Browse a selection of projects that use BioPortal resources
| Electronic Trial Master File - eTMF | |
| This preliminary version of the eTMF content model ontology is designed to support clinical trial regulatory content management. Metadata terms are sourced from NCI thesaurus. The HAIG is a non-profit organization formed to promote content interoperability for electronic content archives in BioPharma and Healthcare. For more info go to www.TheHaig.Org. | |
| People: | Zachariah Schmidt |
|---|---|
| Institution: | HAIG - Health Science Archive Interoperability Group |
| Homepage: | http://www.TheHaig.org |
| Adverse Event Reporting Ontology (AERO) | |
| The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events. | |
| People: | Melanie Courtot |
| Institution: | |
| Homepage: | http://purl.obolibrary.org/obo/aero |
| An Ontology for Drug Discovery Investigations | |
| The goal of DDI project is to develop an ontology for the description of drug discovery investigations. DDI 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, Andrew Hopkins, Richard Bickerton |
| Institution: | Aberystwyth University |
| Homepage: | http://purl.org/ddi/home |
| 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. | |
| People: | |
| Institution: | |
| Homepage: | http://www.anobase.org/ |
| Assay Annotation | |
| Excel template uses BAO to annotated data into PubChem's Deposition System. The template provides dropdown lists for fields where the value is allowed (controlled vocabulary). | |
| People: | S. Schurer, U. Vempati, S. Canny, M. Southern |
| Institution: | TSRI and UM |
| Homepage: | http://www.bioassayontology.org/index.php?option=com_content&view=article&id=97&Itemid=140 |
| BAOSearch | |
| BAOSearch is a web-based application for querying, browsing and downloading small molecule biological screening results, including high-throughput screening (HTS) data.
BAOSearch content was curated from PubChem |
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| People: | Mader C, Datar N, Abeyruwan S, Koleti A, Venkatapuram S, Chung C, Puram D, Vempati U, Sakurai K, Przydzial M, Lemmon V, Visser U, Schürer S. |
| Institution: | University of Miami |
| Homepage: | http://baosearch.ccs.miami.edu/baosearch/ |
| 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/ |
| Bio2RDF | |
| The Bio2RDF project transforms silos of life science data into a globally distributed network of linked data for biological knowledge discovery. | |
| People: | Michel Dumontier, Peter Ansell, Francois Belleau, Allison Callahan, Jacques Corbeil, Jose Cruz-Toledo, Alex De Leon, Steve Etlinger, James Hogan, Nichealla Keath, Jean Morissette, Marc-Alexandre Nolin, Nicole Tourigny, Philippe Rigault and, Paul Roe |
| Institution: | Multi |
| Homepage: | http://bio2rdf.org |
| BioAssay Ontology | |
| The BioAssay Ontology (BAO) is an NIH-funded project to develop standard terminologies and a formal, extensible, knowledge-based description of biological assays and assay data (the ontology). Biocuration is a component of the BAO project to systematically annotate biological assays such as those in PubChem with standardized terminology describing assay concepts defined in the ontology. The BAO project also develops software tools to query and explore data sets in the context of the ontology. | |
| People: | |
| Institution: | University of Miami |
| Homepage: | http://www.bioassayontology.org/ |
| 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. | |
| People: | |
| Institution: | |
| 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. | |
| People: | |
| Institution: | |
| Homepage: | http://biositemaps.ncbcs.org/ |
| BioXSD | |
| BioXSD defines exchange formats of basic bioinformatics types of data. It is a rich but not-too-complicated XML-Schema-based format for biopolymer sequences, feature records, alignments, and references to resources. Semantics if BioXSD type definitions is given via SAWSDL annotation with EDAM, RDFS, and DublinCore. In addition, BioXSD supports rich annotation of data by any public ontology concepts. | |
| People: | Matus Kalas, Edita Kerosiene, Pal Puntervoll, Armin Topfer, Jon Ison, Christophe Blanchet, Kristoffer Rapacki, Inge Jonassen ... |
| Institution: | University of Bergen, Danish Technical University, CNRS, EBI ... |
| Homepage: | http://bioxsd.org |
| Blood Ontology | |
| The Blood Ontology is a set of co-related ontologies being created to gather and represent data about blood according to well-founded ontological principles. | |
| People: | HTLV Interdisciplinar Research Group |
| Institution: | Federal University of Minas Gerais, Hemominas Foundation |
