", "DNA ligase" etc.)
and proteins that are indirectly referred to (the word "protein")
will be matched.
The keyword "eat-4" is entered in
the third row, where the "exact match" box is checked.
The default boolean operator "AND" and the default value of "greater than one occurrences" are applied.
The two diagrams below show parts of the result page for this search. In the first example,
Textpresso
has returned the published homology from the first paper
to characterize the
eat-4
gene (cgc3349 - Lee et al, Journal of Neuroscience, vol. 19, 159-167 (1999)).
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This search utilizes two ontology categories and a keyword. A subgroup of the biological process ontology category, TYPE: "biosynthesis", VALUE: "expression",
is selected from the subgroup menu. This subgroup of the biological process ontology contains only terms that
indicate genetic expression ("over-express", "encode" etc.).
A subgroup of the "Cell or cell group" category, TYPE: "type", VALUE: "name" is selected from the subgroup menu.
This subgroup contains terms that are
cell and cell group names. Further, a specification value of "named" is selected so that only specifically named
cells and cell groups will be
matched ("AVM", "neurons"). The keyword "eat-4" is entered in
the third keyword row, where the "exact match" box is checked.
The default boolean operator "AND" and the default value of "greater than one occurrences" are applied.
The diagram below shows part of the results page for this search.
The search pin-points with high precision sentences discussing the expression of eat-4 in various cells from
Textpresso
corpus of full-text papers!
In fact 10 of the 11 returned sentences for this search answered the question posed. The third sentence,
seen below (cgc3038), talks about where
eat-4
is not
expressed, "... EAT-4 is not expressed in PVC neurons ....".
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This search utilizes two ontology categories and a keyword. The ontology category "phenotype" is
selected in the first row. A specification value of "all" is selected so that specifically named
phenotypes ("Egl", "fertilization defective") and indirectly named phenotypes (the word "phenotype") will be matched.
Th ontology category "allele" is selected in the second row. A specification value of "all" is selected
so that specifically named alleles ("n2559" , "e307") and alleles that are indirectly referred too (the word "allele")
are
matched. The keyword "eat-4" is entered in
the third keyword row, where the "exact match" box is checked.
The default boolean operator "AND" and the default value of "greater than one occurrences" are applied.
The diagram below shows part of the results page for this search. The search was designed to look for phenotypes
of eat-4 resulting from mutations to the gene (thus the category "allele" was selected). Here we see two distinct
phenotypes, multivulval and wild type, cause by eat-4(ky5) and eat-4(ad572) respectively.
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This search utilizes two ontology categories and a keyword. The ontology category "gene" is
selected in the first row. A specification value of "named" is selected so that only specifically named
genes ("let-60", "lin-12" etc.) will be matched. The ontology category "pathway" is selected in the second row.
Two
subgroups of the "pathway" category are selected. The first subcategory, TYPE: "type", VALUE:
"molecular" is selected from the subgroup menu. A second subcategory, TYPE: "course", VALUE: "downstream"
is also selected. This is done by pressing the control key (Ctrl) as you click on the second subcategory.
NOTE: ONLY ONE VALUE FOR EACH SUBCATEGORY MAY BE SELECTED.
The combination of these subgroups matches terms such as ("cascade", "downstream" etc.).
The keyword "lin-12" is entered in the third keyword row, where the "exact match" box is checked.
The default boolean operator "AND" and the default value of "greater than one occurrences" are applied.
The diagram below shows part of the results page for this search.
This query demonstrates the precision of the Advanced Retrieval search engine. The parameter "pathway" was refined
to include only those terms which indicated downstream events at a molecular level. Thus, at least two genes, emb-5 and
sel-10 are quickly identified from the literature as acting downstream of the lin-12 signaling pathway.
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This search utilizes three ontology categories and a keyword. The ontology category "life stage" is
selected in the first row with a specification value of "all" so that life stages that are specifically
named ("1-cell embryo") and/or indirectly refereed too will be matched ("adult").
