Chemical Entities of Biological Interest
Names
More detailed information about this field from each metasource.
Chemical Entities of Biological Interest
metasource: Fairsharing.org
version: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: re3data.org
version: re3data.org: ChEBI; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3H78W last accessed: 2022-11-04
ChEBI
metasource: Fairsharing.org
version: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: re3data.org
version: re3data.org: ChEBI; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3H78W last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:10.906729
Chemical Entities of Biological Interest Ontology
metasource: Biontology / Bioportal
version: 214 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/CHEBI
CHEBI
metasource: Biontology / Bioportal
version: 214 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/CHEBI
ChEBI - Chemical Entities of Biological Interest
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
chebi
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:10.906729
Names
More detailed information about this field from each metasource.
Chemical Entities of Biological Interest
metasource: Fairsharing.orgversion: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: re3data.org
version: re3data.org: ChEBI; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3H78W last accessed: 2022-11-04
ChEBI
metasource: Fairsharing.orgversion: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: re3data.org
version: re3data.org: ChEBI; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3H78W last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:10.906729
Chemical Entities of Biological Interest Ontology
metasource: Biontology / Bioportalversion: 214 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/CHEBI
CHEBI
metasource: Biontology / Bioportalversion: 214 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/CHEBI
ChEBI - Chemical Entities of Biological Interest
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
chebi
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:10.906729
Other names: ChEBI, Chemical Entities of Biological Interest Ontology, CHEBI, ChEBI - Chemical Entities of Biological Interest, chebi
Names
More detailed information about this field from each metasource.
Chemical Entities of Biological Interest
metasource: Fairsharing.orgversion: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: re3data.org
version: re3data.org: ChEBI; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3H78W last accessed: 2022-11-04
ChEBI
metasource: Fairsharing.orgversion: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: re3data.org
version: re3data.org: ChEBI; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3H78W last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:10.906729
Chemical Entities of Biological Interest Ontology
metasource: Biontology / Bioportalversion: 214 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/CHEBI
CHEBI
metasource: Biontology / Bioportalversion: 214 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/CHEBI
ChEBI - Chemical Entities of Biological Interest
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
chebi
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:10.906729
Chemical Entities of Biological Interest (ChEBI) is a free dictionary that describes 'small’ chemical compounds. These compound includes distinct synthetic or natural atoms, molecules, ions, ion pair, radicals, radical ions, complexes, conformers, etc.. These molecular entities can interact with or affect the processes of living organisms.
Description
More detailed information about this field from each metasource.
Chemical Entities of Biological Interest (ChEBI) is a free dictionary that describes 'small’ chemical compounds. These compound includes distinct synthetic or natural atoms, molecules, ions, ion pair, radicals, radical ions, complexes, conformers, etc.. These molecular entities can interact with or affect the processes of living organisms.
metasource: Fairsharing.orgversion: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
A structured classification of chemical compounds of biological relevance.
metasource: Biontology / Bioportalversion: 214 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/CHEBI
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity [1]. The molecular entities in question are either natural products or synthetic products used to intervene in the processes of living organisms. Genome-encoded macromolecules (nucleic acids, proteins and peptides derived from proteins by cleavage) are not as a rule included in ChEBI. In addition to molecular entities, ChEBI contains groups (parts of molecular entities) and classes of entities. ChEBI encompasses an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. ChEBI uses nomenclature, symbolism and terminology endorsed by the following international scientific bodies:- International Union of Pure and Applied Chemistry (http://www.iupac.org/) (IUPAC)- Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (http://www.iubmb.org/) (NC-IUBMB) All data in the database is non-proprietary or is derived from a non-proprietary source. Each data item is fully traceable and explicitly referenced to the original source. ChEBI shows the following data fields:- ChEBI identifer - the unique identifer- ChEBI name - the name recommended for use in biological databases- ChEBI ASCII name - the ChEBI name with any special characters rendered in ASCII format- Definition - a short verbal definition is included in some entries, especially relevant to classes- Structure - graphical representation(s) of a molecular structure and associated molfile(s), IUPAC International Chemical Identifier (InChI) and SMILES strings- Formula - Molecular formula- Parents and children, according to ChEBI Ontology- IUPAC name - a name generated according to the recommendations of IUPAC- Synonyms - other names together with an indication of their source- Database links - manually curated cross-references to other non-proprietary databases- Registry numbers - CAS Registry Number, Beilstein Registry Number, Gmelin Registry Number (if available)- Comment(s) - A free-text comment may be added to some terms, especially in cases where confusing terminology has been historically used. A comment may relate to a single term or to the entry as a whole.The ChEBI terms have been automatically mapped to the UniProt (http://www.ebi.uniprot.org/) database, and for each ChEBI entity the list of UniProt entries containing the relevant terms are available. ChEBI can be accessed through the WWW (http://www.ebi.ac.uk/chebi/) or may be downloaded by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/chebi/).
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of 'small molecular entities'. The term 'molecular entity' encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms (either deliberately, as for drugs, or unintentionally', as for chemicals in the environment). The qualifier 'small' implies the exclusion of entities directly encoded by the genome, and thus as a rule nucleic acids, proteins and peptides derived from proteins by cleavage are not included.
metasource: re3data.orgversion: re3data.org: ChEBI; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3H78W last accessed: 2022-11-04
Dictionary of molecular entities focused on small chemical compounds. "Molecular entity" includes any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:10.906729
Webpage:
http://www.ebi.ac.uk/chebi/Webpage
More detailed information about this field from each metasource.
http://www.ebi.ac.uk/chebi/
metasource: Fairsharing.orgversion: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:10.906729
http://www.ebi.ac.uk/chebi
metasource: Biontology / Bioportalversion: 214 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/CHEBI
https://www.ebi.ac.uk/chebi/
metasource: re3data.orgversion: re3data.org: ChEBI; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3H78W last accessed: 2022-11-04
Licence:
Name: Creative Commons Attribution 4.0 International (CC BY 4.0)Licence name
More detailed information about this field from each metasource.
Creative Commons Attribution 4.0 International (CC BY 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
other
metasource: re3data.orgversion: re3data.org: ChEBI; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3H78W last accessed: 2022-11-04
Licence URL
More detailed information about this field from each metasource.
https://creativecommons.org/licenses/by/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
https://www.ebi.ac.uk/about/terms-of-use
metasource: re3data.orgversion: re3data.org: ChEBI; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3H78W last accessed: 2022-11-04
Publications:
(7)
Publications
More detailed information about this field from each metasource.
ChEBI: a database and ontology for chemical entities of biological interest
PMID: 17932057
metasource: Fairsharing.org
version: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013
PMID: 23180789
metasource: Fairsharing.org
version: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
ChEBI in 2016: Improved services and an expanding collection of metabolites
PMID: 26467479
metasource: Fairsharing.org
version: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
Chemical Entities of Biological Interest: an update
PMID: 19854951
metasource: Fairsharing.org
version: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
ChEBI: an open bioinformatics and cheminformatics resource
PMID: 19496059
metasource: Fairsharing.org
version: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
http://dx.doi.org/10.1093/nar/gks1146
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1186/1758-2946-2-S1-P6
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:10.906729
Publications
More detailed information about this field from each metasource.
ChEBI: a database and ontology for chemical entities of biological interest
PMID: 17932057
metasource: Fairsharing.org
version: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013
PMID: 23180789
metasource: Fairsharing.org
version: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
ChEBI in 2016: Improved services and an expanding collection of metabolites
PMID: 26467479
metasource: Fairsharing.org
version: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
Chemical Entities of Biological Interest: an update
PMID: 19854951
metasource: Fairsharing.org
version: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
ChEBI: an open bioinformatics and cheminformatics resource
PMID: 19496059
metasource: Fairsharing.org
version: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
http://dx.doi.org/10.1093/nar/gks1146
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1186/1758-2946-2-S1-P6
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:10.906729
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ChEBI: a database and ontology for chemical entities of biological interest
PubMed citations: 359.
