The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability

Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery

(2015) Christopher J. Mungall et al.   HUMAN MUTATION

Mouse genome database 2016

(2015) Carol J. Bult et al.   NUCLEIC ACIDS RESEARCH

ENCODE data at the ENCODE portal

(2015) Cricket A. Sloan et al.   NUCLEIC ACIDS RESEARCH

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

flowCL: ontology-based cell population labelling in flow cytometry

(2014) Mélanie Courtot et al.   BIOINFORMATICS

A method for increasing expressivity of Gene Ontology annotations using a compositional approach

(2014) Rachael P Huntley et al.   BMC BIOINFORMATICS

ImmPort: disseminating data to the public for the future of immunology

(2014) Sanchita Bhattacharya et al.   IMMUNOLOGIC RESEARCH

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes

(2014) J. Brad Karpinka et al.   NUCLEIC ACIDS RESEARCH

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

Representing Kidney Development Using the Gene Ontology

(2014) Yasmin Alam-Faruque et al.   PLoS One

The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio

(2014) Ceri E Van Slyke et al.   Journal of Biomedical Semantics

TermGenie – a web-application for pattern-based ontology class generation

(2014) Heiko Dietze et al.   Journal of Biomedical Semantics

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

(2014) Melissa A Haendel et al.   Journal of Biomedical Semantics

CLO: The cell line ontology

(2014) Sirarat Sarntivijai et al.   Journal of Biomedical Semantics

Critical assessment of automated flow cytometry data analysis techniques

(2013) Nima Aghaeepour et al.   NATURE METHODS

Protein Ontology: a controlled structured network of protein entities

(2013) Darren A. Natale et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments

(2013) Paola Roncaglia et al.   Journal of Biomedical Semantics

The neurological disease ontology

(2013) Mark Jensen et al.   Journal of Biomedical Semantics

The Drosophila anatomy ontology

(2013) Marta Costa et al.   Journal of Biomedical Semantics

A strategy for building neuroanatomy ontologies

(2012) David Osumi-Sutherland et al.   BIOINFORMATICS

Cytometry by Time-of-Flight Shows Combinatorial Cytokine Expression and Virus-Specific Cell Niches within a Continuum of CD8+ T Cell Phenotypes

(2012) Evan W. Newell et al.   IMMUNITY

500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton

(2012) P. Mabee et al.   JOURNAL OF APPLIED ICHTHYOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The cell: an image library-CCDB: a curated repository of microscopy data

(2012) David N. Orloff et al.   NUCLEIC ACIDS RESEARCH

ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics

(2012) Douglas G. Howe et al.   NUCLEIC ACIDS RESEARCH

The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

(2012) Laurel Cooper et al.   PLANT AND CELL PHYSIOLOGY

A Unified Anatomy Ontology of the Vertebrate Skeletal System

(2012) Wasila M. Dahdul et al.   PLoS One

A deep profiler's guide to cytometry

(2012) Sean C. Bendall et al.   TRENDS IN IMMUNOLOGY

Uberon, an integrative multi-species anatomy ontology

(2012) Christopher J Mungall et al.   GENOME BIOLOGY

Modeling biomedical experimental processes with OBI

(2012) Ryan R Brinkman et al.   Journal of Biomedical Semantics

The Virtual Fly Brain browser and query interface

(2011) N. Milyaev et al.   BIOINFORMATICS

Logical Development of the Cell Ontology

(2011) Terrence F Meehan et al.   BMC BIOINFORMATICS

CELLPEDIA: a repository for human cell information for cell studies and differentiation analyses

(2011) A. Hatano et al.   Database-The Journal of Biological Databases and Curation

Developing a kidney and urinary pathway knowledge base

(2011) Simon Jupp et al.   Journal of Biomedical Semantics

Modeling sample variables with an Experimental Factor Ontology

(2010) James Malone et al.   BIOINFORMATICS

Elucidation of seventeen human peripheral blood B-cell subsets and quantification of the tetanus response using a density-based method for the automated identification of cell populations in multidimensional flow cytometry data

(2010) Yu Qian et al.   CYTOMETRY PART B-CLINICAL CYTOMETRY

Interplay between Foxd3 and Mitf regulates cell fate plasticity in the zebrafish neural crest

(2010) Kevin Curran et al.   DEVELOPMENTAL BIOLOGY

Hematopoietic cell types: Prototype for a revised cell ontology

(2010) Alexander D. Diehl et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Cross-product extensions of the Gene Ontology

(2010) Christopher J. Mungall et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature

(2010) Wasila M. Dahdul et al.   PLoS One

An improved ontological representation of dendritic cells as a paradigm for all cell types

(2009) Anna Masci et al.   BMC BIOINFORMATICS

An ontology for Xenopus anatomy and development

(2008) Erik Segerdell et al.   BMC DEVELOPMENTAL BIOLOGY

The NIFSTD and BIRNLex Vocabularies: Building Comprehensive Ontologies for Neuroscience

(2008) William J. Bug et al.   NEUROINFORMATICS