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Browse the ontology-based projects in the community: Each project description is linked to BioPortal ontologies that the project uses. Use the ‘Add Project’ link to add your ontology-based project to this list and to link it to BioPortal ontologies. Your project will then appear on the pages that list the details for the ontologies that you selected (e.g., click on "Projects" at the page for the ontology of Mouse adult gross anatomy to check out the projects that use that ontology). We also invite you to review ontologies that you used in your project.
| AnoBase | |
| AnoBase is a database containing genomic/biological information on anopheline mosquitoes, with an emphasis on Anopheles gambiae, the world's most important malaria vector. AnoBase is the continuation of AnoDB, a database established and maintained since 1996 at the Institute of Molecular Biology and Biotechnology (IMBB) of the Foundation of Research and Technology - Hellas (FORTH) in Heraklion, Crete, Greece. | |
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| Homepage: | http://www.anobase.org/ |
| Bgee | |
| Bgee is a database to compare expression patterns between animals. We create homology relationships between anatomical ontologies, and store this information in a multi-species ontology. On the download page of Bgee, you will find the Homologous Organ Group ontology, the developmental Stages ontology, and the Homolonto software for ontology alignment. | |
| People: | Robinson-Rechavi lab |
| Institution: | Universite de Lausanne |
| Homepage: | http://bgee.unil.ch/ |
| BioLit | |
| A web database of open access articles with metadata | |
| People: | Lynn Fink |
| Institution: | UCSD |
| Homepage: | http://biolit.ucsd.edu |
| BioPAX | |
| The goal of the BioPAX group is to develop a common exchange format for biological pathways data. The BioPAX project began at the Fourth BioPathways Consortium Meeting, a satellite of the ISMB'02 Conference held in Edmonton, Canada in August 2002. It was decided that a pathway exchange format would facilitate sharing of pathway information between databases and users and would be a good first step to building an open source pathway information resource. The project got underway in early October 2002 when Chris Hogue (BIND, UToronto), Peter Karp (BioCyc, SRI), and Chris Sander (MSKCC) organized the BioPAX work group. | |
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| Homepage: | http://www.biopax.org/index.html |
| Biositemaps | |
| The Biositemaps Working Group of the NIH Roadmap National Centers of Biomedical Computing (NCBC) (www.ncbcs.org) has developed technologies to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. Each site which intends to contribute to the inventory instantiates a file on its Internet site ‘'biositemap.rdf' which conforms to a defined RDF schema and uses concepts from the Biomedical Resource Ontology to describe the resources. | |
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| Homepage: | http://biositemaps.ncbcs.org/ |
| breast tissue cell lines | |
| Contains a comprehensive list of cell lines derived from breast tissue, both normal and pathological. The ontology in built in OWL with cross relation to classes- genetic variation, pathological condition, genes, chemicals and drugs. The relations built enable semantic query across different classes | |
| People: | Usha Mahadevan & Arathi Raghunath |
| Institution: | Molecular Connection Pvt. Ltd. |
| Homepage: | www.molecularconnections.com |
| CBO | |
| Create Cell Behavior Ontology | |
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| Homepage: | http://www.compucell3d.org |
| Cell line ontology | |
| Cell lines are key experimental models to understand protein interactions and signaling pathways. With a large pool of such data coming from different cell lines of different origin -of normal and -pathological tissues, proper analysis requires segregating data pertaining to specific cell lines. The project envisaged brings together hierarchical trees of organs, mammalian cell lines and diseases in one platform. Certain specific terms from Cell Type (CL) ontology, Foundational Model of Anatomy (FMA) and DOID ontologies are mapped for searchability. Ontology is developed in both OBO and OWL. | |
| People: | Arathi Raghunath, Bharat Bhat, Jignesh Bhate, Usha Mahadevan |
| Institution: | Molecular Connections Pvt. Ltd |
| Homepage: | http://www.molecularconnections.com |
| CTSA Inventory Resource Web Presence (CIRWP) | |
| The CTSA Inventory Resource Web Presence (CIRWP) is a federated, inter-institutional project to facilitate resource discovery. The CIRWP project contains informatics and translational resources from over 40 CTSA and NCBC organizations. The project utilizes the categories provided by the Biomedical Resource Ontology (BRO). Through the CIRWP framework, the BRO facilitates semantic search and discovery of biomedical resources, breaking down barriers to scientific discoveries that will improve human health. | |
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| Homepage: | http://biositemaps.ncbcs.org/cirwp/about.htm |
| dictyBase | |
| An Online Informatics Resource for Dictyostelium. | |
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| Homepage: | http://dictybase.org/ |
| Drug Design Ontology | |