359 articles citing: ChEBI: a database and ontology for chemical entities of biological interest
The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept. PMID:35889831
Establishing a Common Nutritional Vocabulary - From Food Production to Diet. PMID:35811979
Semantics of Dairy Fermented Foods: A Microbiologist's Perspective. PMID:35804753
Nobiletin as a Neuroprotectant against NMDA Receptors: An In Silico Approach. PMID:35745697
Automated Rational Design of Metal-Organic Polyhedra. PMID:35731954
DACPGTN: Drug ATC Code Prediction Method Based on Graph Transformer Network for Drug Discovery. PMID:35721178
Ficus benghalensis promotes the glucose uptake- Evidence with in silico and in vitro. PMID:35673455
Chemical reaction network knowledge graphs: the OntoRXN ontology. PMID:35637523
An evidence-based lexical pattern approach for quality assurance of Gene Ontology relations. PMID:35419584
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. PMID:35388368
Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation. PMID:35350714
Parallel sequence tagging for concept recognition. PMID:35331131
A Genome-Scale Metabolic Model for the Human Pathogen Candida Parapsilosis and Early Identification of Putative Novel Antifungal Drug Targets. PMID:35205348
Structure-based knowledge acquisition from electronic lab notebooks for research data provenance documentation. PMID:35101121
Illuminating the lineage-specific diversification of resin glycoside acylsugars in the morning glory (Convolvulaceae) family using computational metabolomics. PMID:35039851
MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data. PMID:34822401
Machine Learning Assisted Approach for Finding Novel High Activity Agonists of Human Ectopic Olfactory Receptors. PMID:34768977
LitCovid-AGAC: cellular and molecular level annotation data set based on COVID-19. PMID:34638170
Biofluid Metabolomics of Mice Exposed to External Low-Dose Rate Radiation in a Novel Irradiation System, the Variable Dose-Rate External 137Cs Irradiator. PMID:34585931
Plasma Metabolome Profiling by High-Performance Chemical Isotope-Labelling LC-MS after Acute and Medium-Term Intervention with Golden Berry Fruit (Physalis peruviana L.), Confirming Its Impact on Insulin-Associated Signaling Pathways. PMID:34579001
Enhancing the interoperability of glycan data flow between ChEBI, PubChem and GlyGen. PMID:34314492
The Infectious Disease Ontology in the age of COVID-19. PMID:34275487
Databases for Protein-Protein Interactions. PMID:34236665
Composition and Associations of the Infant Gut Fungal Microbiota with Environmental Factors and Childhood Allergic Outcomes. PMID:34060330
Learning adaptive representations for entity recognition in the biomedical domain. PMID:34001263
Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies. PMID:33991093
Identification of PTP1B regulators from Cymbopogon citratus and its enrichment analysis for diabetes mellitus. PMID:33928007
Semantic standards of external exposome data. PMID:33901445
Ontology-driven weak supervision for clinical entity classification in electronic health records. PMID:33795682
An immunologically friendly classification of non-peptidic ligands. PMID:33772585
Learning chemistry: exploring the suitability of machine learning for the task of structure-based chemical ontology classification. PMID:33726837
Few-Shot Induction of Generalized Logical Concepts via Human Guidance. PMID:33501288
Ontologies relevant to behaviour change interventions: a method for their development. PMID:33447665
SeMPI 2.0-A Web Server for PKS and NRPS Predictions Combined with Metabolite Screening in Natural Product Databases. PMID:33383692
Feasible-metabolic-pathway-exploration technique using chemical latent space. PMID:33381845
The 4R's Framework of Nutritional Strategies for Post-Exercise Recovery: A Review with Emphasis on New Generation of Carbohydrates. PMID:33375691
Multipath: An R Package to Generate Integrated Reproducible Pathway Models. PMID:33371258
Outlier concepts auditing methodology for a large family of biomedical ontologies. PMID:33319713
Informing epidemic (research) responses in a timely fashion by knowledge management - a Zika virus use case. PMID:33148605
The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering. PMID:33015004
Automated Annotation of Sphingolipids Including Accurate Identification of Hydroxylation Sites Using MSn Data. PMID:33003696
Integrative transcriptomics analysis of lung epithelial cells and identification of repurposable drug candidates for COVID-19. PMID:32971089
Knowledge Graph Approach to Combustion Chemistry and Interoperability. PMID:32743209
Toward Automated Inventory Modeling in Life Cycle Assessment: The Utility of Semantic Data Modeling to Predict Real-World Chemical Production. PMID:32632354
Building a PubMed knowledge graph. PMID:32591513
FOBI: an ontology to represent food intake data and associate it with metabolomic data. PMID:32556148
DDIEM: drug database for inborn errors of metabolism. PMID:32527280
Effects of Genetic Variation on Urinary Small Molecule Signatures of Mice after Exposure to Ionizing Radiation: A Study of p53 Deficiency. PMID:32521675
Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB). PMID:32463383
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources. PMID:32429287
Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. PMID:32313939
BioHackathon 2015: Semantics of data for life sciences and reproducible research. PMID:32308977
The Role and Promise of Artificial Intelligence in Medical Toxicology. PMID:32215849
A Computational Approach for Mapping Heme Biology in the Context of Hemolytic Disorders. PMID:32211383
Reconstruction and Analysis of Cattle Metabolic Networks in Normal and Acidosis Rumen Tissue. PMID:32168900
An Integrated Multi-Disciplinary Perspectivefor Addressing Challenges of the Human Gut Microbiome. PMID:32155792
DNA N6-Methyladenine Modification in Plant Genomes-A Glimpse into Emerging Epigenetic Code. PMID:32075056
Enhancing the drug ontology with semantically-rich representations of National Drug Codes and RxNorm unique concept identifiers. PMID:31865907
A 2018 workshop: vaccine and drug ontology studies (VDOS 2018). PMID:31865905
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data. PMID:31821406
STS-NLSP: A Network-Based Label Space Partition Method for Predicting the Specificity of Membrane Transporter Substrates Using a Hybrid Feature of Structural and Semantic Similarity. PMID:31781551
Identifying novel sphingosine kinase 1 inhibitors as therapeutics against breast cancer. PMID:31752564
Accurate and Efficient Determination of Unknown Metabolites in Metabolomics by NMR-Based Molecular Motif Identification. PMID:31718151
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
Multi-Target β-Protease Inhibitors from Andrographis paniculata: In Silico and In Vitro Studies. PMID:31319560
FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration. PMID:31304272
iMet: A graphical user interface software tool to merge metabolic networks. PMID:31286073
An ontology for representing hematologic malignancies: the cancer cell ontology. PMID:31272372
PerMM: A Web Tool and Database for Analysis of Passive Membrane Permeability and Translocation Pathways of Bioactive Molecules. PMID:31259547
LION/web: a web-based ontology enrichment tool for lipidomic data analysis. PMID:31141612
Auto-Generated Physiological Chain Data for an Ontological Framework for Pharmacology and Mechanism of Action to Determine Suspected Drugs in Cases of Dysuria. PMID:31119651
Navigating in vitro bioactivity data by investigating available resources using model compounds. PMID:31036807
DNAmod: the DNA modification database. PMID:31016417
Too many tags spoil the metadata: investigating the knowledge management of scientific research with semantic web technologies. PMID:30900066
How to Develop a Drug Target Ontology: KNowledge Acquisition and Representation Methodology (KNARM). PMID:30848456
Liquid Chromatography-Mass Spectrometry-Based Metabolomics of Nonhuman Primates after 4 Gy Total Body Radiation Exposure: Global Effects and Targeted Panels. PMID:30843397
CSgator: an integrated web platform for compound set analysis. PMID:30830479
Metabolic fingerprinting analysis of oil palm reveals a set of differentially expressed metabolites in fatal yellowing symptomatic and non-symptomatic plants. PMID:30830392
Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling. PMID:30736318
OGER++: hybrid multi-type entity recognition. PMID:30666476
Chemlistem: chemical named entity recognition using recurrent neural networks. PMID:30523437
MER: a shell script and annotation server for minimal named entity recognition and linking. PMID:30519990
Harmonizing semantic annotations for computational models in biology. PMID:30462164
C/VDdb: A multi-omics expression profiling database for a knowledge-driven approach in cardiovascular disease (CVD). PMID:30419069
A Structure- and Ligand-Based Virtual Screening of a Database of "Small" Marine Natural Products for the Identification of "Blue" Sigma-2 Receptor Ligands. PMID:30322188
LION LBD: a literature-based discovery system for cancer biology. PMID:30304355
Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling. PMID:30239666
Mind the Gap: Mapping Mass Spectral Databases in Genome-Scale Metabolic Networks Reveals Poorly Covered Areas. PMID:30223552
Linked open data-based framework for automatic biomedical ontology generation. PMID:30200874
Nonhuman Primates with Acute Radiation Syndrome: Results from a Global Serum Metabolomics Study after 7.2 Gy Total-Body Irradiation. PMID:30183511
DrugMetab: An Integrated Machine Learning and Lexicon Mapping Named Entity Recognition Method for Drug Metabolite. PMID:30033622
CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. PMID:30012108
Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism. PMID:29973148
Sachem: a chemical cartridge for high-performance substructure search. PMID:29797000
Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics. PMID:29748461
Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse. PMID:29743102
Signalling maps in cancer research: construction and data analysis. PMID:29688383
OliveNet™: a comprehensive library of compounds from Olea europaea. PMID:29688352
Analyzing user interactions with biomedical ontologies: A visual perspective. PMID:29657560
Ligand Binding Site Structure Influences the Evolution of Protein Complex Function and Topology. PMID:29562182
LAILAPS-QSM: A RESTful API and JAVA library for semantic query suggestions. PMID:29529024
SistematX, an Online Web-Based Cheminformatics Tool for Data Management of Secondary Metabolites. PMID:29301376
Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data. PMID:29291722
Integrating phenotype ontologies with PhenomeNET. PMID:29258588
From word models to executable models of signaling networks using automated assembly. PMID:29175850
Taxonomy-Based Approaches to Quality Assurance of Ontologies. PMID:29158885
Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. PMID:29140462
Entity recognition in the biomedical domain using a hybrid approach. PMID:29122011
A review of parameters and heuristics for guiding metabolic pathfinding. PMID:29086092
Critical Assessment of Small Molecule Identification 2016: automated methods. PMID:29086042
The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production. PMID:29062930
Deciphering lipid structures based on platform-independent decision rules. PMID:29058722
Towards refactoring the Molecular Function Ontology with a UML profile for function modeling. PMID:28978337
iATC-mHyb: a hybrid multi-label classifier for predicting the classification of anatomical therapeutic chemicals. PMID:28938573
BIOSSES: a semantic sentence similarity estimation system for the biomedical domain. PMID:28881973
Imaging mass spectrometry and MS/MS molecular networking reveals chemical interactions among cuticular bacteria and pathogenic fungi associated with fungus-growing ants. PMID:28717220
The self-inhibitory nature of metabolic networks and its alleviation through compartmentalization. PMID:28691704
Predicting anatomic therapeutic chemical classification codes using tiered learning. PMID:28617230
Model-based biotechnological potential analysis of Kluyveromyces marxianus central metabolism. PMID:28444480
Semantic prioritization of novel causative genomic variants. PMID:28414800
CATTLE (CAncer treatment treasury with linked evidence): An integrated knowledge base for personalized oncology research and practice. PMID:28296354
A Lipidomic and Metabolomic Serum Signature from Nonhuman Primates Exposed to Ionizing Radiation. PMID:28220056
Proposed Confidence Scale and ID Score in the Identification of Known-Unknown Compounds Using High Resolution MS Data. PMID:28116700
Technical Challenges in Mass Spectrometry-Based Metabolomics. PMID:27900235
YMDB 2.0: a significantly expanded version of the yeast metabolome database. PMID:27899612
Systems-level analysis of mechanisms regulating yeast metabolic flux. PMID:27789812
Prediction, Detection, and Validation of Isotope Clusters in Mass Spectrometry Data. PMID:27775610
Notions of similarity for systems biology models. PMID:27742665
Progress Towards Computational 3-D Multicellular Systems Biology. PMID:27739051
Exploring Hydrogenotrophic Methanogenesis: a Genome Scale Metabolic Reconstruction of Methanococcus maripaludis. PMID:27736793
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. PMID:27664130
MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models. PMID:27536246
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. PMID:27377652
DrugQuest - a text mining workflow for drug association discovery. PMID:27295093
HITSZ_CDR: an end-to-end chemical and disease relation extraction system for BioCreative V. PMID:27270713
Generation of open biomedical datasets through ontology-driven transformation and integration processes. PMID:27255189
The cellular microscopy phenotype ontology. PMID:27195102
The Ontology for Biomedical Investigations. PMID:27128319
An accurate and precise representation of drug ingredients. PMID:27096073
Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning. PMID:27087307
In silico methods for drug repurposing and pharmacology. PMID:27080087
A physiome interoperability roadmap for personalized drug development. PMID:27051513
Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies. PMID:26988001
Challenges in horizontal model integration. PMID:26968798
Metabolomics in rheumatic diseases: desperately seeking biomarkers. PMID:26935283
libChEBI: an API for accessing the ChEBI database. PMID:26933452
Selectivity profiling of BCRP versus P-gp inhibition: from automated collection of polypharmacology data to multi-label learning. PMID:26855674
Integration and Validation of the Genome-Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism. PMID:26812499
Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products. PMID:26808821
Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders. PMID:26690135
SureChEMBL: a large-scale, chemically annotated patent document database. PMID:26582922
Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction. PMID:26566239
Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. PMID:26559508
Identification of Chemical Toxicity Using Ontology Information of Chemicals. PMID:26508991
PhenoMiner: from text to a database of phenotypes associated with OMIM diseases. PMID:26507285
Cell scale host-pathogen modeling: another branch in the evolution of constraint-based methods. PMID:26500611
ChEBI in 2016: Improved services and an expanding collection of metabolites. PMID:26467479
Physicochemical characteristics of structurally determined metabolite-protein and drug-protein binding events with respect to binding specificity. PMID:26442281
Geroprotectors.org: a new, structured and curated database of current therapeutic interventions in aging and age-related disease. PMID:26342919
Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies. PMID:26320941
Optimal Threshold Determination for Interpreting Semantic Similarity and Particularity: Application to the Comparison of Gene Sets and Metabolic Pathways Using GO and ChEBI. PMID:26230274
Global Metabolomic Identification of Long-Term Dose-Dependent Urinary Biomarkers in Nonhuman Primates Exposed to Ionizing Radiation. PMID:26230079
OCDB: a database collecting genes, miRNAs and drugs for obsessive-compulsive disorder. PMID:26228432
Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013. PMID:26202570
PubChemRDF: towards the semantic annotation of PubChem compound and substance databases. PMID:26175801
