Projects
Browse a selection of projects that use BioPortal resources
Project | Description | Contacts | Institutions | Ontologies |
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Harmonising phenomics information for a better interoperability in the RD field
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are disease (RD) research is a field of medicine increasingly reliant on information technology. Low-cost whole-genome sequencing has revolutionized the... | ordo.orphanet@inserm.fr | ERA-NET Cofund action N° 643578 | 3 |
A Treatment For Covid
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The following project leverages the CODO ontology, to provide treatment for a patient suffering from COVID. | alessandro.magliacane@hotmail.com | Università della Campania Luigi Vanvitelli | 2 |
A Visualization Tool for Refining Mappings between Biomedical Ontologies
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Ontology alignment, the task of identifying mappings between ontologies, is a key task for knowledge sharing between applications that use... | Watson W.K. Chua, Jung-jae Kim, Bui Duc Hieu | Nanyang Technological University | 2 |
Access of OntoKBCF via a CCR-based EHR prototype
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This is an exploration of introducing molecular genetic information into a simulated clinical setting- a Continuity of Care Record (CCR)... | Xia Jing, Stephen Kay, Nicholas Hardiker, Tom Marley, James Cimino | The University of Salford, NIH | 1 |
ACCORDYS
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In the context of prenatal diagnosis of fetal malformation, knowledge of "similar'' and resolved cases (i.e. previous cases with a... | Jean Charlet, Xavier Aim, Andreea Bodnari, Jean-Michel Daube, Louise Delger, Ferdinand Dhombres, Egle Eensoo, Marie Gonzals, Brigitte Grau, Cyril Grouin, Marie-Christine Jaulent, Thomas Lavergne, Anne-Laure Ligozat, Jrme Mainka, Aurlie Nvol, Yves | Inserm, Paris, France | 1 |
ACEnano
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ACEnano ("Analytical and Characterisation Excellence in nanomaterial risk assessment: a tiered approach") aims to develop a widely implementable and robust... | acenano@edelweissconnect.com | 1 | |
ACS-registry
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ACS registry definitions | Gert-Jan Vos MD, PhD | AZN | 1 |
AdaptEHR
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Adaptive EHR (AdaptEHR) is built upon a context-based framework, integrating data from different sources in the patient record and subsequently... | University of California, Los Angeles | 3 | |
Adaptive Automated Scientific Laboratory
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The goal of AdaLab (an Adaptive Automated Scientific Laboratory) framework for semi-automated and automated knowledge discovery by teams of human... | Larisa Soldatova | Brunel University | 2 |
ADHD Ontology
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Concepts and rules for the psychological assessment and management of ADHD. Heuristic knowledge for effective psycho-social interventions. | Joachim Diederich | Psychology Network Pty Ltd | 0 |
Adolescent Brain Cognitive Development Study
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The Data Analysis and Informatics Core (DAIC) of the ABCD project is using the RxNORM ontology in REDCap to collect a medication inventory of all its 10,000 participants. | Hauke Bartsch | UC San Diego | 1 |
Adverse Event Reporting Ontology
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The Adverse Event Reporting Ontology (AERO) is an ontology aimed at providing logical representation of adverse events guidelines, increasing quality and accuracy of reported events. | Melanie Courtot | 6 | |
agriGO
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The agriGO is an integrated web-based GO analysis toolkit for the agricultural community, using the advantages of our previous GO enrichment tool (EasyGO), to meet analysis demands from new technologies and research objectives. | China Agricultural University | 1 | |
AmiGO
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AmiGO is the official web-based set tools for searching and browsing the Gene Ontology database, which consists of a controlled... | Gene Ontology Consortium | 1 | |
An integrated approach to the challenge of sustainable food systems: adaptive and mitigatory strategies to address climate change and malnutrition (SYSTEMIC) WP5
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"The SYSTEMIC network (an integrated approach to the challenge of sustainable food systems: adaptive and mitigatory strategies to address climate... | dupamato@fcna.up.pt | 2 | |
An Ontology for Drug Discovery Investigations
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The goal of DDI project is to develop an ontology for the description of drug discovery investigations. DDI aims to... | Da Qi, Larisa Soldatova, Ross King, Andrew Hopkins, Richard Bickerton | Aberystwyth University | 5 |
Anatomic ontology for human lung maturaton
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Anatomic Ontology for Alveolar Development and Maturation in the Human Lung | Helen Pan | RTI International | 1 |
Animal QTL Database
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Animal QTLdb is a database for QTL and SNP/gene association data from chicken, pig, cattle, goat, sheep, horse, and rainbow trout. | bioinfo-team@animalgenome.org | Iowa State University | 4 |
Animal Trait Correlation Database