| Homepage: | http://mba.eci.ufmg.br/BLO/ |
| 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 |
| caB2B | |
| caB2B, or cancer Bench-to-Bedside, is a tool that enables querying for cancer related information hosted anywhere on caGrid. It allows for Web-based queries, which can be stored for later re-use. caB2B users can semantically search and retrieve information from the NCBO Resource Index. | |
| People: | |
| Institution: | National Cancer Institute |
| Homepage: | https://cabig.nci.nih.gov/tools/caB2B |
| CBO | |
| Create Cell Behavior Ontology | |
| People: | |
| Institution: | |
| 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 |
| Cell line ontology | |
| Ontologies provide a common platform of controlled vocabulary for researchers who need to share information across a particular domain, inclusive of machine-interpretable definitions of basic concepts in the domain and relations among them. The need for ontologies that provide a systematic arrangement of available data and allow cross talk across various related domains is gaining momentum. In this backdrop, we have developed a comprehensive ontology on primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. An extensive network of relations has been built across these concepts to enable different combination of queries. The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format. | |
| People: | Usha Mahadevan |
| Institution: | Molecular Connections Pvt. Ltd. |
| Homepage: | www.molecularconnections.com |
| Chemical Information Ontology | |
| The Chemical Information Ontology (CHEMINF) is an ontology to represent chemical structure and to richly describe chemical properties, whether intrinsic, observed or computed. | |
| People: | Leonid Chepelev, Michel Dumontier, Janna Hastings, Egon Willighagen |
| Institution: | multi |
| Homepage: | http://code.google.com/p/semanticchemistry/ |
| 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. | |
| People: | |
| Institution: | |
| Homepage: | http://biositemaps.ncbcs.org/cirwp/about.htm |
| dictyBase | |
| An Online Informatics Resource for Dictyostelium. | |
| People: | |
| Institution: | |
| Homepage: | http://dictybase.org/ |
| 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/ |
| eagle-i | |
| The eagle-i project is building a searchable network of research resources at research institutions nationwide. We are developing an application ontology for indexing and querying, and this effort is being guided by discussions within the ontology community aimed at promoting interoperability. We will be inventorying laboratories, services, instruments, services, reagents, organisms, persons, protocols, human studies (metadata), tissue/biological sample repositories and training opportunities. The eagle-i application ontology is being used to drive our data tool and search applications, and is available in beta form from google code: http://code.google.com/p/eagle-i/ | |
| People: | Melissa Haendel, Carlo Torniai |
| Institution: | Consortium |
| Homepage: | https://www.eagle-i.org/home/ |
| 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 |
| EMBOSS | |
| The European Molecular Biology Open Software Suite | |
| People: | |
| Institution: | |
| Homepage: | http://emboss.sourceforge.net/ |
| EMBOSS | |
| The European Molecular Biology Open Software Suite (EMBOSS) is a well established, high quality package of open source software tools for molecular biology. | |
| People: | Peter Rice, Alan Bleasby, Jon Ison, Mahmut Uludag |
| Institution: | EMBL-EBI |
| Homepage: | http://emboss.sourceforge.net/ |
| eMERGE - eleMAP | |
| Organized by the National Human Genome Research Institute (NHGRI) with additional funding from the National Institute of General Medical Sciences, the eMERGE Network is a national consortium formed to develop, disseminate, and apply approaches to research that combine DNA biorepositories with electronic medical record (EMR) systems for large-scale, high-throughput genetic research. | |
| People: | |
| Institution: | |
| Homepage: | https://www.gwas.net/eleMAP/ |
| Epilepsiae | |
| EPILEPSIAE- Evolving Platform for Improving the Living Expectations for Patients Suffering from IctAl Events is developing the European Database on Epilepsy, algorithms for seizure prediction in refractory epilepsy, and Brainatcs, a transportable device to warn a patient of a coming seizure | |
| People: | partners from 4 countries |
| Institution: | EU FP7 |
| Homepage: | ww.epilepsiae.eu |
| eSysbio | |
