0. What's behind the scene of Text2knowledge?

T2K is parsing data from Medline, GenBank and Google results. Most of the data is generated automagically. Some human curations are provided. Currently, T2K is hosting the following databases:

  • Gene Name Database: Gene Names, Accession # and Taxonomy ID. ==> Gene Synonym Finder / Gene Mapper
  • Acronym Database: Acronyms, Full names and pmids. ==> Medical Acronym Finder
  • Gene Interaction Database: Gene/Proteins, Interaction type, Context and pmids. ==> GeneQuest
  • Gene Tagger: label a text file with <gene> tag together with taxonomy and sequence information. ==> Gene Tagger

1. What is GeneQuest?

It is a database holding gene interaction information extracted from Medline abstracts.

2. What is Acronym Finder?

It is a database holding acronyms extracted from Medline. all the entries are generated automatically, the higher the score, the more likely it is a valide full name for the acronym. You could also contributing to the database by rating the acronym finder results.

3. What is Gene Synonym Finder / Gene Mapper?

It is a gene name database holding gene name, its Accession number, taxonomy and phenotype (OMIM) information. It is based on both GenBank, OMIM and Medline data. A dump of a specific species' gene name list could be provided upon request.

4. My gene/acronym/synonym/interaction cannot be found.

The system is still under development. The interaction data is still limited. Try both my acronym and synonym finder, I am confident you will find something.

Contact me if you think I missed some important ones.

5. How to Cite T2K databases?

For works that used T2K databases, please cite "Text2Knowledge: http://bioinformatics.org/textknowledge/".

6. What is Gene Tagger?

It is a web tool that take a medical text file or a list of gene names and tag genes with <gene> tag with taxonomy and sequence information. Note that it will take quiet a long time if you are tagging a long paragraphs or a full paper.

7. Help needed.

Evaluate the gene interaction and acronym finder results and send your comments.