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CorrDB is a database for heritability and trait correlation data from cattle, chicken, goat, horse, pig, and sheep. | bioinfo-team@animalgenome.org | Iowa State University | 4 |
Annotation on First Authors' Review Articles
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A directory-based search system for review articles written by their first authors. This service is in Japanese, and users can... | DBCLS | 1 | |
AnoBase
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AnoBase is a database containing genomic/biological information on anopheline mosquitoes, with an emphasis on Anopheles gambiae, the world's most important... | 2 | ||
AQUAEXCEL
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AQUAEXCEL aims to integrate key aquaculture research infrastructures across Europe, in order to promote their coordinated use and development. | FP7, Capacities; Research Infrastructures | 0 | |
Armadyllo QData Commons
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Armadyllo is an patient-centric open community-curated registry of tools for RD and orphan disease research. We aim to explore mtDNA... | Sophia Boettcher | NA | 0 |
ARRS GoldMiner
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ARRS GoldMiner is a biomedical image search engine. | C. Kahn | American Roentgen Ray Society | 3 |
Ascidian Anatomy and Development Ontology
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The first ontologies describing the anatomy and the development of ascidians. | contact@bioself.fr | 10 | |
Assay Annotation
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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). | S. Schurer, U. Vempati, S. Canny, M. Southern | TSRI and UM | 1 |
AstraZeneca HTS annotation
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As a part of the AstraZeneca in kind contribution to the IMI OpenPhacts project, AstraZeneca HTS data is annotated according to the BAO ontology. | L. Zander Balderud, O. Engkvist, M. Bjreland, N. Blomberg | AstraZeneca R&D | 1 |
AWIC Tree
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Animal Use Alternatives Thesaurus Terminology | 0 | ||
BAOSearch
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BAOSearch is a web-based application for querying, browsing and downloading small molecule biological screening results, including high-throughput screening (HTS) data.BAOSearch... | Mader C, Datar N, Abeyruwan S, Koleti A, Venkatapuram S, Chung C, Puram D, Vempati U, Sakurai K, Przydzial M, Lemmon V, Visser U, Schurer S. | University of Miami | 1 |
Beta Cell Genomics database
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Beta cell genomics database provides searches and tools to explore detailed information about genes, transcripts, gene interactions, genomic regions, and beta cell related functional genomics studies. | Beta Cell Biology Consortium | University of Pennsylvania | 24 |
Bgee
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Bgee is a database to compare expression patterns between animals. We create homology relationships between anatomical ontologies, and store this... | Robinson-Rechavi lab | Universite de Lausanne | 10 |
Bio.Tools
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Bio.Tools is an open community-curated registry of bioinformatics tools and data resources. It is developed and maintained within the ELIXIR Europe project, in collaboration with the global bioinformatics community. | registry-core@elixir-dk.org | ELIXIR-EXCELERATE WP1, ELIXIR Denmark, ELIXIR France, ELIXIR Norway, ELIXIR Estonia, ELIXIR Czechia, Debian Med community, SEQwiki community, and other communities | 1 |
Bio2RDF
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The Bio2RDF project transforms silos of life science data into a globally distributed network of linked data for biological knowledge discovery. | 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 | Multi | 1 |
BioAssay Express
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BioAssay Express allows to explore the similarity of assays within and between organizations. browse and group assays based upon meaningful,... | Alex M. Clark, Nadia K. Litterman, Janice E. Kranz, Peter Gund, Kellan Gregory, Barry A. Bunin | Collaborative Drug Discovery | 3 |
BioAssay Ontology
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The BioAssay Ontology (BAO) is an NIH-funded project to develop standard terminologies and a formal, extensible, knowledge-based description of biological... | University of Miami | 6 | |
Biochemical Substructure Ontology
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Biochemical Substructure Ontology | 0 | ||
Bioconductor
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Bioconductor is an open source, open development software project to provide tools for the analysis and comprehension of high-throughput genomic data. It is based primarily on the R programming language. | 1 | ||
biocVI
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Document Triage: Identify relevant PubMed citations describing genetic mutations affecting protein-protein interactions, and Relation Extraction: Extract experimentally verified PPI affected by the presence of a genetic mutation. | 1 | ||
Biodiversity Ontology
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OntoBio is a biodiversity ontology developed by INPA and being jointly expanded by us at ICMC-USP. Its main objective is... | Flor Karina Mamani | University of São Paulo (USP), National Institute for Amazonian Research (INPA) | 0 |