| eSysbio is an online system for collaborative life science research. It provides a secure Web-based workspace where researchers can analyse and share their data. The aims of eSysbio are: 1. To enable efficient interdisciplinary life science research 2. To ease analysis of complex biological data 3. To allow efficient use of public data and analysis tools 4. To automatically document in silico experiments for reproducible science For the analyses of their data, users of eSysbio can use any external tools that have an interoperable SOAP Web service interface. In addition, users can use their custom R scripts, or those shared with other users. It allows complex analyses by composing Web services and R scripts into custom workflows. | |
| People: | Prabu Venkatamaran, Hakon Sagehaug, Matus Kalas, Pawel Sztromwasser, Anne-Kristin Stavrum, Armin Topfer, Michael Dondrup, Francisco Roque, Siv Hollup, Kjell Petersen, Inge Jonassen, Pal Puntervoll |
| Institution: | University of Bergen |
| Homepage: | http://esysbio.org/about |
| Evaluation of LOINC Document Ontology | |
| Use of LOINC Document Ontology to facilitate NLP projects, Health Information Exchange and secondary use of data | |
| People: | |
| Institution: | National Institute of Health Clinical Center |
| Homepage: | http://code.google.com/p/loinc-document-ontology-repository |
| FGED-MGED Ontology | |
| The Functional Genomics Data (FGED) Society has incorporated the MGED Ontology (MO) into OBI for use in annotating functional genomics studies especially with the MAGE-TAB format. | |
| People: | |
| Institution: | |
| Homepage: | http://www.fged.org/projects/ontology/ |
| Fishmap | |
| FishMap is a unified and centralized resource for storage, retrieval, and display of genomic information of zebrafish. | |
| People: | |
| Institution: | |
| 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 |
| Institution: | |
| Homepage: | http://flybase.org/ |
| Fundamental Biology of Sudden Cardiac Death and Its Application to Identify Patients at Risk (PROSE-ICD) | |
| This study examines the role of genetic, protein and electrocardiographic markers measured longitudinally in predicting the risk of SCD and overall mortality in patients with implantable defibrillators placed for primary prevention. | |
| People: | Gordon Tomaselli (PI) |
| Institution: | Johns Hopkins Hospital, Washington Hospital Center, Virginia College of Medicine |
| Homepage: | http://www.hopkinsmedicine.org/heart_vascular_institute/clinical_trials/sudden_cardiac_death/prose_icd.html |
| 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 |
| Institution: | |
| 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. | |
| People: | |
| Institution: | |
| Homepage: | http://www.gramene.org/ |
| Hewan Invertebrata | |
| Ontology hewan Invertebrata | |
| People: | Vasko Edo Gultom |
| Institution: | |
| Homepage: | www.vaskoedo.co.cc |
| HOM - Health Ontology Mapper | |
| HOM’s open source components provide a key framework for mapping data, requesting data and delivering data to and from data standards. HOM has been integrated directly with the i2b2 Workbench, providing a robust system for both single institution deployments and federated query systems across institutions using both caGRID and Harvard SHRINE. | |
| People: | Rob Wynden, Prakash Lakshminarayanan, Ketty Mobed |
| Institution: | UCSF |
| Homepage: | http://www.healthontologymapper.org/ |
| http://bioportal.bioontology.org/ontologies/1672 | |
| Demonstrate a novel approach to updating and expanding upon information present in drug product labels that is useful for determining a drug’s safety. The approach will use natural language processing and scientific discourse ontologies to build a linked open data store of scientific information that updates or elaborates on medication safety statements present in drug product labels. | |
| People: | Scientific Discourse Task Force |
| Institution: | W3C Health Care and Life Sciences Interest Group |
| Homepage: | http://www.w3.org/wiki/HCLSIG/SWANSIOC |
| 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 |
| Hypertrophic Cardiomyopathy consortium | |
| The Hypertrophic Cardiomyopathy Consortium is a network of investigators focused on the research, diagnosis, and treatment of HCM. The Consortium includes investigators from Johns Hopkins University and several other institutions throughout the world. The consortium seeks to define a large cohort in which all patients have undergone a thorough clinical evaluation. This typically includes history and physical examination by a cardiologist, 12-lead ECG, echocardiography including advanced techniques such as tissue Doppler and strain imaging. Additionally, Holter monitoring, signal averaged ECG, cardiac MRI, electrophysiological testing, coronary angiograms and genetic data may be available for a large number of patients. The consortium includes over 6000 patients with a confirmed diagnosis of HCM. | |