SEEK: a systems biology data and model management platform. PMID:26160520
The Chemical Validation and Standardization Platform (CVSP): large-scale automated validation of chemical structure datasets. PMID:26155308
A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case. PMID:26100720
Many InChIs and quite some feat. PMID:26081259
Computational Metabolomics Operations at BioCyc.org. PMID:26011592
Biocuration at the Saccharomyces genome database. PMID:25997651
Visualisation of BioPAX Networks using BioLayout Express (3D). PMID:25949802
Chemical Entity Recognition and Resolution to ChEBI. PMID:25937941
Abstraction networks for terminologies: Supporting management of "big knowledge". PMID:25890687
A comparison of conditional random fields and structured support vector machines for chemical entity recognition in biomedical literature. PMID:25810779
A document processing pipeline for annotating chemical entities in scientific documents. PMID:25810778
LeadMine: a grammar and dictionary driven approach to entity recognition. PMID:25810776
The CHEMDNER corpus of chemicals and drugs and its annotation principles. PMID:25810773
CheNER: a tool for the identification of chemical entities and their classes in biomedical literature. PMID:25810772
Combining computational models, semantic annotations and simulation experiments in a graph database. PMID:25754863
Describing the breakbone fever: IDODEN, an ontology for dengue fever. PMID:25646954
Reconstruction and analysis of a genome-scale metabolic model of the oleaginous fungus Mortierella alpina. PMID:25582171
Using a genome-scale metabolic model of Enterococcus faecalis V583 to assess amino acid uptake and its impact on central metabolism. PMID:25527553
The application of the open pharmacological concepts triple store (open PHACTS) to support drug discovery research. PMID:25522365
Finding gene regulatory network candidates using the gene expression knowledge base. PMID:25490885
EXACT2: the semantics of biomedical protocols. PMID:25472549
LigDig: a web server for querying ligand-protein interactions. PMID:25433696
Bioinformatics: the next frontier of metabolomics. PMID:25389922
DEOP: a database on osmoprotectants and associated pathways. PMID:25326239
A reappraisal of how to build modular, reusable models of biological systems. PMID:25275523
Annotated chemical patent corpus: a gold standard for text mining. PMID:25268232
Identification of structural features in chemicals associated with cancer drug response: a systematic data-driven analysis. PMID:25161239
KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems. PMID:25115331
The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation. PMID:25068035
Automated LC-HRMS(/MS) approach for the annotation of fragment ions derived from stable isotope labeling-assisted untargeted metabolomics. PMID:24965664
Egas: a collaborative and interactive document curation platform. PMID:24923820
Metabolomic Characterization of Knockout Mutants in Arabidopsis: Development of a Metabolite Profiling Database for Knockout Mutants in Arabidopsis. PMID:24828308
Phenotype ontologies and cross-species analysis for translational research. PMID:24699242
Computational tools for the secondary analysis of metabolomics experiments. PMID:24688685
Thematic series on biomedical ontologies in JBMS: challenges and new directions. PMID:24602198
KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics. PMID:24564846
Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing. PMID:24484917
The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources. PMID:24438387
Prediction of drugs target groups based on ChEBI ontology. PMID:24350241
Semantic integration of gene expression analysis tools and data sources using software connectors. PMID:24341380
The environment ontology: contextualising biological and biomedical entities. PMID:24330602
Extending the "web of drug identity" with knowledge extracted from United States product labels. PMID:24303301
SWEETLEAD: an in silico database of approved drugs, regulated chemicals, and herbal isolates for computer-aided drug discovery. PMID:24223973
Quantification of the impact of PSI:Biology according to the annotations of the determined structures. PMID:24139526
Evaluation and cross-comparison of lexical entities of biological interest (LexEBI). PMID:24124474
GPCR ontology: development and application of a G protein-coupled receptor pharmacology knowledge framework. PMID:24078711
A modular framework for biomedical concept recognition. PMID:24063607
The human urine metabolome. PMID:24023812
The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species. PMID:23937709
Flux balance analysis of cyanobacterial metabolism: the metabolic network of Synechocystis sp. PCC 6803. PMID:23843751
In silico modeling of shear-stress-induced nitric oxide production in endothelial cells through systems biology. PMID:23708369
Metabolic tinker: an online tool for guiding the design of synthetic metabolic pathways. PMID:23580552
Recent progress in the development of metabolome databases for plant systems biology. PMID:23577015
Bioanalysis of eukaryotic organelles. PMID:23570618
PharmaTrek: A Semantic Web Explorer for Open Innovation in Multitarget Drug Discovery. PMID:23548981
From ontology to semantic similarity: calculation of ontology-based semantic similarity. PMID:23533360
Integration of clinical data with a genome-scale metabolic model of the human adipocyte. PMID:23511207
The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. PMID:23482073
EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. PMID:23479348
Controlled vocabularies and ontologies in proteomics: overview, principles and practice. PMID:23429179
Ontology for vector surveillance and management. PMID:23427646
Application of Top-Down and Bottom-up Systems Approaches in Ruminant Physiology and Metabolism. PMID:23372424
Visualization of protein interaction networks: problems and solutions. PMID:23368786
Chapter 3: Small molecules and disease. PMID:23300405
The Internet as Scientific Knowledge Base: Navigating the Chem-Bio Space. PMID:23293679
ChemEx: information extraction system for chemical data curation. PMID:23282330
Automated compound classification using a chemical ontology. PMID:23273256
Building an efficient curation workflow for the Arabidopsis literature corpus. PMID:23221298
Redefining Cheminformatics with Intuitive Collaborative Mobile Apps. PMID:23198002
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. PMID:23180789
Reconciliation of metabolites and biochemical reactions for metabolic networks. PMID:23172809
Gene Ontology annotations and resources. PMID:23161678
A UML profile for the OBO relation ontology. PMID:23095840
MetNet Online: a novel integrated resource for plant systems biology. PMID:23066841
Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes. PMID:23046642
Towards improving phenotype representation in OWL. PMID:23046625
Ontologies as integrative tools for plant science. PMID:22847540
Bayesian ontology querying for accurate and noise-tolerant semantic searches. PMID:22843981
A text-mining system for extracting metabolic reactions from full-text articles. PMID:22823282
Concept annotation in the CRAFT corpus. PMID:22776079
Public domain databases for medicinal chemistry. PMID:22731701
Improving disease gene prioritization by comparing the semantic similarity of phenotypes in mice with those of human diseases. PMID:22719993
Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics. PMID:22711793
Bioinformatics advances in saliva diagnostics. PMID:22699264
Mass spectrometry-based metabolomics to elucidate functions in marine organisms and ecosystems. PMID:22690147
Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. PMID:22663945
Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity. PMID:22645535
MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity. PMID:22591066
A chemical specialty semantic network for the Unified Medical Language System. PMID:22577759
Improving integrative searching of systems chemical biology data using semantic annotation. PMID:22401035
Uberon, an integrative multi-species anatomy ontology. PMID:22293552
Propagating semantic information in biochemical network models. PMID:22289386
KB-Rank: efficient protein structure and functional annotation identification via text query. PMID:22270457
Self-organizing ontology of biochemically relevant small molecules. PMID:22221313
Physical properties of biological entities: an introduction to the ontology of physics for biology. PMID:22216106
New concepts for building vocabulary for cell image ontologies. PMID:22188658
A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature. PMID:22151823
Exact score distribution computation for ontological similarity searches. PMID:22078312
PathCase-SB architecture and database design. PMID:22070889
SCRIPDB: a portal for easy access to syntheses, chemicals and reactions in patents. PMID:22067445
YMDB: the Yeast Metabolome Database. PMID:22064855
Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology. PMID:22041276
Improving ontologies by automatic reasoning and evaluation of logical definitions. PMID:22032770
BioPAX support in CellDesigner. PMID:22021903
OSCAR4: a flexible architecture for chemical text-mining. PMID:21999457
The representation of protein complexes in the Protein Ontology (PRO). PMID:21929785
GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution. PMID:21914205
Using the Saccharomyces Genome Database (SGD) for analysis of genomic information. PMID:21901739
Minimum information about a bioactive entity (MIABE). PMID:21878981
The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions. PMID:21878109
Integrating systems biology models and biomedical ontologies. PMID:21835028
Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics. PMID:21791100
Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning. PMID:21789201
Retrieval, alignment, and clustering of computational models based on semantic annotations. PMID:21772260
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
PhenomeNET: a whole-phenome approach to disease gene discovery. PMID:21737429
Informatics and standards for nanomedicine technology. PMID:21721140
AMDORAP: non-targeted metabolic profiling based on high-resolution LC-MS. PMID:21702951
Mining metabolites: extracting the yeast metabolome from the literature. PMID:21687783
MarkUs: a server to navigate sequence-structure-function space. PMID:21672961
GLAMM: Genome-Linked Application for Metabolic Maps. PMID:21624891
Sharing and archiving nucleic acid structure mapping data. PMID:21610212
ChemMine tools: an online service for analyzing and clustering small molecules. PMID:21576229
ChemicalTagger: A tool for semantic text-mining in chemistry. PMID:21575201
Resource description framework technologies in chemistry. PMID:21569523
Extending biochemical databases by metabolomic surveys. PMID:21566124
Ontologies and standards in bioscience research: for machine or for human. PMID:21519400
Consensus-phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells. PMID:21483477
A new approach to assess and predict the functional roles of proteins across all known structures. PMID:21445639
Linking the Resource Description Framework to cheminformatics and proteochemometrics. PMID:21388575
The human serum metabolome. PMID:21359215
Advances in structure elucidation of small molecules using mass spectrometry. PMID:21289855
MEMOSys: Bioinformatics platform for genome-scale metabolic models. PMID:21276275
Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. PMID:21261995
Systematic integration of experimental data and models in systems biology. PMID:21114840
Integration of metabolic databases for the reconstruction of genome-scale metabolic networks. PMID:20712863
Ranked retrieval of Computational Biology models. PMID:20701772
The CoFactor database: organic cofactors in enzyme catalysis. PMID:20679331
Natural Language Processing methods and systems for biomedical ontology learning. PMID:20647054
RKB: a Semantic Web knowledge base for RNA. PMID:20626922
The metabolic network of Synechocystis sp. PCC 6803: systemic properties of autotrophic growth. PMID:20616194
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. PMID:20587024
PUDGE: a flexible, interactive server for protein structure prediction. PMID:20525783
Saliva Ontology: an ontology-based framework for a Salivaomics Knowledge Base. PMID:20525291
Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network. PMID:20498836
MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data. PMID:20457745
Phenotype ontologies for mouse and man: bridging the semantic gap. PMID:20427557
Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis. PMID:20426876
Bioinformatics and molecular modeling in glycobiology. PMID:20364395
CDK-Taverna: an open workflow environment for cheminformatics. PMID:20346188
Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining. PMID:20331846
Quantitative assessment of the expanding complementarity between public and commercial databases of bioactive compounds. PMID:20298516
Evolution of the Sequence Ontology terms and relationships. PMID:20226267
NanoParticle Ontology for cancer nanotechnology research. PMID:20211274
GeneComps and ChemComps: a new CTD metric to identify genes and chemicals with shared toxicogenomic profiles. PMID:20198196
Cross-product extensions of the Gene Ontology. PMID:20152934
Fast and efficient searching of biological data resources--using EB-eye. PMID:20150321
PlantMetabolomics.org: a web portal for plant metabolomics experiments. PMID:20147492
A network-theoretic approach for decompositional translation across Open Biological Ontologies. PMID:20144734
Integrating phenotype ontologies across multiple species. PMID:20064205
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase. PMID:20043185
Composite annotations: requirements for mapping multiscale data and models to biomedical ontologies. PMID:19964601
Linking human diseases to animal models using ontology-based phenotype annotation. PMID:19956802
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. PMID:19907644
Gene expression atlas at the European bioinformatics institute. PMID:19906730
The immune epitope database 2.0. PMID:19906713
Saccharomyces Genome Database provides mutant phenotype data. PMID:19906697
Non-redundant patent sequence databases with value-added annotations at two levels. PMID:19884134
Chemical Entities of Biological Interest: an update. PMID:19854951
The IntAct molecular interaction database in 2010. PMID:19850723
Initial implementation of a comparative data analysis ontology. PMID:19812726
KA-SB: from data integration to large scale reasoning. PMID:19796402
Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli. PMID:19783351
Lowering industry firewalls: pre-competitive informatics initiatives in drug discovery. PMID:19609266
libAnnotationSBML: a library for exploiting SBML annotations. PMID:19561017
MIRO and IRbase: IT tools for the epidemiological monitoring of insecticide resistance in mosquito disease vectors. PMID:19547750
Approaches to neuroscience data integration. PMID:19505888
Practical application of ontologies to annotate and analyse large scale raw mouse phenotype data. PMID:19426459
Leveraging existing biological knowledge in the identification of candidate genes for facial dysmorphology. PMID:19208187
MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions. PMID:19147664
A survey of visualization tools for biological network analysis. PMID:19040716
Cascaded classifiers for confidence-based chemical named entity recognition. PMID:19025690
Genome and proteome annotation: organization, interpretation and integration. PMID:19019817
Chemical databases for environmental health and clinical research. PMID:18996453
dictyBase--a Dictyostelium bioinformatics resource update. PMID:18974179
HMDB: a knowledgebase for the human metabolome. PMID:18953024
Modeling multi-typed structurally viewed chemicals with the UMLS Refined Semantic Network. PMID:18952946
ConsensusPathDB--a database for integrating human functional interaction networks. PMID:18940869
Presenting and exploring biological pathways with PathVisio. PMID:18817533
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks. PMID:18782832
Arabidopsis reactome: a foundation knowledgebase for plant systems biology. PMID:18591350
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. PMID:18467421
An anatomy ontology to represent biological knowledge in Dictyostelium discoideum. PMID:18366659
Correcting ligands, metabolites, and pathways. PMID:17132165 -
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013
PubMed citations: 270.
