Submissions tagged with text mining
(16 documents)
Normalization and Matching of Chemical Compound Names
The identification of a chemical compound solely based on its name requires comprehensive chemical knowledge and often extensive searches in chemical databases. However, it is crucial for the integ…
Received 04 June 2009 16:05 UTC; Posted 05 June 2009
Posted to: Chemistry, Bioinformatics
Using Textpresso for Information Retrieval, Fact Extraction
Ten years ago WormBase1 started as a repository for sequence data for the modelorganism Caenorhabditis elegans and has since striven to include the curation of allgenetic and molecular data p…
Received 01 June 2009 17:44 UTC; Posted 02 June 2009
Posted to: Genetics & Genomics, Bioinformatics
Integrating Text Mining into the MGI Biocuration Workflow
A major challenge for the development of resources for functional and comparative genomics is the extraction of data from the biomedical literature. Although text retrieval and extraction for biol…
Received 20 May 2009 11:36 UTC; Posted 20 May 2009
Posted to: Bioinformatics
Biocuration Workflow Catalogue
As the first phase of a knowledge engineering study of biocuration workflows, we performed a preliminary task-modeling exercise on seven separate bioinformatics systems. This involved constructing …
Received 13 May 2009 18:00 UTC; Posted 13 May 2009
Posted to: Bioinformatics
Reflect: Augmented Browsing for the Life Scientist
Anyone who regularly reads life science literature often comes across names of genes, proteins, or small molecules that they would like to know more about. To make this process easier, we have deve…
Received 02 May 2009 01:44 UTC; Posted 04 May 2009
Posted to: Biotechnology, Chemistry, Genetics & Genomics, Molecular Cell Biology, Bioinformatics
Bringing Text Miners and Biologists Closer Together
The boosting of Biomedical Text Mining (BioTM) research in the last few years has led the way for finally bridging out the gap between text miners and biologists. Beyond the development of enhanced…
Received 27 April 2009 21:29 UTC; Posted 28 April 2009
Posted to: Bioinformatics
GOAssay: from Gene Ontology to Assays IDentifiers – Towards Automatic Functional Annotation of PubChem BioAssays
OBJECTIVES: We report on a experiment to functionally annotate PubChem assays using the Gene Ontology Categorizer (GOCat). METHODS and MATERIALS: The assays are processed to filter out non func…
Received 24 April 2009 20:48 UTC; Posted 28 April 2009
Posted to: Chemistry, Genetics & Genomics, Bioinformatics
UIMA in the Biocuration Workflow: A coherent framework for cooperation between biologists and computational linguists
As collaborating partners, Barcelona Media Innovation Centre and GRIB (Universitat Pompeu Fabra) seek to combine strengths from Computational Linguistics and Biomedicine to produce a robust Text Mi…
Received 24 April 2009 16:05 UTC; Posted 24 April 2009
Posted to: Bioinformatics
Direct submission system and literature annotation of rice genes in Oryzabase
Oryzabase (http://www.shigen.nig.ac.jp/rice/oryzabase/) is a comprehensive rice science database 1. It houses a variety of genetic resources, relevan…
Received 24 April 2009 04:20 UTC; Posted 24 April 2009
Posted to: Genetics & Genomics, Bioinformatics, Plant Biology
Text mining for Swiss-Prot curation: A story of success and failure
A text mining group has been set up at the Swiss Institute of Bioinformatics, with objective to develop and adapt information retrieval and extraction tools to help Swiss-Prot curators in their dai…
Received 24 April 2009 09:36 UTC; Posted 24 April 2009
Posted to: Bioinformatics