| The goal of DDO project is to develop an ontology for the description of drug discovery investigations. DDO aims to follow to the OBO (Open Biomedical Ontologies) Foundry principles, uses relations laid down in the OBO Relation Ontology, and be compliant with Ontology for biomedical investigations (OBI). | |
| People: | Da Qi, Larisa Soldatova, Ross King |
| Institution: | Aberystwyth University |
| Homepage: | http://users.aber.ac.uk/ddq/ddo/wiki |
| DSS | |
| Decision Support for Arthropod-borne Infectious Diseases. The Ontology portion of our project is still under construction. | |
| People: | David Penhall, Saul Lozano-Fuentes |
| Institution: | Colorado State University |
| Homepage: | http://www.rams-aid.org/ |
| EFO | |
| The Experimental Factor Ontology (EFO) is an application focused ontology modelling the experimental factors in ArrayExpress. The ontology has been developed to increase the richness of the annotations that are currently made in the ArrayExpress repository, to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The methodology employed in the development of EFO involves construction of mappings to multiple existing domain specific ontologies, such as the Disease Ontology and Cell Type Ontology. This is achieved using a combination of automated and manual curation steps and the use of a phonetic matching algorithm. The ontology is evaluated with use cases from the ArrayExpress repository and used in our query interface http://www.ebi.ac.uk/microarray-as/atlas/ | |
| People: | James Malone, Helen Parkinson |
| Institution: | EBI |
| Homepage: | http://www.ebi.ac.uk/efo |
| Electrophysiology Ontology | |
| The Electrophysiology (EP) Ontology is part of Project 2 of the Cardiovascular Research Grid (CVRG), an NHLBI funded effort to develop a national infrastructure for managing, sharing, and analyzing a broad range of cardiac data. The EP Ontology will contain terms for describing single-channel electrophysiological experiments and data obtained using voltage-clamp, current clamp and fluorescence imaging techniques applied at the cell level and multi-channel fluorescence imaging techniques applied at the cell, tissue and whole heart levels. | |
| People: | Dr. Raimond L. Winslow, Stephen J. Granite |
| Institution: | The Johns Hopkins University |
| Homepage: | http://www.cvrgrid.org |
| Fishmap | |
| FishMap is a unified and centralized resource for storage, retrieval, and display of genomic information of zebrafish. | |
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| Homepage: | http://fishmap.igib.res.in/ |
| FlyBase | |
| The FlyBase project is carried out by a consortium of Drosophila researchers and computer scientists at: Harvard University, University of Cambridge (UK), Indiana University and the University of New Mexico. | |
| People: | http://flybase.org/static_pages/docs/consortium.html |
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| Homepage: | http://flybase.org/ |
| Gene Ontology Consortium | |
| The GO Consortium is the set of model organism and protein databases and biological research communities actively involved in the development and application of the Gene Ontology. | |
| People: | http://www.geneontology.org/GO.consortiumlist.shtml#fulllist |
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| Homepage: | http://www.geneontology.org/ |
| Gramene | |
| As an information resource, Gramene's purpose is to provide added value to data sets available within the public sector, which will facilitate researchers' ability to understand the grass genomes and take advantage of genomic sequence known in one species for identifying and understanding corresponding genes, pathways and phenotypes in other grass species. | |
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| Homepage: | http://www.gramene.org/ |
| Human Protein Ontology | |
| This project aims at developing a protein ontology of human proteins for different semantic queries. Proteins are categorized based on their molecular function, involvement in biological or physiological processes as per GO terms and other public sources and to disease associations. Proteins are mapped to their splice variants, orthologs and paralogs. Mapping isoforms of family proteins and components of a functional complex are also addressed. Disease associations are mapped to DOID terms and splice variants to PRO ontology terms. The ontology is built in Protégé OWL and allows querying for molecules by any of the above mentioned categories. About 500 proteins of different functions will be annotated as a sample set in this phase of the project. | |
| People: | Arathi Raghunath, Bharat Bhat, Jignesh Bhate, Usha Mahadevan |
| Institution: | Molecular Connections Pvt. Ltd |
| Homepage: | http://www.molecularconnections.com |
| Influenza Ontology | |
| The Influenza Ontology is an application ontology covering the numerous aspects if influenza virus basic research, and surveillance. The influenza ontology extends the Infectious Disease Ontology (IDO). | |
| People: | Burke Squires, Lynn Schriml, Joanne Luciano |
| Institution: | UT Southwestern, Univ of Maryland, MITRE |
| Homepage: | http://influenzaontologywiki.igs.umaryland.edu/wiki/index.php/Main_Page |
| Mouse Genome Informatics | |
| MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. The projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, and MouseCyc Project at MGI. | |
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| Homepage: | http://www.informatics.jax.org/ |