270 articles citing: The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013
A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics. PMID:35888710
DES-Amyloidoses "Amyloidoses through the looking-glass": A knowledgebase developed for exploring and linking information related to human amyloid-related diseases. PMID:35877764
Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics. PMID:35776534
Archeochemistry reveals the first steps into modern industrial brewing. PMID:35661112
Representing Normal and Abnormal Physiology as Routes of Flow in ApiNATOMY. PMID:35547570
COVID-19 Drug Repurposing: A Network-Based Framework for Exploring Biomedical Literature and Clinical Trials for Possible Treatments. PMID:35335943
Reconstruction of a generic genome-scale metabolic network for chicken: Investigating network connectivity and finding potential biomarkers. PMID:35316277
Understanding the activating mechanism of the immune system against COVID-19 by Traditional Indian Medicine: Network pharmacology approach. PMID:35305722
From Platform to Knowledge Graph: Evolution of Laboratory Automation. PMID:35252980
Pharmacological Effects of Cisplatin Combination with Natural Products in Cancer Chemotherapy. PMID:35163459
Combining word embeddings to extract chemical and drug entities in biomedical literature. PMID:34920708
Establishment of quantitative RNAi-based forward genetics in Entamoeba histolytica and identification of genes required for growth. PMID:34843592
MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data. PMID:34822401
Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches. PMID:34821250
mapMECFS: a portal to enhance data discovery across biological disciplines and collaborative sites. PMID:34749736
High-confidence structural annotation of metabolites absent from spectral libraries. PMID:34650271
An ontology network for Diabetes Mellitus in Mexico. PMID:34625104
Non-β-Lactam Allosteric Inhibitors Target Methicillin-Resistant Staphylococcus aureus: An In Silico Drug Discovery Study. PMID:34438984
Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden. PMID:34342533
NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism. PMID:34340747
IDSM ChemWebRDF: SPARQLing small-molecule datasets. PMID:33980298
Methods for Molecular Modelling of Protein Complexes. PMID:33950384
NLM-Chem, a new resource for chemical entity recognition in PubMed full text literature. PMID:33767203
Fast searches of large collections of single-cell data using scfind. PMID:33649586
An empirical meta-analysis of the life sciences linked open data on the web. PMID:33479214
Review on natural products databases: where to find data in 2020. PMID:33431011
COCONUT online: Collection of Open Natural Products database. PMID:33423696
Functional Characterization of the Lin28/let-7 Circuit During Forelimb Regeneration in Ambystoma mexicanum and Its Influence on Metabolic Reprogramming. PMID:33330447
Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra. PMID:33230292
Towards a foundational representation of potential drug-drug interaction knowledge. PMID:33139970
PIMD: An Integrative Approach for Drug Repositioning Using Multiple Characterization Fusion. PMID:33075523
Decomposing the molecular complexity of brewing. PMID:32885047
Knowledge-Based Decision Support in Healthcare via Near Field Communication. PMID:32878204
SBML Level 3: an extensible format for the exchange and reuse of biological models. PMID:32845085
OmicsON - Integration of omics data with molecular networks and statistical procedures. PMID:32726348
BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint. PMID:32703160
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources. PMID:32429287
DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases. PMID:32308806
Suggestions for Standardized Identifiers for Fatty Acyl Compounds in Genome Scale Metabolic Models and Their Application to the WormJam Caenorhabditis elegans Model. PMID:32231124
The Future of Origin of Life Research: Bridging Decades-Old Divisions. PMID:32110893
Automated Methods Enable Direct Computation on Phenotypic Descriptions for Novel Candidate Gene Prediction. PMID:31998331
Analysis of Low Molecular Weight Substances and Related Processes Influencing Cellular Cholesterol Efflux. PMID:31933239
OHMI: the ontology of host-microbiome interactions. PMID:31888755
STS-NLSP: A Network-Based Label Space Partition Method for Predicting the Specificity of Membrane Transporter Substrates Using a Hybrid Feature of Structural and Semantic Similarity. PMID:31781551
SXGBsite: Prediction of Protein-Ligand Binding Sites Using Sequence Information and Extreme Gradient Boosting. PMID:31771119
The Immune Epitope Database and Analysis Resource Program 2003-2018: reflections and outlook. PMID:31761977
Stable Isotope-Assisted Plant Metabolomics: Combination of Global and Tracer-Based Labeling for Enhanced Untargeted Profiling and Compound Annotation. PMID:31708958
Enabling semantic queries across federated bioinformatics databases. PMID:31697362
The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation. PMID:31685817
PPR-SSM: personalized PageRank and semantic similarity measures for entity linking. PMID:31664891
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
Enabling Web-scale data integration in biomedicine through Linked Open Data. PMID:31531395
NERChem: adapting NERBio to chemical patents via full-token features and named entity feature with chemical sub-class composition. PMID:31414701
NaPLeS: a natural products likeness scorer-web application and database. PMID:31399811
Graphical Model Selection for Gaussian Conditional Random Fields in the Presence of Latent Variables. PMID:31391793
ROBOT: A Tool for Automating Ontology Workflows. PMID:31357927
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. PMID:31225582
Literature-Based Enrichment Insights into Redox Control of Vascular Biology. PMID:31223421
ODAE: Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions. PMID:31074377
DNAmod: the DNA modification database. PMID:31016417
Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database. PMID:30963208
Visual and Semantic Enrichment of Analytical Chemistry Literature Searches by Combining Text Mining and Computational Chemistry. PMID:30835438
A Model Integration Pipeline for the Improvement of Human Genome-Scale Metabolic Reconstructions. PMID:30808160
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. PMID:30787451
BO-LSTM: classifying relations via long short-term memory networks along biomedical ontologies. PMID:30616557
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. PMID:30576488
Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans. PMID:30488036
Human Disease Ontology 2018 update: classification, content and workflow expansion. PMID:30407550
The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance. PMID:30349549
Classification, Ontology, and Precision Medicine. PMID:30304648
A community-driven reconstruction of the Aspergillus niger metabolic network. PMID:30275963
Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism. PMID:30228271
DES-Mutation: System for Exploring Links of Mutations and Diseases. PMID:30190574
MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions. PMID:30137210
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases. PMID:30084866
Creating a Structured AOP Knowledgebase via Ontology-Based Annotations. PMID:30057931
Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints. PMID:29949965
Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center. PMID:29917015
Tocotrienol-Rich Fraction of Palm Oil Improves Behavioral Impairments and Regulates Metabolic Pathways in AβPP/PS1 Mice. PMID:29889072
GNOMICS: A one-stop shop for biomedical and genomic data. PMID:29888054
Reverse Screening Methods to Search for the Protein Targets of Chemopreventive Compounds. PMID:29868550
A guideline for reporting experimental protocols in life sciences. PMID:29868256
QTLTableMiner++: semantic mining of QTL tables in scientific articles. PMID:29801439
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis. PMID:29762782
PomBase: The Scientific Resource for Fission Yeast. PMID:29761456
Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa. PMID:29688451
FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability. PMID:29688354
Navigating the disease landscape: knowledge representations for contextualizing molecular signatures. PMID:29684165
Propagating annotations of molecular networks using in silico fragmentation. PMID:29668671
The role of the Human Metabolome Database in inborn errors of metabolism. PMID:29663269
NMReDATA, a standard to report the NMR assignment and parameters of organic compounds. PMID:29656574
Where to search top-K biomedical ontologies? PMID:29579141
IMPPAT: A curated database of Indian Medicinal Plants, Phytochemistry And Therapeutics. PMID:29531263
Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature. PMID:29523070
Recon3D enables a three-dimensional view of gene variation in human metabolism. PMID:29457794
Using OWL reasoning to support the generation of novel gene sets for enrichment analysis. PMID:29444698
Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine. PMID:29402212
A computationally driven analysis of the polyphenol-protein interactome. PMID:29396566
InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk. PMID:29363423
Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism. PMID:29322929
In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host. PMID:29276507
Chemical reaction vector embeddings: towards predicting drug metabolism in the human gut microbiome. PMID:29218869
The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes. PMID:29169408
Using semantics for representing experimental protocols. PMID:29132408
Drug target ontology to classify and integrate drug discovery data. PMID:29122012
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. PMID:29106569
Computational approaches to chemical hazard assessment. PMID:29101769
Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D. PMID:29086112
The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. PMID:29086040
The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production. PMID:29062930
Bitter or not? BitterPredict, a tool for predicting taste from chemical structure. PMID:28935887
Type 1 Diabetes: Urinary Proteomics and Protein Network Analysis Support Perturbation of Lysosomal Function. PMID:28819457
DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species. PMID:28729549
Knowledge base and mini-expert platform for the diagnosis of inborn errors of metabolism. PMID:28726811
MINERVA-a platform for visualization and curation of molecular interaction networks. PMID:28725475
Metabolic modeling to identify engineering targets for Komagataella phaffii: The effect of biomass composition on gene target identification. PMID:28691262
Drug repurposing for aging research using model organisms. PMID:28620943
Drug repositioning for enzyme modulator based on human metabolite-likeness. PMID:28617219
Dead simple OWL design patterns. PMID:28583177
PharmML in Action: an Interoperable Language for Modeling and Simulation. PMID:28575551
MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive. PMID:28535296
Unique identifiers for small molecules enable rigorous labeling of their atoms. PMID:28534867
ChloroKB: A Web Application for the Integration of Knowledge Related to Chloroplast Metabolic Network. PMID:28442501
DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. PMID:28387604
Better living through ontologies at the Immune Epitope Database. PMID:28365732
Support for phosphoinositol 3 kinase and mTOR inhibitors as treatment for lupus using in-silico drug-repurposing analysis. PMID:28284231
A Comprehensive Gene Expression Meta-analysis Identifies Novel Immune Signatures in Rheumatoid Arthritis Patients. PMID:28210261
Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. PMID:28200013
An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge. PMID:28158609