BioImage Informatics Index
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BIII (BioImage Informatics Index, biii.eu) is an open community registry of tools, workflows, and training materials for bioimage analysis, developed... | wg4-edam_ontology@irbbarcelona.org.glip.com, matus.kalas@uib.no | NEUBIAS (Network of EUropean BioImage AnalystS) | 1 |
BioImaging Search Engine
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BISE (BioImaging Search Engine, biii.eu) is an open community registry of tools, workflows, and training materials for bioimage analysis, developed... | wg4-edam_ontology@irbbarcelona.org.glip.com, matus.kalas@uib.no | NEUBIAS (Network of EUropean BioImage AnalystS) | 1 |
Bioinformatics Web Service Ontology
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The Bioinformatics Web Services ontology (OBIws) is an ontology that extends the Ontology for Biomedical Investigations (OBI) to build an Ontology that supports consistent annotation of Bioinformatics Web services. | Jie Zheng, Alok Dhamanaskar | University of Pennsylvania, University of Georgia | 4 |
BioInterchange
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Interchange data using the Resource Description Framework (RDF) and let BioInterchange automagically create RDF triples from your TSV, XML, GFF3,... | 1 | ||
BioInterchange 2.0
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BioInterchange 2.0 normalizes your genomic datasets in one canonical data model. That means that data analysis algorithms can be implemented... | kim@codamono.com | CODAMONO, Toronto, Ontario, Canada | 1 |
BioLit
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A web database of open access articles with metadata | Lynn Fink | UCSD | 0 |
Biological Observation Matrix Linked Data
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A mapping from BIOM (HDF5) to Linked Data, with an example dataset and HDF52RDF converter. The long-term aim is to be able to publish big metagenomic data in a Semantic Web friendly way | mikel.egana@ehu.es | UPV/EHU | 1 |
Biomedical Image Ontology
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BIM is an open biomedical image feature ontology, it provides semantic vocabularies to represent the biomedical images and their features.... | ahmad chan | university of New Brunswick | 0 |
Biomedical Semantic QA
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Biomedical Semantic QA | mmfalrod@gmail.com | ULisboa | 3 |
BioPAX
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The goal of the BioPAX group is to develop a common exchange format for biological pathways data.The BioPAX project began... | 0 | ||
BioSimulations
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BioSimulations is a free platform for sharing and re-using biomodels, simulations, and visualizations. | info@biosimulations.org | Center for Reproducible Biomedical Modeling | 3 |
BioSimulators
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BioSimulators is a free collection of containerized biosimulation tools that provide consistent interfaces and a guide to choosing a simulator. | info@biosimulators.org | Center for Reproducible Biomedical Modeling | 3 |
Biositemaps
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The Biositemaps Working Group of the NIH Roadmap National Centers of Biomedical Computing (NCBC) (www.ncbcs.org) has developed technologies to address... | NIH/NCBC | 1 | |
BioXSD
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BioXSD defines exchange formats of basic bioinformatics types of data. It is a rich, but not too complicated XML-Schema-based format... | Matus Kalas, Edita Karosiene, Pal Puntervoll, Sveinung Gundersen, Jon Ison, Christophe Blanchet, Kristoffer Rapacki, Inge Jonassen ... | University of Bergen, Danish Technical University, CNRS, EBI ... | 1 |
Blood Ontology
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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. | HTLV Interdisciplinar Research Group | Federal University of Minas Gerais, Hemominas Foundation | 7 |
BNDMR
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The french national database to gather rare disease information for all french citizens and all rare diseases. | Remy Choquet, Paul Landais, Albane de Carrara, Meriem Maaroufi, Claude Messiaen, Yannick Fonjallaz, Minh Macabiau, Jean-Philippe Necker | French ministry of health | 1 |
Botryllus schlosseri anatomy and development ontology
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The first ontology describing the anatomy and the development of Botryllus schlosseri. Working group : Lucia Manni, Fabio Gasparini, Kohji Hotta, Katherine J. Ishizuka J, Lorenzo Ricci, Stefano Tiozzo, Ayelet Voskoboynik, Delphine Dauga | Delphine DAUGA, contact@bioself-communication.com | 0 | |
Brain Safe
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Research | Robert | GHU | 1 |
breast tissue cell lines
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Contains a comprehensive list of cell lines derived from breast tissue, both normal and pathological. The ontology in built... | Usha Mahadevan & Arathi Raghunath | Molecular Connection Pvt. Ltd. | 0 |
caB2B
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caB2B, or cancer Bench-to-Bedside, is a tool that enables querying for cancer related information hosted anywhere on caGrid. It... | National Cancer Institute | 1 | |
Can suicide theory guided natural language processing of clinical progress notes improve existing prediction models of Veteran suicide mortality?