The ontology category "time relation" is selected in the second row with no subcategories selected so that it will
match any term in the time relation category ("early", "temporal" etc.).
The ontology category "biological process" is selected in the third row. A subgroup of the biological
process ontology category, TYPE: "biosynthesis", VALUE: "expression", is selected from the subgroup menu.
This subgroup of the biological process ontology contains only terms that indicate genetic expression ("encode",
"over-express" etc.).
The keyword "lin-12" is entered in the fourth row, where the "exact match" box is checked.
The default boolean operator "AND" and the default value of "greater than one occurrences" are applied.
The diagram below shows part of the results page for this search.
By combining both the "life stage" and "time relation" ontology categories, one can search for
when
during
C. elegans
development a particular event occurs. Below are results from three separate publications (cgc2972, cgc1670, cgc1909)
that
indicate that lin-12 is expressed during embryonic and post-embryonic development, and specifically during the development
of the ventral nerve cord (cgc2972).
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This search utilizes one ontology categories and four keywords.
The ontology category "biological process" is selected in the first row. A subgroup of the biological
process ontology category, TYPE: "biosynthesis", VALUE: "translation", is selected from the subgroup menu.
This subgroup of the biological process ontology contains only terms that associated with protein translation
("translate", "transplice" etc.).
The keyword "lin-2a" is entered in the second row, where the "exact match" box is checked.
In rows three, four and five the keywords "lin-2b", "lin-2c" and "lin-2d" are entered respectively with the
"exact match" box checked in each row. In the last three rows the boolean operator is set to "OR".
The default value of "greater than one occurrences" is applied.
The diagram below shows part of the results page for this search.
A trick is used in this search to looked for splice variants of the
lin-2
gene. Taking advantage of the xxx-1a,
xxx-1b, xxxx-1c etc. naming convention for splice variants for a given gene and the "OR" boolean operator, one can
search specifically for any mention of these splice variants in a sentence. This has an advantage over
other search engines
where one may search for splice variants of a gene using a wild card (i.e. lin-2*), which in addition to any
lin-2 splice variants may also return results matching
lin-22
or
lin-26
for example. Thus
Textpresso
facilitates the formulation of exact queries. Please note however, the use of the boolean operator "OR"
means that the "biological process" category is not
required
in the returned hits.
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This search utilizes four ontology categories and two keywords.
The ontology category "biological process" is selected in the first row. The number of times that
a "biological process" category term will be matched in a sentence is set to "greater than" "1".
The ontology category "gene" is selected in the second row. A specification value of "named" is
selected so that only specifically named genes ("let-60", "lin-12" etc.) will be matched.
The ontology category "involvement" is selected in the third row.
The ontology category "pathway" is selected in the fourth row.
The keyword "ras" is entered in the fifth row, where the "exact match" box is checked.
In row six the keyword "let-60" is entered are entered with the "exact match" box checked and the
boolean operator set to "NOT".
The diagram below shows part of the results page for this search. The combination of the "gene" and "involvement"
categories with the keyword "ras" form the core components of this query. Further, two tricks are used in this
search to increase the accuracy of the query. The first is the addition of the "pathway" category, which serves
to refine the search to ras
signaling
. Secondly, to reduce the number of false positives, the
let-60
Ras gene is excluded from the search. From a sample of the results page below, we can identify at least four genes
thought to be involved in Ras signaling (lin-39, sur-6, ksr-1 and sur-8).
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This search utilizes three ontology categories and one keywords.
The ontology category "cell and cell group" is selected in the first row.
The ontology category "effect" is selected in the second row.
The ontology category "pathway" is selected in the third row.
The keyword "ras" is entered in the fourth row, where the "exact match" box is checked.
The diagram below shows part of the results page for this search. This time the category "effect" is
used in combination with "cell and cell group". The same trick is used as above, the category "pathway"
is specified with the keyword "ras" which refines the query to Ras signaling. The sample results show
that the Ras signaling pathway appears to effect at least two different cell groups, the AWC neurons and
the Vulval Precursor Cells.
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