Protein Bioinformatics Databases and Resources. PMID:28150231
Global open data management in metabolomics. PMID:28092796
Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD). PMID:28079125
Molecular Mechanism of Binding between 17β-Estradiol and DNA. PMID:28066533
Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation. PMID:28031032
Construction of antimicrobial peptide-drug combination networks from scientific literature based on a semi-automated curation workflow. PMID:28025336
Developing the Quantitative Histopathology Image Ontology (QHIO): A case study using the hot spot detection problem. PMID:28003147
Provenance information as a tool for addressing engineered nanoparticle reproducibility challenges. PMID:27936809
Exposome-Explorer: a manually-curated database on biomarkers of exposure to dietary and environmental factors. PMID:27924041
EuPathDB: the eukaryotic pathogen genomics database resource. PMID:27903906
Glycosaminoglycanomics: where we are. PMID:27900575
MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes. PMID:27899624
Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction. PMID:27895706
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. PMID:27867422
DrugCentral: online drug compendium. PMID:27789690
Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns. PMID:27774140
A capillary electrophoresis coupled to mass spectrometry pipeline for long term comparable assessment of the urinary metabolome. PMID:27694997
Modeling biochemical pathways in the gene ontology. PMID:27589964
Integration of targeted metabolomics and transcriptomics identifies deregulation of phosphatidylcholine metabolism in Huntington's disease peripheral blood samples. PMID:27524956
Mapping the patent landscape of synthetic biology for fine chemical production pathways. PMID:27489206
Ontology-based Vaccine and Drug Adverse Event Representation and Theory-guided Systematic Causal Network Analysis toward Integrative Pharmacovigilance Research. PMID:27458549
First Proposal of Minimum Information About a Cellular Assay for Regenerative Medicine. PMID:27405781
Fast metabolite identification with Input Output Kernel Regression. PMID:27307628
The Proteasix Ontology. PMID:27259807
A stable genetic polymorphism underpinning microbial syntrophy. PMID:27258948
The BioHub Knowledge Base: Ontology and Repository for Sustainable Biosourcing. PMID:27246819
Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events. PMID:27213033
Reactome from a WikiPathways Perspective. PMID:27203685
Argo: enabling the development of bespoke workflows and services for disease annotation. PMID:27189607
Electronic cigarette exposure triggers neutrophil inflammatory responses. PMID:27184092
BELTracker: evidence sentence retrieval for BEL statements. PMID:27173525
The Chinchilla Research Resource Database: resource for an otolaryngology disease model. PMID:27173523
Chemical entity recognition in patents by combining dictionary-based and statistical approaches. PMID:27141091
MBROLE 2.0-functional enrichment of chemical compounds. PMID:27084944
Extending gene ontology in the context of extracellular RNA and vesicle communication. PMID:27076901
MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions. PMID:27076900
Requirements for the formal representation of pathophysiology mechanisms by clinicians. PMID:27051514
Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation. PMID:27011785
Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies. PMID:26988001
Principles of metadata organization at the ENCODE data coordination center. PMID:26980513
libChEBI: an API for accessing the ChEBI database. PMID:26933452
A Computational Solution to Automatically Map Metabolite Libraries in the Context of Genome Scale Metabolic Networks. PMID:26909353
The UniProtKB guide to the human proteome. PMID:26896845
Predicting the functions of a protein from its ability to associate with other molecules. PMID:26767846
Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases. PMID:26716837
Emerging semantics to link phenotype and environment. PMID:26713234
The evolution of standards and data management practices in systems biology. PMID:26700851
Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods. PMID:26694353
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. PMID:26615188
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
Analysis of volatile organic compounds in exhaled breath to diagnose ventilator-associated pneumonia. PMID:26608483
DESM: portal for microbial knowledge exploration systems. PMID:26546514
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. PMID:26527732
MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. PMID:26527720
RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource. PMID:26500754
A Glimpse to Background and Characteristics of Major Molecular Biological Networks. PMID:26491677
ChEBI in 2016: Improved services and an expanding collection of metabolites. PMID:26467479
Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. PMID:26467476
Ontology-based representation and analysis of host-Brucella interactions. PMID:26445639
Illuminating the dark matter in metabolomics. PMID:26430243
Searching molecular structure databases with tandem mass spectra using CSI:FingerID. PMID:26392543
Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology. PMID:26387907
Geroprotectors.org: a new, structured and curated database of current therapeutic interventions in aging and age-related disease. PMID:26342919
Computational approaches to natural product discovery. PMID:26284671
Minimum Information about a Biosynthetic Gene cluster. PMID:26284661
SurvCurv database and online survival analysis platform update. PMID:26249811
BioModels: Content, Features, Functionality, and Use. PMID:26225232
Human metabolic atlas: an online resource for human metabolism. PMID:26209309
Chemical databases: curation or integration by user-defined equivalence? PMID:26194583
A large-scale crop protection bioassay data set. PMID:26175909
PubChemRDF: towards the semantic annotation of PubChem compound and substance databases. PMID:26175801
Biomedical imaging ontologies: A survey and proposal for future work. PMID:26167381
The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease. PMID:26119816
Disease insights through cross-species phenotype comparisons. PMID:26092691
ONION: Functional Approach for Integration of Lipidomics and Transcriptomics Data. PMID:26053255
The SwissLipids knowledgebase for lipid biology. PMID:25943471
Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes. PMID:25941533
Annotation-based feature extraction from sets of SBML models. PMID:25904997
Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework. PMID:25894391
Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems. PMID:25887162
BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology. PMID:25879798
The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI. PMID:25855807
Neurochemical Metabolomics Reveals Disruption to Sphingolipid Metabolism Following Chronic Haloperidol Administration. PMID:25850894
eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment. PMID:25815161
Optimising chemical named entity recognition with pre-processing analytics, knowledge-rich features and heuristics. PMID:25810777
CheNER: a tool for the identification of chemical entities and their classes in biomedical literature. PMID:25810772
Improving chemical entity recognition through h-index based semantic similarity. PMID:25810770
Open-access metabolomics databases for natural product research: present capabilities and future potential. PMID:25789275
Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows. PMID:25789153
Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions. PMID:25785184
Ontology application and use at the ENCODE DCC. PMID:25776021
An ontology approach to comparative phenomics in plants. PMID:25774204
The Open Physiology workflow: modeling processes over physiology circuitboards of interoperable tissue units. PMID:25759670
Polyol specificity of recombinant Arabidopsis thaliana sorbitol dehydrogenase studied by enzyme kinetics and in silico modeling. PMID:25755662
A 'rule of 0.5' for the metabolite-likeness of approved pharmaceutical drugs. PMID:25750602
Improving collaboration by standardization efforts in systems biology. PMID:25538939
The application of the open pharmacological concepts triple store (open PHACTS) to support drug discovery research. PMID:25522365
The InterPro protein families database: the classification resource after 15 years. PMID:25428371
Gene Ontology Consortium: going forward. PMID:25428369
MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities. PMID:25378329
T3DB: the toxic exposome database. PMID:25378312
PomBase 2015: updates to the fission yeast database. PMID:25361970
The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease. PMID:25355511
UniProt: a hub for protein information. PMID:25348405
The human DEPhOsphorylation database DEPOD: a 2015 update. PMID:25332398
Updates in Rhea--a manually curated resource of biochemical reactions. PMID:25332395
The complex portal--an encyclopaedia of macromolecular complexes. PMID:25313161
The immune epitope database (IEDB) 3.0. PMID:25300482
The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology. PMID:25276334
NutriChem: a systems chemical biology resource to explore the medicinal value of plant-based foods. PMID:25106869
MediaDB: a database of microbial growth conditions in defined media. PMID:25098325
Semantic Web repositories for genomics data using the eXframe platform. PMID:25093072
Text-mining-assisted biocuration workflows in Argo. PMID:25037308
Network thermodynamic curation of human and yeast genome-scale metabolic models. PMID:25028891
Processing biological literature with customizable Web services supporting interoperable formats. PMID:25006225
Integrative analysis of longitudinal metabolomics data from a personal multi-omics profile. PMID:24958148
Ontology-supported research on vaccine efficacy, safety and integrative biological networks. PMID:24909153
A method for increasing expressivity of Gene Ontology annotations using a compositional approach. PMID:24885854
XTMS: pathway design in an eXTended metabolic space. PMID:24792156
A rule-based ontological framework for the classification of molecules. PMID:24735706
Efficient ring perception for the Chemistry Development Kit. PMID:24479757
Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2. PMID:24468196
Integrated text mining and chemoinformatics analysis associates diet to health benefit at molecular level. PMID:24453957
The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. PMID:24319146
BacMet: antibacterial biocide and metal resistance genes database. PMID:24304895
iPfam: a database of protein family and domain interactions found in the Protein Data Bank. PMID:24297255
FireDB: a compendium of biological and pharmacologically relevant ligands. PMID:24243844
The Reactome pathway knowledgebase. PMID:24243840
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. PMID:24234451
BacDive--the Bacterial Diversity Metadatabase. PMID:24214959
DrugBank 4.0: shedding new light on drug metabolism. PMID:24203711
The functional therapeutic chemical classification system. PMID:24177719
The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications. PMID:24103152
KNIME-CDK: Workflow-driven cheminformatics. PMID:24103053
OntoQuery: easy-to-use web-based OWL querying. PMID:24008420
Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance. PMID:23935056
Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery. PMID:23892182
An analysis of a 'community-driven' reconstruction of the human metabolic network. PMID:23888127
Metingear: a development environment for annotating genome-scale metabolic models. PMID:23766418
Small-volume analysis of cell-cell signaling molecules in the brain. PMID:23748227
The ChEMBL database as linked open data. PMID:23657106 -
ChEBI in 2016: Improved services and an expanding collection of metabolites
PubMed citations: 269.