| People: | Theodore Abraham, MD |
| Institution: | Johns Hopkins University |
| Homepage: | http://www.hcm-consortium.org |
| Immune Epitope Database | |
| The IEDB contains data related to antibody and T cell epitopes for humans, non-human primates, rodents, and other animal species. | |
| People: | http://www.immuneepitope.org/acknowledgements.php |
| Institution: | La Jolla Institute for Allergy & Immunology |
| Homepage: | http://www.immuneepitope.org/ |
| Immunology Database and Analysis Portal (ImmPort) | |
| ImmPort, the Immunology Database and Analysis Portal, is a one stop shop to access reference and experiment data for immunologists. ImmPort provides advanced information technology support in the production, analysis, archiving, and exchange of scientific data for the diverse community of life science researchers supported by NIAID/DAIT. | |
| People: | Richard H. Scheuermann, et al. |
| Institution: | U.T. Southwestern Medical Center |
| Homepage: | www.immport.org |
| 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 |
| Influenza Research Database (IRD) | |
| The mission of the Influenza Research Database (IRD) is to provide a resource for the influenza virus research community that will facilitate an understanding of the influenza virus and how it interacts with the host organism, leading to new treatments and preventive actions. This resource will contain avian and non-human mammalian influenza surveillance data, human clinical data associated with virus extracts, phenotypic characteristics of viruses isolated from extracts, and all genomic and proteomic data available in public repositories for influenza viruses. The resource will link host surveillance and clinical data to sequence and phenotypic data for all well characterized influenza virus strains. Data obtained from public data sources for well characterized virus strains will be supplemented with IRD generated data. The IRD will provide a suite of tools for analysis of all types of influenza data and a personal work bench on which each scientist can store lists of important data selected from that available on IRD. | |
| People: | Richard H. Scheuermann, et al. |
| Institution: | U.T. Southwestern Medical Center |
| Homepage: | www.fludb.org |
| Integrative Tools for Protozoan Parasite Research (ITPPR) | |
| The Integrative Tools for Protozoan Parasite Research project is using OBI to develop forms to capture structured meta-data about studies (e.g., genotyped isolates of parasites, phenotypes of transgenic parasites) for EuPathDB and to provide terms for annotating bioinformatics web services available through Galaxy. | |
| People: | Christian Stoeckert |
| Institution: | University of Pennsylvania |
| Homepage: | http://www.bioontology.org/node/604/ |
| ISA software suite | |
| An open source ISA software suite and an extensible hierarchical data structure implemented by a growing number of international public resources. It caters to data as diverse as stem cell, toxicogenomics, environmental gene surveys, microbial diversity studies, and a variety of metabolomics and metagenomics-based studies. But it maintains cross-domain compatibility in the way the experimental context is described. | |
| People: | International collaborative effort |
| Institution: | Multiple institutions; leads at University of Oxford, UK |
| Homepage: | http://isa-tools.org |
| LogMap | |
| Logic-based and Scalable Ontology Matching. LogMap is a highly scalable ontology matching system with `built-in' reasoning and diagnosis capabilities. Currently, LogMap is the only matching system that can sucessfully deal with semantically rich ontologies containing tens (and even hundreds) of thousands of classes. Furthermore, LogMap is able to produce a `clean' set of output mappings in many cases. Our experiments with the ontologies NCI, FMA and SNOMED CT con firm that our system can efficiently match even the largest existing bio-medical ontologies. | |
| People: | Ernesto Jimenez Ruiz and Bernardo Cuenca Grau |
| Institution: | University of Oxford |
| Homepage: | http://www.cs.ox.ac.uk/isg/projects/LogMap/ |
| Medical Dictionary | |
| Medical annotator & dictionary | |
| People: | |
| Institution: | Dalhousie University |
| Homepage: | http://cs.dal.ca |
| Mental Functioning Ontology | |
