AIMC Topic: Software

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Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects.

Database : the journal of biological databases and curation
UNLABELLED: With biodiversity research activities being increasingly shifted to the web, the need for a system of persistent and stable identifiers for physical collection objects becomes increasingly pressing. The Consortium of European Taxonomic Fa...

BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences.

Database : the journal of biological databases and curation
UNLABELLED: Extracting meaningful relationships with semantic significance from biomedical literature is often a challenging task. BioCreative V track4 challenge for the first time has organized a comprehensive shared task to test the robustness of t...

Tutorial on Protein Ontology Resources.

Methods in molecular biology (Clifton, N.J.)
The Protein Ontology (PRO) is the reference ontology for proteins in the Open Biomedical Ontologies (OBO) foundry and consists of three sub-ontologies representing protein classes of homologous genes, proteoforms (e.g., splice isoforms, sequence vari...

Development of a Web-Enabled SVR-Based Machine Learning Platform and its Application on Modeling Transgene Expression Activity of Aminoglycoside-Derived Polycations.

Combinatorial chemistry & high throughput screening
OBJECTIVE: Support Vector Regression (SVR) has become increasingly popular in cheminformatics modeling. As a result, SVR-based machine learning algorithms, including Fuzzy-SVR and Least Square-SVR (LS-SVR) have been developed and applied in various r...

Exploring Genome-Wide Expression Profiles Using Machine Learning Techniques.

Methods in molecular biology (Clifton, N.J.)
Although contemporary high-throughput -omics methods produce high-dimensional data, the resulting wealth of information is difficult to assess using traditional statistical procedures. Machine learning methods facilitate the detection of additional p...

Collection of Simulated Data from a Thalamocortical Network Model.

Neuroinformatics
A major challenge in experimental data analysis is the validation of analytical methods in a fully controlled scenario where the justification of the interpretation can be made directly and not just by plausibility. In some sciences, this could be a ...

Complementary Sources of Protein Functional Information: The Far Side of GO.

Methods in molecular biology (Clifton, N.J.)
The GO captures many aspects of functional annotations, but there are other alternative complementary sources of protein function information. For example, enzyme functional annotations are described in a range of resources from the Enzyme Commission...

The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations.

Methods in molecular biology (Clifton, N.J.)
The Evidence and Conclusion Ontology (ECO) is a community resource for describing the various types of evidence that are generated during the course of a scientific study and which are typically used to support assertions made by researchers. ECO des...

A Gene Ontology Tutorial in Python.

Methods in molecular biology (Clifton, N.J.)
This chapter is a tutorial on using Gene Ontology resources in the Python programming language. This entails querying the Gene Ontology graph, retrieving Gene Ontology annotations, performing gene enrichment analyses, and computing basic semantic sim...