269 articles citing: ChEBI in 2016: Improved services and an expanding collection of metabolites
Network approaches for modeling the effect of drugs and diseases. PMID:35704883
PeakForest: a multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management. PMID:35699774
Duodenal Metabolic Profile Changes in Heat-Stressed Broilers. PMID:35681802
PIKAChU: a Python-based informatics kit for analysing chemical units. PMID:35672769
Volatile Organic Compounds Frequently Identified after Hyperbaric Hyperoxic Exposure: The VAPOR Library. PMID:35629974
BioChemDDI: Predicting Drug-Drug Interactions by Fusing Biochemical and Structural Information through a Self-Attention Mechanism. PMID:35625486
A method for intracerebroventricular cannulation of young broiler chicks. PMID:35620758
A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural Mesothelioma. PMID:35558518
IMEx Databases: Displaying Molecular Interactions into a Single, Standards-Compliant Dataset. PMID:35507258
Tumor Glucose and Fatty Acid Metabolism in the Context of Anthracycline and Taxane-Based (Neo)Adjuvant Chemotherapy in Breast Carcinomas. PMID:35433453
SwissBioPics-an interactive library of cell images for the visualization of subcellular location data. PMID:35411389
PyMiner: A method for metabolic pathway design based on the uniform similarity of substrate-product pairs and conditional search. PMID:35404943
Harmonizing model organism data in the Alliance of Genome Resources. PMID:35380658
JaponicusDB: rapid deployment of a model organism database for an emerging model species. PMID:35380656
A Comprehensive View on the Quercetin Impact on Colorectal Cancer. PMID:35335239
Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx. PMID:35322036
COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions. PMID:35320266
Profiling Urinary Sulfate Metabolites With Mass Spectrometry. PMID:35281273
Prion protein with a mutant N-terminal octarepeat region undergoes cobalamin-dependent assembly into high-molecular weight complexes. PMID:35271850
FlyBase: a guided tour of highlighted features. PMID:35266522
A Modular and Expandable Ecosystem for Metabolomics Data Annotation in R. PMID:35208247
The gold complex auranofin: new perspectives for cancer therapy. PMID:35201489
The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization. PMID:35193494
Plant Responses Underlying Timely Specialized Metabolites Induction of Brassica Crops. PMID:35185956
Towards the prediction of non-peptidic epitopes. PMID:35180214
Zebrafish information network, the knowledgebase for Danio rerio research. PMID:35166825
Different Schiff Bases-Structure, Importance and Classification. PMID:35164049
Multimodal reasoning based on knowledge graph embedding for specific diseases. PMID:35150235
Interpretation of the DOME Recommendations for Machine Learning in Proteomics and Metabolomics. PMID:35119864
Agent-based models for detecting the driving forces of biomolecular interactions. PMID:35115584
Genome-Scale Modeling Specifies the Metabolic Capabilities of Rhizophagus irregularis. PMID:35076269
The SwissSimilarity 2021 Web Tool: Novel Chemical Libraries and Additional Methods for an Enhanced Ligand-Based Virtual Screening Experience. PMID:35054998
Minimal Information about MHC Multimers (MIAMM). PMID:35042788
Structural basis of cyclic oligoadenylate binding to the transcription factor Csa3 outlines cross talk between type III and type I CRISPR systems. PMID:35038453
Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. PMID:35037224
An Overview of Biomedical Ontologies for Pandemics and Infectious Diseases Representation. PMID:34868401
High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032. PMID:34867870
VectorBase.org updates: bioinformatic resources for invertebrate vectors of human pathogens and related organisms. PMID:34864248
Author-sourced capture of pathway knowledge in computable form using Biofactoid. PMID:34860157
eQuilibrator 3.0: a database solution for thermodynamic constant estimation. PMID:34850162
Expression Atlas update: gene and protein expression in multiple species. PMID:34850121
The Aliment to Bodily Condition knowledgebase (ABCkb): a database connecting plants and human health. PMID:34838100
Drug Therapeutic-Use Class Prediction and Repurposing Using Graph Convolutional Networks. PMID:34834320
MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data. PMID:34822401
RDFizing the biosynthetic pathway of E.coli O-antigen to enable semantic sharing of microbiology data. PMID:34809564
PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions. PMID:34788826
The Human Disease Ontology 2022 update. PMID:34755882
Rhea, the reaction knowledgebase in 2022. PMID:34755880
GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction. PMID:34748537
HERMES: a molecular-formula-oriented method to target the metabolome. PMID:34725482
Complex Portal 2022: new curation frontiers. PMID:34718729
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. PMID:34718728
Text Mining for Building Biomedical Networks Using Cancer as a Case Study. PMID:34680062
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. PMID:34676613
NPCDR: natural product-based drug combination and its disease-specific molecular regulation. PMID:34664659
NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products. PMID:34662515
A Catalog of Natural Products Occurring in Watermelon-Citrullus lanatus. PMID:34595201
In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology. PMID:34570957
An updated, computable MEDication-Indication resource for biomedical research. PMID:34556781
The Cancer Epitope Database and Analysis Resource: A Blueprint for the Establishment of a New Bioinformatics Resource for Use by the Cancer Immunology Community. PMID:34504503
Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions. PMID:34502252
gutMGene: a comprehensive database for target genes of gut microbes and microbial metabolites. PMID:34500458
Sumatriptan Anaphylaxis: A Headache of an Allergy. PMID:34484909
FORUM: Building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases. PMID:34478489
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Ten simple rules for creating reusable pathway models for computational analysis and visualization. PMID:34411100
Exploring Chemical Information in PubChem. PMID:34370395
Integrated human/SARS-CoV-2 metabolic models present novel treatment strategies against COVID-19. PMID:34353886
Impact of Weaning and Maternal Immune Activation on the Metabolism of Pigs. PMID:34336923
Potential drugs against COVID-19 revealed by gene expression profile, molecular docking and molecular dynamic simulation. PMID:34306168
CFTR Lifecycle Map-A Systems Medicine Model of CFTR Maturation to Predict Possible Active Compound Combinations. PMID:34299207
Characterization of the Exometabolome of Nitrosopumilus maritimus SCM1 by Liquid Chromatography-Ion Mobility Mass Spectrometry. PMID:34276593
MassSpecBlocks: a web-based tool to create building blocks and sequences of nonribosomal peptides and polyketides for tandem mass spectra analysis. PMID:34233741
Visual comprehension and orientation into the COVID-19 CIDO ontology. PMID:34224898
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus. PMID:34188046
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research. PMID:34159360
Mixology: a tool for calculating required masses and volumes for laboratory solutions. PMID:34136652
Predicting biological pathways of chemical compounds with a profile-inspired approach. PMID:34118870
Interpreting the lipidome: bioinformatic approaches to embrace the complexity. PMID:34091802
Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective. PMID:34083542
Aspergillus Metabolome Database for Mass Spectrometry Metabolomics. PMID:34063531
COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model. PMID:34015823
An overview of graph databases and their applications in the biomedical domain. PMID:34003247
Reactome and the Gene Ontology: Digital convergence of data resources. PMID:33964129
Predicting the Structure and Dynamics of Membrane Protein GerAB from Bacillus subtilis. PMID:33917581
Reassessing the Use of Undecanoic Acid as a Therapeutic Strategy for Treating Fungal Infections. PMID:33835367
Simulating the enzymes of ganglioside biosynthesis with Glycologue. PMID:33828618
Xanthophylls from the Sea: Algae as Source of Bioactive Carotenoids. PMID:33801636
Comparative population genomic analyses of transporters within the Asgard archaeal superphylum. PMID:33770091
A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives. PMID:33741955
Learning chemistry: exploring the suitability of machine learning for the task of structure-based chemical ontology classification. PMID:33726837
Chemotranscriptomic Profiling Defines Drug-Specific Signatures of the Glycopeptide Antibiotics Dalbavancin, Vancomycin and Chlorobiphenyl-Vancomycin in a VanB-Type-Resistant Streptomycete. PMID:33717038
Distinct lipid profile, low-level inflammation, and increased antioxidant defense signature in HIV-1 elite control status. PMID:33659876
Hybrid semantic recommender system for chemical compounds in large-scale datasets. PMID:33622374
Public data sources to support systems toxicology applications. PMID:33604492
Curation of over 10 000 transcriptomic studies to enable data reuse. PMID:33599246
Cancers in Agreement? Exploring the Cross-Talk of Cancer Metabolomic and Transcriptomic Landscapes Using Publicly Available Data. PMID:33494351
The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research. PMID:33494105
Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB. PMID:33445429
Ontological modeling and analysis of experimentally or clinically verified drugs against coronavirus infection. PMID:33441564
Linking chemical and disease entities to ontologies by integrating PageRank with extracted relations from literature. PMID:33430995
Community Approaches for Integrating Environmental Exposures into Human Models of Disease. PMID:33369481
A review on viral data sources and search systems for perspective mitigation of COVID-19. PMID:33348368
Outlier concepts auditing methodology for a large family of biomedical ontologies. PMID:33319713
The Gene Ontology resource: enriching a GOld mine. PMID:33290552
Towards a unified open access dataset of molecular interactions. PMID:33262342
UniProt: the universal protein knowledgebase in 2021. PMID:33237286
DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations. PMID:33209251
The Transporter Classification Database (TCDB): 2021 update. PMID:33170213
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models. PMID:33156326
PK-DB: pharmacokinetics database for individualized and stratified computational modeling. PMID:33151297
DrugCentral 2021 supports drug discovery and repositioning. PMID:33151287
Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production. PMID:33134082
Antifouling Activity of Meroterpenes Isolated from the Ascidian Aplidium aff. densum. PMID:33094389
StreptomeDB 3.0: an updated compendium of streptomycetes natural products. PMID:33051671
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
Chasing the Major Sphingolipids on Earth: Automated Annotation of Plant Glycosyl Inositol Phospho Ceramides by Glycolipidomics. PMID:32961698
Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production. PMID:32942174
Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project. PMID:32939051
Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management. PMID:32883995
Microbial natural product databases: moving forward in the multi-omics era. PMID:32856641
Investigations of Dimethylglycine, Glycine Betaine, and Ectoine Uptake by a Betaine-Carnitine-Choline Transporter Family Transporter with Diverse Substrate Specificity in Vibrio Species. PMID:32817090
A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets. PMID:32716361
Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook. PMID:32662816
A behind-the-scenes tour of the IEDB curation process: an optimized process empirically integrating automation and human curation efforts. PMID:32615639
A kinetic mechanism for enhanced selectivity of membrane transport. PMID:32614861