| The Mental Functioning Ontology is an ontology for mental functioning, including mental processes such as cognition and traits such as intelligence, and related diseases and disorders. It is developed in the context of the Ontology for General Medical Science and the Basic Formal Ontology. The project is being developed in collaboration between the University of Geneva, Switzerland, and the University at Buffalo, USA. | |
| People: | Janna Hastings, Werner Ceusters, Barry Smith, Kevin Mulligan |
| Institution: | University of Geneva, University at Buffalo |
| Homepage: | http://code.google.com/p/mental-functioning-ontology/ |
| Mobile RadLex | |
| A mobile browser of RadLex for the Android Phone. Free to download on the Android Market. :D | |
| People: | Mantas |
| Institution: | |
| Homepage: | http://mantascode.com/?p=453 |
| 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. | |
| People: | |
| Institution: | |
| 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 |
| nano-TAB | |
| The nano-TAB standard specifies the format for representing and sharing information about nanomaterials, small molecules and biological specimens along with their assay characterization data (including metadata, and summary data) using spreadsheet or TAB-delimited files. The nano-TAB specification provides descriptive information on ISA-TAB as applied to nanotechnology. | |
| People: | |
| Institution: | |
| Homepage: | https://wiki.nci.nih.gov/display/ICR/nano-TAB |
| 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: | NCBO |
| 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: | NCBO |
| Institution: | Stanford University |
| Homepage: | http://www.bioontology.org/resources-index |
| NeuMORE | |
| Develop an ontology in recovery domain. | |
| People: | |
| Institution: | University of South Alabama |
| Homepage: | http://cis.usouthal.edu/ |
| 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 |
| Institution: | |
| Homepage: | http://neuinfo.org |
| OntoCAT | |
| High level abstraction API (Java/REST/R) for interacting with ontology resources including local ontology files in standard OWL and OBO formats (via OWL API) and public ontology repositories: EBI Ontology Lookup Service (OLS) and NCBO BioPortal. | |
| People: | Tomasz Adamusiak, Helen Parkinson, Natalja Kurbatova, Misha Kapushesky, Morris Swertz |
| Institution: | EMBL-EBI, University of Groningen |
| Homepage: | http://www.ontocat.org |
| OntoCOG | |
| Ontology based web service for COG enrichment study by using Fisher's exact test. | |
| People: | Yu Lin, Yongqun He, Zuoshuang Xiang |
| Institution: | University of Michigan |
| Homepage: | http://ontocog.hegroup.org/ |
| Ontologi Hewan Invertebrata | |
| I am A Student Bachelor Of IT. | |
| People: | VASKO EDO GULTOM |
| Institution: | USU |
| Homepage: | http://www.vaskoedo.co.cc |
| Ontologi Hewan Invertebrata | |
| ok. i had create it for benefit in future also science too. so greatful to rdf/owl in semantic web. | |
| People: | VASKO EDO GULTOM |
| Institution: | universitas sumatera utara |
| Homepage: | http://www.vaskoedo.co.cc |
| Ontology of Data Mining (OntoDM) | |
| OntoDM is a general-purpose ontology for the domain of data mining. The ontology includes the information processing processes that occur in the domain of data mining, participants in the processes and their specifications. OntoDM is highly transferable and extendable due to its adherence to accepted standards, and compliance with existing ontology resources. The generality in scope allows wide number of applications of the ontology, such as semantic annotation of data mining scenarios, ontology based support for QSARs, etc. | |
| People: | Pance Panov, Saso Dzeroski, Larisa Soldatova |
| Institution: | Jozef Stefan Institute |
| Homepage: | http://kt.ijs.si/panovp/OntoDM/ |
| 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). | |
| People: | |
| Institution: | |
| Homepage: | http://paramecium.cgm.cnrs-gif.fr/ |
| Patient/Research Participant Permissions Ontology | |
| An ontology to capture patients' and research participants' research permissions, consents and routine care permissions. | |
| People: | |
| Institution: | MUSC |
| Homepage: | http://open.recomdata.com/rpms.php |
| Pediatric Terminology | |
| Terms associated with pediatrics, representing information related to child health and development from pre-birth through 21 years of age. | |
| People: | Ranjana Srivastava, Daniel Lyman, Ipsita Das |
| Institution: | National Institute of Child Health and Human Development |
| Homepage: | http://www.nichd.nih.gov/health/clinicalresearch/terminology/ |
| Phenoscape | |
