Links
From BioAssay Ontology
Links to Useful Resources
Click onto the links into the relevant categories below.
BAO Glossary
Biology / Assay / Reagents
Ontology Repositories / Resources
- EBI OLS
- Open NCBO BioPortal National Center for Biomedical Ontologies
- OntoBee
- OBO Foundry Collaborative open source ontologies
- RCS Ontologies
Bio Ontologies
- Cell Line Ontology from Molecular Connections
- Cell System Markup Language
- Chemical Entities of Biological Interest (ChEBI) Ontology
- Experimental Factor Ontology at EBI
- Gene Ontology GO
- Morphster
- Neuroscience Information Framework (NIF)
- OBI Ontology for Biomedical Investigations
- Open Clinical Ontologies
Other Useful Ontologies
- EDAM (EMBRACE Data and Methods)
- IEEE SUO Standard Upper Ontology
- Ontologies from the Dumontier Lab
- Relation Ontology
Biology Standards and References
- FGED Standards *MIAME *MINSEQE *MAGE-TAB *MAGE *MGED Ontology
- MIAME Minimum Information About a Microarray Experiment
- MIACA Nature Paper and Supporting Material
- BioPAX
- Guidelines of the STRENDA Commission Beilstein
- IUPAC Gold Book
- MIACA Schema
- MIBBI
Ontology Development
- Semantic Web Best Practices
- Conceptual Graphs
- Ontology Design Patterns
- Modeling Documents by Combining Semantic Concepts with Unsupervised Statistical Learning
- Barry Smith List of Publications
Software Tools and Semantic Technologies
Experiment / lab / biology
- Bio GPS
- BioGuide
- CMAP Tools (Construct, navigate, share and criticize knowledge models - concept maps)
- Connectivity Map
- ConceptGen
- Explaining Entailments (Protege)
- GO Annotation tools
- Ingenuity Systems
- Investigation/Study/Assay (ISA) Infrastructure
- XperimentR (Imperial College)
Ontology / Semantic technology
- NCBO Annotator
- OBO Edit
- Pellet OWL Reasoner
- Protege
- RacerPro 2.0 Semantic Reasoner
- SPARQL Query Language for RDF
- Revelytix Semantic technology solutions
- BEL Framework Technology platform for managing, publishing, and using structured life-science knowledge
Semantic Web Standards
- OWL Web Ontology Language
- Semantic Web
- Sig.ma Semantic Mashup
- Semantic Web Ontologies
- SKOS Simple Knowledge Organization System
- SKOS Simple Knowledge Organization System Reference
- Suggested Upper Merged Ontologies SUMO
- SUMO OBO Mapping
Semantic Web Projects
Tutorials
- Barry Smith's Ontology Course
- Marek Obitko (Ontologies and Semantic Web; Prediction with Neural Networks)
- NCBO Seminar Series
SLAS (former SBS)
Assay Technologies / Assay Development
- NIH Chemical Genomics Center (NCGC) Assay Guide
Chemistry and Biology Database Resources / Data Repositories
- Comparative Toxicogenomics Database Links disease to chemicals, genes, pathways Introduction to CTD
- BIOBASE Biological Databases
- Unison Genentech Compendium of protein sequences and extensive precomputed predictions
- Biocarta Interactive graphic models of molecular and cellular pathways
- GEO Gene Expression Omnibus NCBI Microarray Repository
- GPCRDB Information system for GPCRs
- IUPHAR The International Union of Basic and Clinical Pharmacology Database on GPCR, Ion Channels and Nuclear Receptors
- KEGG Kyoto Encyclopedia of Genes and Genomes
- Membranome A database of all human membrane proteins
- Molecule Pages from Nature's Signaling Gateway
- GPCR-OKB, oligomer knowledge database GPCR oligomerization database
- OPM Orientation of Proteins in Membranes Database
- PID Pathway Inteaction Database
- PIR Protein Information Resource
- PubChem NCBI BioAssay Repository
- REACTOME an open-source, open access pathway database
- STRING Known and Predicted Protein-Protein Interactions
- Structural Classification of Proteins
- Antibody Registry (NIF)
Cheminformatics Web
additional tools and related projects
- Alfresco Share site (requires invite - ask Stephan)
- SWENG Confluence Wiki (requires CCS LDAP access)