Longitudinal wastewater sampling in buildings reveals temporal dynamics of metabolites. PMID:32598361
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). PMID:32598315
CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis. PMID:32533075
Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN. PMID:32499584
Using Reactome to build an autophagy mechanism knowledgebase. PMID:32486891
Differential Effects of Post-Weaning Diet and Maternal Obesity on Mouse Liver and Brain Metabolomes. PMID:32481497
X-ray Structure-Based Chemoinformatic Analysis Identifies Promiscuous Ligands Binding to Proteins from Different Classes with Varying Shapes. PMID:32471121
High-throughput screening of clinically approved drugs that prime nonviral gene delivery to human Mesenchymal stem cells. PMID:32467728
The World of Cyclic Dinucleotides in Bacterial Behavior. PMID:32466317
A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function. PMID:32449511
Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker. PMID:32440005
Applying knowledge-driven mechanistic inference to toxicogenomics. PMID:32387679
novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model. PMID:32313937
Metabolomics Adaptation of Juvenile Pacific Abalone Haliotis discus hannai to Heat Stress. PMID:32286374
A structured model for immune exposures. PMID:32283555
Structured reviews for data and knowledge-driven research. PMID:32283553
Integration of mass spectral fingerprinting analysis with precursor ion (MS1) quantification for the characterisation of botanical extracts: application to extracts of Centella asiatica (L.) Urban. PMID:32281154
Improving lipid mapping in Genome Scale Metabolic Networks using ontologies. PMID:32215752
New markers for sepsis caused by Pseudomonas aeruginosa during burn infection. PMID:32170472
Incorporation of a unified protein abundance dataset into the Saccharomyces genome database. PMID:32128557
Biological Activity Profiles of Multitarget Ligands from X-ray Structures. PMID:32059498
HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes. PMID:32034905
Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords. PMID:31984130
Metabolic Pathways Associated With Term Labor Induction Course in African American Women. PMID:31983215
Compartment and hub definitions tune metabolic networks for metabolomic interpretations. PMID:31972021
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. PMID:31950984
Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation. PMID:31921009
Heritability estimates for 361 blood metabolites across 40 genome-wide association studies. PMID:31911595
Integrative omics approaches provide biological and clinical insights: examples from mitochondrial diseases. PMID:31895050
The human DEPhOsphorylation Database DEPOD: 2019 update. PMID:31836896
Experiment design driven FAIRification of omics data matrices, an exemplar. PMID:31831744
BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities. PMID:31783634
FlySilico: Flux balance modeling of Drosophila larval growth and resource allocation. PMID:31748517
Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery. PMID:31735951
Creating a Reliable Mass Spectral-Retention Time Library for All Ion Fragmentation-Based Metabolomics. PMID:31717785
The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences. PMID:31701143
MetaboLights: a resource evolving in response to the needs of its scientific community. PMID:31691833
PDBe: improved findability of macromolecular structure data in the PDB. PMID:31691821
The reactome pathway knowledgebase. PMID:31691815
Enzyme annotation in UniProtKB using Rhea. PMID:31688925
Cisplatin-resistant triple-negative breast cancer subtypes: multiple mechanisms of resistance. PMID:31684899
Plant Reactome: a knowledgebase and resource for comparative pathway analysis. PMID:31680153
SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update. PMID:31665520
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. PMID:31665441
PPR-SSM: personalized PageRank and semantic similarity measures for entity linking. PMID:31664891
Metabolic Modeling of Streptococcus mutans Reveals Complex Nutrient Requirements of an Oral Pathogen. PMID:31662430
Chemical Diversity and Classification of Secondary Metabolites in Nine Bryophyte Species. PMID:31614655
Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration. PMID:31611808
Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features. PMID:31605112
ModelBricks-modules for reproducible modeling improving model annotation and provenance. PMID:31602314
Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems. PMID:31548717
Application of the SwissDrugDesign Online Resources in Virtual Screening. PMID:31540350
VARIDT 1.0: variability of drug transporter database. PMID:31495872
Model annotation and discovery with the Physiome Model Repository. PMID:31492098
Enhancing Clinical Data and Clinical Research Data with Biomedical Ontologies - Insights from the Knowledge Representation Perspective. PMID:31419826
The ABCD database: a repository for chemically defined antibodies. PMID:31410491
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. PMID:31395883
Quantifying the impact of public omics data. PMID:31383865
Artificial Intelligence for Drug Toxicity and Safety. PMID:31383376
Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes. PMID:31273253
Interoperable chemical structure search service. PMID:31254167
MolMeDB: Molecules on Membranes Database. PMID:31250015
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm. PMID:31236786
Systematic Isolation and Structure Elucidation of Urinary Metabolites Optimized for the Analytical-Scale Molecular Profiling Laboratory. PMID:31188566
PathMe: merging and exploring mechanistic pathway knowledge. PMID:31092193
BitterSweet: Building machine learning models for predicting the bitter and sweet taste of small molecules. PMID:31073241
A Bioinformatics View of Glycan⁻Virus Interactions. PMID:31018588
DNAmod: the DNA modification database. PMID:31016417
CFM-ID 3.0: Significantly Improved ESI-MS/MS Prediction and Compound Identification. PMID:31013937
Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community. PMID:31003499
Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies. PMID:30858527
Beyond Pathway Analysis: Identification of Active Subnetworks in Rett Syndrome. PMID:30847002
How Sustainable are Biomedical Ontologies? PMID:30815087
Automated evaluation of consistency within the PubChem Compound database. PMID:30778259
mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics. PMID:30688441
BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification. PMID:30612223
SugarSketcher: Quick and Intuitive Online Glycan Drawing. PMID:30563078
Connecting nutrition composition measures to biomedical research. PMID:30541615
PDX Finder: A portal for patient-derived tumor xenograft model discovery. PMID:30535239
Prioritising candidate genes causing QTL using hierarchical orthologous groups. PMID:30423067
BioSamples database: an updated sample metadata hub. PMID:30407529
The Gene Ontology Resource: 20 years and still GOing strong. PMID:30395331
UniProt: a worldwide hub of protein knowledge. PMID:30395287
BRENDA in 2019: a European ELIXIR core data resource. PMID:30395242
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. PMID:30371894
DrugCentral 2018: an update. PMID:30371892
MatrixDB: integration of new data with a focus on glycosaminoglycan interactions. PMID:30371822
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. PMID:30357405
The Immune Epitope Database (IEDB): 2018 update. PMID:30357391
From Affective Science to Psychiatric Disorder: Ontology as a Semantic Bridge. PMID:30349491
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
Updates in Rhea: SPARQLing biochemical reaction data. PMID:30272209
BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis. PMID:30256983
Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations. PMID:30246165
Growing and cultivating the forest genomics database, TreeGenes. PMID:30239664
Structural basis of the filamin A actin-binding domain interaction with F-actin. PMID:30224736
Annotation and detection of drug effects in text for pharmacovigilance. PMID:30105604
A Cloud-Based Metabolite and Chemical Prioritization System for the Biology/Disease-Driven Human Proteome Project. PMID:30094994
A new bioinformatics tool to help assess the significance of BRCA1 variants. PMID:29996917
Reverse Screening Methods to Search for the Protein Targets of Chemopreventive Compounds. PMID:29868550
The Cellosaurus, a Cell-Line Knowledge Resource. PMID:29805321
iPath3.0: interactive pathways explorer v3. PMID:29718427
MetExplore: collaborative edition and exploration of metabolic networks. PMID:29718355
Community-driven roadmap for integrated disease maps. PMID:29688273
JAMI: a Java library for molecular interactions and data interoperability. PMID:29642846
Ligand Binding Site Structure Influences the Evolution of Protein Complex Function and Topology. PMID:29562182
STRENDA DB: enabling the validation and sharing of enzyme kinetics data. PMID:29498804
Interleukins and their signaling pathways in the Reactome biological pathway database. PMID:29378288
Identification of Inhibitors Targeting Ferredoxin-NADP⁺ Reductase from the Xanthomonas citri subsp. citri Phytopathogenic Bacteria. PMID:29295539
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. PMID:29186578
The European Bioinformatics Institute in 2017: data coordination and integration. PMID:29186510
SuperDRUG2: a one stop resource for approved/marketed drugs. PMID:29140469
HMDB 4.0: the human metabolome database for 2018. PMID:29140435
WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. PMID:29136241
Drug target ontology to classify and integrate drug discovery data. PMID:29122012
TCMID 2.0: a comprehensive resource for TCM. PMID:29106634
PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database. PMID:29106626
NPASS: natural product activity and species source database for natural product research, discovery and tool development. PMID:29106619
SABIO-RK: an updated resource for manually curated biochemical reaction kinetics. PMID:29092055
SYNBIOCHEM Synthetic Biology Research Centre, Manchester - A UK foundry for fine and speciality chemicals production. PMID:29062953
The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production. PMID:29062930
Aspergillus Secondary Metabolite Database, a resource to understand the Secondary metabolome of Aspergillus genus. PMID:28779078
biochem4j: Integrated and extensible biochemical knowledge through graph databases. PMID:28708831
The yeast noncoding RNA interaction network. PMID:28701522
Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery. PMID:28602100
From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics. PMID:28520864
IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models. PMID:28389638
Mixing omics: combining genetics and metabolomics to study rheumatic diseases. PMID:28148918
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules-Search Options and Applications in Food Science. PMID:27929431
CEBS: a comprehensive annotated database of toxicological data. PMID:27899660
Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. PMID:27899649
The neXtProt knowledgebase on human proteins: 2017 update. PMID:27899619
Plant Reactome: a resource for plant pathways and comparative analysis. PMID:27799469
Updates in Rhea - an expert curated resource of biochemical reactions. PMID:27789701
Exploring human disease using the Rat Genome Database. PMID:27736745
Metabolomics and Cheminformatics Analysis of Antifungal Function of Plant Metabolites. PMID:27706030
A scientist's guide for submitting data to ZFIN. PMID:27443940
Recon 2.2: from reconstruction to model of human metabolism. PMID:27358602
Toward Community Standards and Software for Whole-Cell Modeling. PMID:27305665
libChEBI: an API for accessing the ChEBI database. PMID:26933452
The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. PMID:26740669
The European Bioinformatics Institute in 2016: Data growth and integration. PMID:26673705 -
Chemical Entities of Biological Interest: an update
PubMed citations: 132.