| What are the developmental and genetic bases of evolutionary differences in morphology across species? Currently it is difficult to approach this question due to a lack of computational tools that allow researchers to integrate developmental genetic and comparative morphological/anatomical data. We are addressing this by developing a database of evolutionarily variable morphological characters for a large clade of fishes (the Ostariophysi) and connecting this database to the large collection of mutant phenotypes in the ZFIN database, the central database of the zebrafish model organism community. The evolutionary and mutant phenotypes are being described using common ontologies. The database with its web-interface, together with the extended ontologies and data curation tools, will allow researchers to ask novel questions about the genetic and developmental regulation of evolutionary morphological transitions. Tool and database development are being guided by use cases, or driving research questions, defined by the devo-evo community. These tools are being developed under an open-source, open-development model, and in such a way that they can be used for additional biological systems in the future. This project is a unique collaboration between evolutionary and model organism biologists including two national centers (NESCent and NCBO), the ZFIN model organism database, the Cypriniformes Tree of Life project, the DeepFin Research Coordination Network, and the morphological image databases used by the evolutionary biology community. | |
| People: | Paula Mabee, Monte Westerfield, Todd Vision, Hilmar Lapp, Wasila Dahdul, James Balhoff, Peter Midford |
| Institution: | National Evolutionary Synthesis Center, University of South Dakota, University of Oregon, University of North Carolina at Chapel Hill |
| Homepage: | http://www.phenoscape.org/ |
| Plant Ontology | |
| The Plant Ontology is a controlled vocabulary (ontology) that describes plant anatomical and morphological structures and growth and developmental stages for all plants. The goal of the PO is to establish a semantic framework for meaningful cross-species queries across gene expression and phenotype datasets from plant genomics and genetics experiments. | |
| People: | |
| Institution: | Oregon State University |
| Homepage: | http://www.plantontology.org/index.html |
| Portfolio Management Application (PMA) | |
| PMA is a system for tracking grants and producing reports - Users can access grant data through a query interface and a variety of pre-defined forms and reports | |
| People: | |
| Institution: | |
| Homepage: | http://bioportal.bioontology.org/ontologies/44666 |
| Protege | |
| Protégé is a free, open source ontology editor and knowledge-base framework | |
| People: | |
| Institution: | |
| 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/ |
| PubChem | |
| Chemical biology resource providing biological activities of small molecules and substances. | |
| People: | Good |
| Institution: | NCBI |
| Homepage: | http://pubchem.ncbi.nlm.nih.gov |
| RAD | |
| My RAD for PhD | |
| People: | farhanjk |
| Institution: | Dalhousie University |
| Homepage: | http://www.facebook.com/farhanjamalkhan |
| RadLex | |
| RadLex is a controlled terminology for radiology. | |
| People: | |
| Institution: | RSNA |
| Homepage: | http://radlex.org |
| RightField | |
| RightField is an open-source tool for adding ontology term selection to Excel spreadsheets. For each annotation field, RightField can specify a range of allowed terms from a chosen ontology (subclasses, individuals or combinations). The resulting spreadsheet presents these terms to the users as a simple drop-down list. This reduces the adoption barrier for using community ontologies as the annotation is made by the scientist that generated the data rather than a third party, and the annotation is collected at the time of data collection. | |
| People: | Stuart Owen, Katy Wolstencroft, Matthew Horridge, Carole Goble |
| Institution: | University of Manchester |
| Homepage: | http://rightfield.org.uk |
| SADI | |
| SADI is a framework to create Semantic Web services using OWL classes as service inputs and outputs | |
| People: | Christopher Baker, Melanie Courtot, Jose Cruz-Toledo, Michel Dumontier, Steve Etlinger, Nichealla Keath, Artjom Klein, Luke McCarthy, Silvane Paixao, Ben Vandervalk, Natalia Villanueva-Rosales, Mark Wilkinson |
| Institution: | Multi |
| Homepage: | http://sadiframework.org |
| SBGN | |
| Systems Biology Graphical Notation (SBGN), is a visual language developed by a community of biochemists, modelers and computer scientists to allow the represention of networks of biochemical interactions in a standard, unambiguous manner. | |
| People: | SBGN Editors |