| Multiscale Ontology for Skin Physiology | |
| The purpose of this project is to investigate the representation of physiological processes in the skin across levels of spatial scale. | |
| People: | Tariq Abdulla |
| Institution: | Loughborough University |
| Homepage: | http://www.lboro.ac.uk |
| NCBO Annotator | |
| A Web service that tags free text with ontology concepts. NCBO uses these Web services to annotate resources in the NCBO Resource Index to create an ontology index of these resources. This Web service can be accessed through BioPortal or used directly in your software. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). Our service methodology leverages ontologies to create annotations of raw text and returns them using semantic web standards. | |
| People: | Clement Jonquet |
| Institution: | Stanford University |
| Homepage: | http://www.bioontology.org/annotator-service |
| NCBO Resource Index | |
| The NCBO Resource Web service is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data resources related to particular ontology concepts. The annotations are generated using the NCBO Annotator and presented through integration with BioPortal, enabling researchers to search for biomedical resources associated (annotated) with specific ontology terms. The NCBO Resources web service uses a concept recognizer (currently provided by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand these using ontology is_a relations in the ontology. The system's indexing workflow processes the text metadata of diverse resource elements such as gene expression data sets, descriptions of radiology images, clinical trial reports, and PubMed article abstracts to annotate and index them with concepts from appropriate ontologies. Researchers can then search biomedical data sources using ontology concepts. | |
| People: | Clement Jonquet |
| Institution: | Stanford University |
| Homepage: | http://www.bioontology.org/resources-index |
| Neural ElectroMagnetic Ontologies (NEMO) | |
| NEMO is developing ontologies for representation and integration of event-related brain potentials (ERPs). To support this work, we are developing an integrated tool environment for storage and management of ERP data, ontologies, and ontology-based markup and analysis of data. | |
| People: | Gwen Frishkoff, Dejing Dou, Paea LePendu, Robert Frank, Haishan Liu, Allen Malony, Jason Sydes |
| Institution: | University of Oregon |
| Homepage: | http://nemo.nic.uoregon.edu |
| Neuroscience Information Framework | |
| The Neuroscience Information Framework (NIF; http://nif.nih.gov) is a dynamic inventory of Web-based neuroscience resources, data, and tools accessible via any computer connected to the Internet. An initiative of the NIH Blueprint for Neuroscience Research, NIF advances neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment. The NIF project is designed to serve the biomedical research community. The more participation from the community, the better the NIF. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through the NIF. We offer a variety of methods for making resources searchable through the NIF. For more information or to recommend a resource, follow the link to Register Your Resource, or send us an e-mail at curation@neuinfo.org. Collaborating institutions working on the current version of NIF include University of California, San Diego, California Institute of Technology, George Mason University, Yale University Medical College, and Washington University. | |
| People: | Maryann Martone, Jeffrey Grethe, Amarnath Gupta, Gordon Shepherd, Giorgio Ascoli, Paul Sternberg, David Van Essen |
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| Homepage: | http://neuinfo.org |
| OntoCAT | |
| OntoCAT or Ontology Common API Tasks is a java library aiming to overcome the hurdle of querying multiple existing ontology resources. It supports both major ontology browsers: NCBO BioPortal and EBI Ontology Lookup Service (OLS), providing a convenient wrapper around their Web Services. It also supports querying of local OWL and OBO resources making use of OWL API. OntoCAT provides the same standardised, uniform interface for all of them. | |
| People: | Tomasz Adamusiak, Helen Parkinson, Morris Swertz |
| Institution: | EMBL-EBI |
| Homepage: | http://ontocat.sourceforge.net/ |
| ParameciumDB | |
| ParameciumDB is a new model organism database associated with the genome sequencing project. Built with core components of the Generic Model Organism Database (GMOD) project, ParameciumDB currently contains the macronuclear genome sequence and annotations, linked to available genetic data (RNA interference data and stock collection). | |
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| Homepage: | http://paramecium.cgm.cnrs-gif.fr/ |
| Protege | |
| Protégé is a free, open source ontology editor and knowledge-base framework | |
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| Homepage: | http://protege.stanford.edu |
| Protein Ontology Project | |
| PO integrates protein data formats and provide a structured and unified vocabulary to represent proteins. PO provides integration of heterogeneous protein and biological data sources. | |
| People: | Amandeep S. Sidhu |
| Institution: | BIOMAP Project Lab |
| Homepage: | http://proteinontology.org.au/ |
| RadLex | |
| RadLex is a controlled terminology for radiology. | |
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| Institution: | RSNA |
