[HTML][HTML] An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Background A major bottleneck in our understanding of the molecular underpinnings of life
is the assignment of function to proteins. While molecular experiments provide the most …
is the assignment of function to proteins. While molecular experiments provide the most …
[HTML][HTML] The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global,
community-driven effort to evaluate and improve the computational annotation of protein …
community-driven effort to evaluate and improve the computational annotation of protein …
[PDF][PDF] UTurku: drug named entity recognition and drug-drug interaction extraction using SVM classification and domain knowledge
The DDIExtraction 2013 task in the SemEval conference concerns the detection of drug
names and statements of drug-drug interactions (DDI) from text. Extraction of DDIs is important …
names and statements of drug-drug interactions (DDI) from text. Extraction of DDIs is important …
Neural network and random forest models in protein function prediction
Over the past decade, the demand for automated protein function prediction has increased
due to the volume of newly sequenced proteins. In this paper, we address the function …
due to the volume of newly sequenced proteins. In this paper, we address the function …
[PDF][PDF] Syntactic analyses and named entity recognition for PubMed and PubMed Central—up-to-the-minute
Although advanced text mining methods specifically adapted to the biomedical domain are
continuously being developed, their applications on large scale have been scarce. One of …
continuously being developed, their applications on large scale have been scarce. One of …
Cell line name recognition in support of the identification of synthetic lethality in cancer from text
Motivation: The recognition and normalization of cell line names in text is an important task
in biomedical text mining research, facilitating for instance the identification of synthetically …
in biomedical text mining research, facilitating for instance the identification of synthetically …
Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling
We present a system for automatically identifying a multitude of biomedical entities from the
literature. This work is based on our previous efforts in the BioCreative VI: Interactive Bio-ID …
literature. This work is based on our previous efforts in the BioCreative VI: Interactive Bio-ID …
[PDF][PDF] UTU: Disease mention recognition and normalization with CRFs and vector space representations
In this paper we present our system participating in the SemEval-2014 Task 7 in both subtasks
A and B, aiming at recognizing and normalizing disease and symptom mentions from …
A and B, aiming at recognizing and normalizing disease and symptom mentions from …
End-to-end system for bacteria habitat extraction
We introduce an end-to-end system capable of named-entity detection, normalization and
relation extraction for extracting information about bacteria and their habitats from biomedical …
relation extraction for extracting information about bacteria and their habitats from biomedical …
[PDF][PDF] Integrating large-scale text mining and co-expression networks: Targeting NADP (H) metabolism in E. coli with event extraction
S Kaewphan, S Kreula, S Van Landeghem… - Proceedings of the Third …, 2012 - utupub.fi
We present an application of EVEX, a literature-scale event extraction resource, in the
concrete biological use case of NADP (H) metabolism regulation in Escherichia coli. We make …
concrete biological use case of NADP (H) metabolism regulation in Escherichia coli. We make …