| Institution: | COMBINE |
| Homepage: | http://www.sbgn.org |
| SBML | |
| The SBML (systems biology markup language) is a machine-readable, standard exchange format for computational models. It is developed collaboratively with the modelling community to meet their evolving needs. | |
| People: | SBML Editors |
| Institution: | COMBINE |
| Homepage: | http://sbml.org/ |
| SBO | |
| Systems Biology Ontology | |
| People: | |
| Institution: | |
| 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. | |
| People: | |
| Institution: | |
| Homepage: | http://www.sanger.ac.uk/Projects/S_pombe/ |
| SED-ML | |
| The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for encoding simulation experiments, following the requirements defined in the MIASE guidelines. SED-ML allows the definition of the model(s) to be used, the experimental task(s) to be run, and the result(s) to be produced. | |
| People: | SED-ML editors |
| Institution: | COMBINE |
| Homepage: | http://sed-ml.org/ |
| SEEK | |
| SEEK is the SysMO Assets Catalogue. It contains information about who holds what data, models, protocols and expertise, and where those assets are held. The SEEK is the main web-based access point to the system and provides an access control layer to enable researchers to restrict access to collaborators, colleagues or other individuals until they are ready to share with the whole consortium or the wider community. | |
| People: | Stuart Owen, Katy Wolstencroft, Olga Krebbs, Quyen Nguyen, Franco du Preeze, Jacky Snoep, Carole Goble |
| Institution: | University of Manchester, Heidelberg Institute of Technology |
| Homepage: | http://www.sysmo-db.org/seek |
| semanticscience integrated ontology | |
| The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for diverse knowledge representation across physical, processual and informational entities. | |
| People: | Michel Dumontier |
| Institution: | Carleton University |
| Homepage: | http://semanticscience.org |
| Semtools | |
| The Semantic Tools for Data Management (Semtools) project is tackling critical issues in the management and use of heterogeneous scientific data. Existing approaches to managing data and associated metadata fail to adequately capture the semantics of the scientific process, thereby impeding the utility of those data for important scientific issues. In Semtools, we will provide new capabilities for data access, discovery, integration, and visualization by developing software tools that utilize semantically annotated data and metadata. | |
| People: | Leinfelder, Jones, Schildhauer, O'Brien, Bowers |
| Institution: | NCEAS - UCSB |
| Homepage: | https://semtools.ecoinformatics.org/ |
| 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. | |
| People: | |
| Institution: | |
| 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. | |
| People: | |
| Institution: | |
| Homepage: | http://www.arabidopsis.org/ |
| The CardioVascular Research Grid (CVRG) | |
| The aim of the CardioVascular Research Grid (CVRG) project is to create an infrastructure for sharing cardiovascular data and data analysis tools. The CVRG will support national and international multi-institutional collaborations in cardiovascular science, and will build on and extend tools developed in the caBIG and BIRN projects. The CVRG project is supported by the National Heart Lung & Blood Institute. The project is based at the Institute for Computational Medicine at Johns Hopkins University, in collaboration with the Center for Comprehensive Informatics at Emory University. | |
| People: | Raimond Winslow, PhD |
| Institution: | Johns Hopkins University, Emory University, |
| Homepage: | http://www.cvrgrid.org |
| The Cognitive Atlas | |
| The Cognitive Atlas is a collaborative knowledge building project that aims to develop an ontology of mental processes and relate them to the mental tasks that are used to measure them. | |
| People: | Russell Poldrack |
| Institution: | University of Texas at Austin/UCLA |
| Homepage: | http://www.cognitiveatlas.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 Drug Interaction Knowledge Base | |
| The Drug Interaction Knowledge Base (DIKB) is a clinically-oriented, evidence-based, knowledge base designed to support pharmacoepidemiology and clinical decision support. The DIKB contains quantitative and qualitative assertions about drug mechanisms and pharmacokinetic drug-drug interactions for over 60 drugs; primarily psychotropics and HMG-CoA reductase inhibitors (statins). | |
| People: | Richard D Boyce |
| Institution: | University of Pittsburgh |
| Homepage: | http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/front-page.html |
