[Description, 13K]
| [Contents] | [Simple Retrieval] |
For more detailed information on the concepts behind Textpresso, see the About Textpresso section. For examples of searches you can perform with Textpresso, see the Examples section.
| [Contents] | [Simple Retrieval] |
Searches can be performed by entering keywords into the Textpresso search field, much like popular search engines such as Google and PubMed . Additionally, searches can also be performed by selecting classes from the Textpresso Ontology . But what exactly is an ontology?
An ontology is a set of vocabularies or a dictionary. The members of each ontology class are groups of words that have similar meanings, where the ontology class name represents the "sense" of those words. For example, the ontology class "Regulation" contains words such as "repress", "enhance", "suppress" and the ontology class "Gene" contains all known C. elegans three-letter gene names and the word "gene". The corpus of text is annotated with the ontology terms, where if term in the ontology is matched in the corpus of text, that word is tagged with the appropriate ontology term. Therefore, searching the text corpus by ontology classes allows the user a much broader and intuitive search that with keywords alone.
There are two main categories of ontology classes used in the Textpresso search engine; (i) words that describe biological entities (such as the "gene", "phenotype", "allele" and "cell" ontology classes) and (ii) words that describe the relationship between entities (such as the "regulation", "purpose", "localization" and "association" ontology classes). A third category of ontology classes exists that is design for use in semantic analysis and is not search-able in the Textpresso system. Below is a table of the current ontology classes search-able in Textpresso.
| Biological Entities | Relationships Between Entities |
| Allele | Action |
| Cell or Cell Group | Association |
| Cellular Component * | Biological Process * |
| Clone | Characterization |
| Drugs | Comparison |
| Entity Feature | Consort |
| Gene | Descriptor |
| Life Stage * | Effect |
| Molecular Function | Involvement |
| Mutant | Localization |
| Nucleic Acid | Method |
| Organism | Pathway |
| Phenotype | Purpose |
| Sex | Regulation |
| Strain | Spatial Relation |
| Transgene | Time Relation |
| * The Textpresso system incorporates the controlled vocabulary developed by the Gene Ontology Consortium to describe the biology of a gene product in any organism. There are three ontologies that describe the molecular function of a gene product, the biological process in which the gene product participates, and the cellular component where the gene product can be found. |
The extensive use of ontologies to search text differentiates Textpresso from other Information Extraction systems. In order to search effectively by ontologies however, the user must understand throughly the sense meaning of each of the ontology classes. See the Ontology section for a complete list of ontology classes, their definitions and examples.
The following sections give detailed instructions on how to perform searches using the Textpresso system, from the most basic text retrieval to sophisticated information extraction. The Textpresso search engine is specifically designed for ease and clarity of use. The system can also be customized by the user to suit his/her individual preferences.
Finally, Textpresso is a dynamic and evolving project at WormBase . The Textpresso ontology continues to grow with curator-level input and as more biological information becomes available. We also depend heavily on user feedback to develop and refine the Textpresso search tools and features. If you would like to comment or contribute to Textpresso, please email Textpresso !
| [Contents] | [Simple Retrieval] |