132 articles citing: Chemical Entities of Biological Interest: an update
Alleviating Environmental Health Disparities Through Community Science and Data Integration. PMID:35664667
OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization. PMID:35615022
Latin American databases of natural products: biodiversity and drug discovery against SARS-CoV-2. PMID:35481202
MetaboListem and TABoLiSTM: Two Deep Learning Algorithms for Metabolite Named Entity Recognition. PMID:35448463
Predictive metabolomics of multiple Atacama plant species unveils a core set of generic metabolites for extreme climate resilience. PMID:35288949
Computational Approaches for Cancer-Fighting: From Gene Expression to Functional Foods. PMID:34439361
Composition and Associations of the Infant Gut Fungal Microbiota with Environmental Factors and Childhood Allergic Outcomes. PMID:34060330
An immunologically friendly classification of non-peptidic ligands. PMID:33772585
ChemProps: A RESTful API enabled database for composite polymer name standardization. PMID:33712066
Executable biochemical space for specification and analysis of biochemical systems. PMID:32915842
HAIKU: A Semantic Framework for Surveillance of Healthcare-Associated Infections. PMID:32288895
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. PMID:31647099
GCAC: galaxy workflow system for predictive model building for virtual screening. PMID:30717669
Automatic identification of relevant chemical compounds from patents. PMID:30698776
GNOMICS: A one-stop shop for biomedical and genomic data. PMID:29888054
Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database. PMID:29777317
Evolution of biomedical ontologies and mappings: Overview of recent approaches. PMID:27642503
Advanced SPARQL querying in small molecule databases. PMID:27275187
Cancer Metabolomics and the Human Metabolome Database. PMID:26950159
SureChEMBL: a large-scale, chemically annotated patent document database. PMID:26582922
Ambiguity of non-systematic chemical identifiers within and between small-molecule databases. PMID:26579214
Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants. PMID:26557642
ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. PMID:26481353
ChEBI in 2016: Improved services and an expanding collection of metabolites. PMID:26467479
PubChemRDF: towards the semantic annotation of PubChem compound and substance databases. PMID:26175801
Many InChIs and quite some feat. PMID:26081259
Mimoza: web-based semantic zooming and navigation in metabolic networks. PMID:25889977
Recognition of chemical entities: combining dictionary-based and grammar-based approaches. PMID:25810767
Patterns of metabolite changes identified from large-scale gene perturbations in Arabidopsis using a genome-scale metabolic network. PMID:25670818
Synthetic biology outside the cell: linking computational tools to cell-free systems. PMID:25538941
The application of the open pharmacological concepts triple store (open PHACTS) to support drug discovery research. PMID:25522365
Annotated chemical patent corpus: a gold standard for text mining. PMID:25268232
OntoVIP: an ontology for the annotation of object models used for medical image simulation. PMID:25038553
Systematic applications of metabolomics in metabolic engineering. PMID:24957776
A controlled vocabulary for pathway entities and events. PMID:24951798
On InChI and evaluating the quality of cross-reference links. PMID:24742140
Drug2Gene: an exhaustive resource to explore effectively the drug-target relation network. PMID:24618344
Guidelines for managing data and processes in bone and cartilage tissue engineering. PMID:24564199
Cheminformatics and the Semantic Web: adding value with linked data and enhanced provenance. PMID:24432050
HuPSON: the human physiology simulation ontology. PMID:24267822
The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands. PMID:24234439
Annotating cancer variants and anti-cancer therapeutics in reactome. PMID:24213504
Evaluation and cross-comparison of lexical entities of biological interest (LexEBI). PMID:24124474
OntoQuery: easy-to-use web-based OWL querying. PMID:24008420
Extracting reaction networks from databases-opening Pandora's box. PMID:23946492
metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research. PMID:23935057
Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology. PMID:23895341
Unlocking the potential of survival data for model organisms through a new database and online analysis platform: SurvCurv. PMID:23826631
Query enhancement through the practical application of ontology: the IEDB and OBI. PMID:23734660
Pathway databases: making chemical and biological sense of the genomic data flood. PMID:23706629
Analysis Tool Web Services from the EMBL-EBI. PMID:23671338
LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics. PMID:23667450
Enhancement of chemical entity identification in text using semantic similarity validation. PMID:23658791
FYPO: the fission yeast phenotype ontology. PMID:23658422
The MetaboLights repository: curation challenges in metabolomics. PMID:23630246
A pathway approach to investigate the function and regulation of SREBPs. PMID:23516131
The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics. PMID:23514033
Brain: biomedical knowledge manipulation. PMID:23505292
UniChem: a unified chemical structure cross-referencing and identifier tracking system. PMID:23317286
ISA-TAB-Nano: a specification for sharing nanomaterial research data in spreadsheet-based format. PMID:23311978
Annotating Human P-Glycoprotein Bioassay Data. PMID:23293680
Automated compound classification using a chemical ontology. PMID:23273256
Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses. PMID:23256535
Consistency of systematic chemical identifiers within and between small-molecule databases. PMID:23237381
Building an efficient curation workflow for the Arabidopsis literature corpus. PMID:23221298
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. PMID:23180789
The EBI enzyme portal. PMID:23175605
HMDB 3.0--The Human Metabolome Database in 2013. PMID:23161693
On the ontology based representation of cell lines. PMID:23144907
MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data. PMID:23109552
The Comparative Toxicogenomics Database: update 2013. PMID:23093600
IUPHAR-DB: updated database content and new features. PMID:23087376
Open biomedical pluralism: formalising knowledge about breast cancer phenotypes. PMID:23046572
An overview of computational life science databases & exchange formats of relevance to chemical biology research. PMID:22934944
Ontologies as integrative tools for plant science. PMID:22847540
Mining the pharmacogenomics literature--a survey of the state of the art. PMID:22833496
Mapping between databases of compounds and protein targets. PMID:22821596
Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction. PMID:22768925
The immune epitope database: a historical retrospective of the first decade. PMID:22681406
Structure-based classification and ontology in chemistry. PMID:22480202
Aptamer Base: a collaborative knowledge base to describe aptamers and SELEX experiments. PMID:22434840
Semantically enabling pharmacogenomic data for the realization of personalized medicine. PMID:22256869
Rhea--a manually curated resource of biochemical reactions. PMID:22135291
The UniProt-GO Annotation database in 2011. PMID:22123736
The IntAct molecular interaction database in 2012. PMID:22121220
TDR Targets: a chemogenomics resource for neglected diseases. PMID:22116064
ProtChemSI: a network of protein-chemical structural interactions. PMID:22110041
Saccharomyces Genome Database: the genomics resource of budding yeast. PMID:22110037
PDBe: Protein Data Bank in Europe. PMID:22110033
UniPathway: a resource for the exploration and annotation of metabolic pathways. PMID:22102589
SABIO-RK--database for biochemical reaction kinetics. PMID:22102587
The Gene Ontology: enhancements for 2011. PMID:22102568
WikiPathways: building research communities on biological pathways. PMID:22096230
MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. PMID:22086950
MetaCrop 2.0: managing and exploring information about crop plant metabolism. PMID:22086948
PathCase-SB architecture and database design. PMID:22070889
SCRIPDB: a portal for easy access to syntheses, chemicals and reactions in patents. PMID:22067445
PomBase: a comprehensive online resource for fission yeast. PMID:22039153
OSCAR4: a flexible architecture for chemical text-mining. PMID:21999457
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on. PMID:21999342
The BioLexicon: a large-scale terminological resource for biomedical text mining. PMID:21992002
The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web. PMID:21991315
Knowledge sharing and collaboration in translational research, and the DC-THERA Directory. PMID:21969471
ChEMBL: a large-scale bioactivity database for drug discovery. PMID:21948594
Bioinformatics and systems biology of the lipidome. PMID:21939287
Chemical structural novelty: on-targets and off-targets. PMID:21916467
Application of computational systems biology to explore environmental toxicity hazards. PMID:21846611
Informatics and standards for nanomedicine technology. PMID:21721140
Software and resources for computational medicinal chemistry. PMID:21707404
Meeting report of the RNA Ontology Consortium January 8-9, 2011. PMID:21677862
Ontological realism: A methodology for coordinated evolution of scientific ontologies. PMID:21637730
ARISTO: ontological classification of small molecules by electron ionization-mass spectrometry. PMID:21622952
Chemical Entity Semantic Specification: Knowledge representation for efficient semantic cheminformatics and facile data integration. PMID:21595881
Combinations of protein-chemical complex structures reveal new targets for established drugs. PMID:21573205
The Protein Data Bank in Europe (PDBe): bringing structure to biology. PMID:21460450
The annotation of the asparagine N-linked glycosylation pathway in the Reactome database. PMID:21199820
SPIKE: a database of highly curated human signaling pathways. PMID:21097778
IUPHAR-DB: new receptors and tools for easy searching and visualization of pharmacological data. PMID:21087994
Human and chicken TLR pathways: manual curation and computer-based orthology analysis. PMID:21052677
PDBe: Protein Data Bank in Europe. PMID:21045060
Further developments towards a genome-scale metabolic model of yeast. PMID:21029416
The Protein Ontology: a structured representation of protein forms and complexes. PMID:20935045
ChemProt: a disease chemical biology database. PMID:20935044
Semantic similarity for automatic classification of chemical compounds. PMID:20885779
MatrixDB, the extracellular matrix interaction database. PMID:20852260
The systematic annotation of the three main GPCR families in Reactome. PMID:20671204
Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research. PMID:20615486
Multiple ontologies in action: composite annotations for biosimulation models. PMID:20601121
PINT: Pathways INtegration Tool. PMID:20538652
PUDGE: a flexible, interactive server for protein structure prediction. PMID:20525783
The Ontology Lookup Service: bigger and better. PMID:20460452
The European Bioinformatics Institute's data resources. PMID:19934258 -
ChEBI: an open bioinformatics and cheminformatics resource
PubMed citations: 15.
15 articles citing: ChEBI: an open bioinformatics and cheminformatics resource
Fungal secondary metabolites in food and pharmaceuticals in the era of multi-omics. PMID:35546367
Quantitative Lipidomic Analysis of Takotsubo Syndrome Patients' Serum. PMID:35514439
DrugQuest - a text mining workflow for drug association discovery. PMID:27295093
ANISEED 2015: a digital framework for the comparative developmental biology of ascidians. PMID:26420834
A 'rule of 0.5' for the metabolite-likeness of approved pharmaceutical drugs. PMID:25750602
Three ontologies to define phenotype measurement data. PMID:22654893
Guidelines for information about therapy experiments: a proposal on best practice for recording experimental data on cancer therapy. PMID:22226027
MMMDB: Mouse Multiple Tissue Metabolome Database. PMID:22139941
The Reactome BioMart. PMID:22012987
The BioLexicon: a large-scale terminological resource for biomedical text mining. PMID:21992002
Sharing and archiving nucleic acid structure mapping data. PMID:21610212
Extending biochemical databases by metabolomic surveys. PMID:21566124
Reactome: a database of reactions, pathways and biological processes. PMID:21067998
Using views of Systems Biology Cloud: application for model building. PMID:20730508
PUDGE: a flexible, interactive server for protein structure prediction. PMID:20525783
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molecular entity
metasource: Fairsharing.org
version: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: re3data.org
version: re3data.org: ChEBI; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3H78W last accessed: 2022-11-04
molecular structure
metasource: Fairsharing.org
version: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: re3data.org
version: re3data.org: ChEBI; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3H78W last accessed: 2022-11-04
natural product
metasource: Fairsharing.org
version: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
small molecule
metasource: Fairsharing.org
version: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
taxonomic classification
metasource: Fairsharing.org
version: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
structure databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
small molecules
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:10.906729
taxonomy
metasource: re3data.org
version: re3data.org: ChEBI; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3H78W last accessed: 2022-11-04
chemical biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:10.906729
Tags
More detailed information about this field from each metasource.
molecular entity
metasource: Fairsharing.orgversion: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: re3data.org
version: re3data.org: ChEBI; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3H78W last accessed: 2022-11-04
molecular structure
metasource: Fairsharing.orgversion: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: re3data.org
version: re3data.org: ChEBI; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3H78W last accessed: 2022-11-04
natural product
metasource: Fairsharing.orgversion: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
small molecule
metasource: Fairsharing.orgversion: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
taxonomic classification
metasource: Fairsharing.orgversion: FAIRsharing.org: ChEBI; Chemical Entities of Biological Interest; DOI: https://doi.org/10.25504/FAIRsharing.62qk8w; Last edited: Feb. 11, 2020, 10:11 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
structure databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
small molecules
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:10.906729
taxonomy
metasource: re3data.orgversion: re3data.org: ChEBI; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3H78W last accessed: 2022-11-04
chemical biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:10.906729
molecular entity molecular structure natural product small molecule taxonomic classification structure small molecule taxonomy chemical biology
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