| 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. | |
| People: | |
| Institution: | |
| Homepage: | http://www.human-phenotype-ontology.org/index.php/hpo_home.html |
| The Ontological Discovery Environment | |
| A web-based environment that discovers ontological structure from empirical data. | |
| People: | Elissa Chesler, Erich Baker, Michael Langston, Jeremy Jay |
| Institution: | The Jackson Laboratory |
| Homepage: | http://ontologicaldiscovery.org |
| Tools for Comparative Phenomics | |
| Here, we provide a number of tools for the integration, analysis and exploration of phenotypes across species. We currently provide these tools: PhenomeNet: PhenomeNet is a cross-species phenotype network in which nodes are compared based on phenotypic similarity. PhenomeBrowser: The PhenomeBrowser is a web-interface to explore the PhenomeNet. PhenomeBLAST: PhenomeBLAST is an ontology-based tool that provides a practical implementation of cross-species alignments of phenotypes using ontologies. We make both a command-line tool and a web-server available. | |
| People: | |
| Institution: | |
| Homepage: | http://code.google.com/p/phenomeblast/ |
| Toxicological ontology | |
| toxicological ontology | |
| People: | |
| Institution: | OpenTox FP7 EU project |
| Homepage: | www.opentox.org |
| Vector Surveillance and Management Ontology | |
| Produce candidate ontologies for vector surveillance and vector management with incorporation into a computer system | |
| People: | Saul Lozano-Fuentes, Lars Eisen |
| Institution: | Colorado State University |
| Homepage: | rams-aid.org |
| 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. | |
| People: | |
| Institution: | |
| Homepage: | http://www.vectorbase.org/index.php |
| Vertebrate Bridging Ontology (VBO) | |
| An ontology of homologies between anatomical structures across species within the subphylum Vertebrata | |
| People: | Ravensara Travillian |
| Institution: | European Bioinformatics Institute |
| Homepage: | https://sourceforge.net/projects/vbo/files/ |
| Virus Pathogen Resource (ViPR) | |
| Database and analysis resource for human pathogenic viruses, including sequence, surveillance and host response data. | |
| People: | Richard H. Scheuermann, et al. |
| Institution: | U.T. Southwestern Medical Center |
| Homepage: | www.viprbrc.org |
| VIVO | |
| VIVO is an open source semantic web application originally developed and implemented at Cornell. When installed and populated with researcher interests, activities, and accomplishments, it enables the discovery of research and scholarship across disciplines at one institution or across many. VIVO supports browsing and a search function which returns faceted results for rapid retrieval of desired information. Content in any local VIVO installation may be maintained manually, brought into VIVO in automated ways from local systems of record, such as HR, grants, course, and faculty activity databases, or from database providers such as publication aggregators and funding agencies. VIVO enables the discovery of researchers across institutions via linked open data (see http://linkeddata.org), as demonstrated by http://vivosearch.org and the VIVO searchlight browser plugin (http://vivosearchlight.org). Participants in the network will include institutions with local installations of VIVO or those using other research discovery and profiling applications that can provide RDF data expressed using the VIVO ontology, such as Harvard Profiles (http://profiles.catalyst.harvard.edu/). The information accessible through VIVO's search and browse capability will reside and be controlled locally, within institutional VIVOs or other semantic web-compliant applications. The VIVO ontology may be used independently of the VIVO application, and source code for the VIVO application, called Vitro (http://vitro.mannlib.cornell.edu), may be downloaded as an standalone ontology editor and semantic web application. | |
| People: | (see project homepage) |
| Institution: | (see project homepage) |
| Homepage: | http://vivoweb.org |
| 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 |
| web service | |
| It is a healthcare analysis system | |
| People: | |
| Institution: | Health |
| Homepage: | http://healthcare.org |
| wFleaBase | |
| wFleaBase is a repository of data and an electronic information service provided for the Daphnia Genomics Consortium (DGC) and the general scientific community. | |
| People: | |
| Institution: | |
| 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. | |
| People: | |
| Institution: | |
| Homepage: | http://www.wormbase.org/ |