AIMC Topic: Molecular Sequence Annotation
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DextMP: deep dive into text for predicting moonlighting proteins.
Bioinformatics (Oxford, England)
Jul 15, 2017
MOTIVATION: Moonlighting proteins (MPs) are an important class of proteins that perform more than one independent cellular function. MPs are gaining more attention in recent years as they are found to play important roles in various systems including...
agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update.
Nucleic acids research
Jul 3, 2017
The agriGO platform, which has been serving the scientific community for >10 years, specifically focuses on gene ontology (GO) enrichment analyses of plant and agricultural species. We continuously maintain and update the databases and accommodate th...
miRNAmeConverter: an R/bioconductor package for translating mature miRNA names to different miRBase versions.
Bioinformatics (Oxford, England)
Feb 15, 2017
SUMMARY: The miRBase database is the central and official repository for miRNAs and the current release is miRBase version 21.0. Name changes in different miRBase releases cause inconsistencies in miRNA names from version to version. When working wit...
Update notifications for the BioCyc collection of databases.
Database : the journal of biological databases and curation
Jan 1, 2017
https://BioCyc.org , https://EcoCyc.org , https://MetaCyc.org.
Biocuration in the structure-function linkage database: the anatomy of a superfamily.
Database : the journal of biological databases and curation
Jan 1, 2017
UNLABELLED: With ever-increasing amounts of sequence data available in both the primary literature and sequence repositories, there is a bottleneck in annotating molecular function to a sequence. This article describes the biocuration process and met...
Tutorial on Protein Ontology Resources.
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
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...
The Vision and Challenges of the Gene Ontology.
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
The overarching goal of the Gene Ontology (GO) Consortium is to provide researchers in biology and biomedicine with all current functional information concerning genes and the cellular context under which these occur. When the GO was started in the 1...
Complementary Sources of Protein Functional Information: The Far Side of GO.
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
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.)
Jan 1, 2017
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...
Annotation Extensions.
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
The specificity of knowledge that Gene Ontology (GO) annotations currently can represent is still restricted by the legacy format of the GO annotation file, a format intentionally designed for simplicity to keep the barriers to entry low and thus enc...
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