Standout Papers
Citation Impact
Citing Papers
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level
2010
Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements
2009
BioBERT: a pre-trained biomedical language representation model for biomedical text mining
2019 Standout
The variant call format and VCFtools
2011 Standout
The UK Biobank resource with deep phenotyping and genomic data
2018 StandoutNature
The cell line ontology-based representation, integration and analysis of cell lines used in China
2019
Phevor Combines Multiple Biomedical Ontologies for Accurate Identification of Disease-Causing Alleles in Single Individuals and Small Nuclear Families
2014
The relationship between proteome size, structural disorder and organism complexity
2011
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery
2014
DISEASES: Text mining and data integration of disease–gene associations
2014
An Expanded View of Complex Traits: From Polygenic to Omnigenic
2017 Standout
The Gene Ontology Resource: 20 years and still GOing strong
2018 Standout
DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants
2016 Standout
INOH: ontology-based highly structured database of signal transduction pathways
2011
Genetic effects on gene expression across human tissues
2017 StandoutNature
High-throughput functional annotation and data mining with the Blast2GO suite
2008 Standout
Variation Ontology for annotation of variation effects and mechanisms
2013
Multi-dimensionality of chronic pain of the oral cavity and face
2013
BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results
2011
The Pfam Protein Families Database
2002 Standout
BioLit: integrating biological literature with databases
2008
NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data
2015
PubChemRDF: towards the semantic annotation of PubChem compound and substance databases
2015
agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update
2017 Standout
ChEMBL: a large-scale bioactivity database for drug discovery
2011 Standout
Radiomics: Images Are More than Pictures, They Are Data
2015 Standout
The Units Ontology: a tool for integrating units of measurement in science
2012
A standard variation file format for human genome sequences
2010
ClinVar: public archive of relationships among sequence variation and human phenotype
2013 Standout
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible
2016 Standout
Considerations for sociotechnical design: experiences with an electronic patient record in a clinical context
1998
Database resources of the National Center for Biotechnology Information: update
2003 Standout
Annotation of Figures from the Biomedical Imaging Literature
2014
The landscape of long noncoding RNAs in the human transcriptome
2015 Standout
OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders
2014 Standout
Multimodal biomedical AI
2022 Standout
The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web
2011
PubChem Substance and Compound databases
2015 Standout
The Human Phenotype Ontology
2010
Functional MRI at the crossroads
2008
VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases
2014
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
2013 Standout
WikiPathways: Pathway Editing for the People
2008
Uberon, an integrative multi-species anatomy ontology
2012
Functional mapping and annotation of genetic associations with FUMA
2017 Standout
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources
2010
Modeling biomedical experimental processes with OBI
2010
Evolving BioAssay Ontology (BAO): modularization, integration and applications
2014
Coming of age: ten years of next-generation sequencing technologies
2016 Standout
Telehealth
2017 Standout
The Pfam protein families database
2009 Standout
The ChEMBL database in 2017
2016 Standout
Enhancing patient safety and quality of care by improving the usability of electronic health record systems: recommendations from AMIA
2013
Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets
2016 Standout
Evolution of the Sequence Ontology terms and relationships
2010
Disease Ontology: a backbone for disease semantic integration
2011
The Human Phenotype Ontology: A Tool for Annotating and Analyzing Human Hereditary Disease
2008
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update
2016 Standout
MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data
2012 Standout
ClinVar: public archive of interpretations of clinically relevant variants
2015 Standout
The Unified Medical Language System (UMLS): integrating biomedical terminology
2003 Standout
Hepatic Stellate Cells: Protean, Multifunctional, and Enigmatic Cells of the Liver
2008 Standout
GREAT improves functional interpretation of cis-regulatory regions
2010 Standout
The immune epitope database (IEDB) 3.0
2014 Standout
Chemical Entities of Biological Interest: an update
2009
Towards revealing the functions of all genes in plants
2013
The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY
2017 Standout
SMART on FHIR: a standards-based, interoperable apps platform for electronic health records
2016
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
2017 StandoutScience
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences
2021 Standout
miRDB: an online database for prediction of functional microRNA targets
2019 Standout
Systematic Review: Impact of Health Information Technology on Quality, Efficiency, and Costs of Medical Care
2006 Standout
Neuropathic Pain: From Mechanisms to Treatment
2020 Standout
Machine Learning in Medicine
2019 Standout
Classification of Intrinsically Disordered Regions and Proteins
2014 Standout
PubChem 2023 update
2022 Standout
Manual curation is not sufficient for annotation of genomic databases
2007
Additional Gene Ontology structure for improved biological reasoning
2006
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis
2018 Standout
The Unified Medical Language System
1993
Experience sampling during fMRI reveals default network and executive system contributions to mind wandering
2009 Standout
The revised International Association for the Study of Pain definition of pain: concepts, challenges, and compromises
2020 Standout
The DisGeNET knowledge platform for disease genomics: 2019 update
2019 Standout
OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets
2017
The Protein Feature Ontology: a tool for the unification of protein feature annotations
2008
Concept of Sample in OMICS Technology
2006
PubChem in 2021: new data content and improved web interfaces
2020 Standout
Modeling sample variables with an Experimental Factor Ontology
2010
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets
2020 Standout
Human Disease Ontology 2018 update: classification, content and workflow expansion
2018
DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)
2022 Standout
EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats
2013
Works of Werner Ceusters being referenced
Models for representation of terminologies and coding systems in medicine.
1993
Foundations for a realist ontology of mental disease
2010
A novel view on information content of concepts in a large ontology and a view on the structure and the quality of the ontology
2004
Relations in biomedical ontologies
2005 Standout
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
2007 Standout
Ontological realism: A methodology for coordinated evolution of scientific ontologies
2010
Classifying orofacial pains: a new proposal of taxonomy based on ontology
2011
Mistakes in Medical Ontologies: Where Do They Come From and How Can They Be Detected?
2004
Toward an ontological treatment of disease and diagnosis.
2009
Perspectives on next steps in classification of oro‐facial pain – part 1: role of ontology
2015
A realism-based approach to the evolution of biomedical ontologies.
2006
From Natural Language to Formal Language: when MultiTALE meets GALEN
1997
HL7 RIM: an incoherent standard.
2006