| Homepage: | http://radlex.org |
| SBO | |
| Systems Biology Ontology | |
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| Homepage: | http://www.ebi.ac.uk/sbo/ |
| Schizosaccharomyces pombe | |
| This database contains all S. pombe (fission yeast) known and predicted protein coding genes, pseudogenes, transposons, tRNAs, rRNAs, snRNAs, snoRNAs and other known and predicted non-coding RNAs. Curation of new and existing literature is ongoing and changes are incorporated weekly. User feedback is welcome. Please send updates, comments and corrections to help us improve the resource using the feedback forms on each gene page. | |
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| Homepage: | http://www.sanger.ac.uk/Projects/S_pombe/ |
| SGD | |
| SGD(TM) is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast. | |
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| Homepage: | http://www.yeastgenome.org/ |
| TAIR | |
| The Arabidopsis Information Resource (TAIR) collects information and maintains a database of genetic and molecular biology data for Arabidopsis thaliana, a widely used model plant. | |
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| Homepage: | http://www.arabidopsis.org/ |
| The Comparative Data Analysis Ontology | |
| The objective of this project is to develop an ontology for the description of information relevant to experiments in evolutionary biology. A practical example of comparative analysis would be inferring the locations of genes and regulatory sites in the human genome by comparing it with the chimp and mouse genomes. When comparative analysis is done within an evolutionary framework, it becomes "evolutionary comparative analysis": the items to be compared are treated as homologs that have evolved along paths of common descent (represented by a tree) according to dynamics that reflect an evolutionary process of change. Various types of biological traits (molecular, morphological, behavioral) can be analyzed in this way. Thus, evolutionary comparative analysis involves distinctive concepts regarding homologous "characters" (the "same" trait as represented in different species), phylogenetic histories, and models of state-transitions of characters. To accomodate diverse types of characters, we will import concepts from other ontologies (e.g., amino acids from an amino acid ontology). The ontology is being developed by a small team of scientists in the context of the Evolutionary Informatics working group at the National Evolutionary Synthesis Center (team members include Julie Thompson, Enrico Pontelli, Francisco Prosdocimi, and Brandon Chisham). The working group has a project wiki at https://www.nescent.org/wg_evoinfo. The draft ontology, in OWL format, is described and available at http://www.evolutionaryontology.org | |
| People: | Arlin Stoltzfus, Julie Thompson, Francisco Prosdocimi, Brandon Chisham, Enrico Pontelli |
| Institution: | NMSU, NIST, University of Strasbourg |
| Homepage: | http://www.evolutionaryontology.org |
| The Human Phenotype Ontology | |
| The human phenotype ontology (HPO) intends to offer a tool that will allow large-scale computational analysis of the human phenome. The HPO currently contains over 9500 terms, each of which describes an individual phenotypic anomaly. The terms are arranged in a directed acyclic graph and are connected by “is-a” edges, such that a term represents a more specific or limited instance of its parent term(s). All relationships in the HPO are is_a relationships, i.e. a simple class-subclass relationships. For instance, Abnormality of the feet is_a Abnormality of the lower limbs. The relationships are transitive, meaning that they are inherited up all paths to the root. Organ abnormality is the main subontology of the HPO and contains descriptions of clinical abnormalities. Additional subontologies are provided to describe inheritance patterns and onset/clinical course. | |
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| Homepage: | http://www.human-phenotype-ontology.org/index.php/hpo_home.html |
| VectorBase | |
| VectorBase is one of eight Bioinformatics Resource Centers funded by NIAID to provide web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases. | |
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| Homepage: | http://www.vectorbase.org/index.php |
| VO: Vaccine Ontology | |
| The Vaccine Ontology (VO, http://www.violinet.org/vaccineontology) is a community-based ontology that targets to model vaccines, vaccine components, and host responses to vaccines, and other vaccine-related information. | |
| People: | Yongqun "Oliver" He |
| Institution: | University of Michigan |
| Homepage: | http://www.violinet.org/vaccineontology |
| wFleaBase | |
| wFleaBase is a repository of data and an electronic information service provided for the Daphnia Genomics Consortium (DGC) and the general scientific community. | |
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| Homepage: | http://wfleabase.org/ |
| WormBase | |
| WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and some related nematodes. Founded in 2000, the WormBase Consortium is led by Paul Sternberg of CalTech, Richard Durbin of the Wellcome Trust Sanger Institute, Lincoln Stein of Cold Spring Harbor, and John Spieth of the Washington University Genome Sequencing Center. | |
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| Homepage: | http://www.wormbase.org/ |