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This project intends to extract from clinical progress notes factors that are central to the 3-step theory of suicide (3ST),... | esther.meerwijk@va.gov | VA Palo Alto Health Care System | 1 |
Cancer ImmunOnthology
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Onthology focusing on cancer-immune system interactions | 0 | ||
Care Coordination of Older Adults: Process, Outcomes, and Cost
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Develop care coordination ontology that describes the activities used by nurses to coordinate care among patients. Then using Natural Language... | Lori Popeyjoy (PopejoyL@missouri.edu), Mohammed Khalilia, Mihail Popescu, Colleen Galambos, Vanessa Lyons, Marilyn Rantz, Lanis Hicks, Frank Stetzer | University of Missouri | 1 |
CARRE
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Personalized patient empowerment and shared decision support for cardiorenal disease and comorbidities | The CARRE Project | 0 | |
CBO
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Create Cell Behavior Ontology | 1 | ||
CEDAR FAIR Funder Form
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This is a metadata form (for the FAIR Funder Implementation Study) that relies on EDAM's list of research topics. | John Graybeal | Stanford Center for Biomedical Informatics Research | 1 |
Cell cycle events
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Notable Cell Cycle events that can be tested with HTS-HCS modes | unc chapel hill | 3 | |
Cell line ontology
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Ontologies provide a common platform of controlled vocabulary for researchers who need to share information across a particular domain, inclusive... | Usha Mahadevan | Molecular Connections Pvt. Ltd. | 3 |
Cellosaurus
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The Cellosaurus is an online knowledge base on cell lines, which attempts to document all cell lines used in biomedical research. | Cellosaurus@sib.swiss | SIB - Swiss Institute of Bioinformatics | 5 |
Center for Enhanced Data Annotation and Retrieval
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CEDAR makes data submission smarter and faster, so biomedical researchers and analysts create and use better metadata. Through better interfaces,... | John Graybeal | 0 | |
CGAP GO Browser
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With the CGAP GO browser, you can browse through the GO vocabularies, and find human and mouse genes assigned to each term.GO data updated every few months. | Cancer Genome Anatomy Project | 1 | |
ChEMBL-RDF
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RDF version of the CC-BY-SA ChEMBL database developed at the EBI in the group of John Overington. | Maastricht University | 2 | |
Chemical Information Ontology
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The Chemical Information Ontology (CHEMINF) is an ontology to represent chemical structure and to richly describe chemical properties, whether intrinsic, observed or computed. | Leonid Chepelev, Michel Dumontier, Janna Hastings, Egon Willighagen | multi | 1 |
Children's Health Exposure Analysis Resource
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CHEAR is intended to: Expand the number of studies that include environmental exposure analysis, Implement the exposome concept in children’s... | 15 | ||
Chinese Diabetes Mellitus Ontology
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CDMO is an OWL 2 ontology designed to cover the diabetes mellitus knowledge represented in chinese language. It's top level was adapted from SNOMED-CT, and strive for mapping with other medical ontologies, such as SNOMED-CT, HPO, DOID, DRON. | Yun Liu, liuyun@njmu.edu.cn; Jie Hu, hujie@njmu.edu.cn | Department of Medical Informatics, Nanjing Medical University, Nanjing, Jiangsu, China | 0 |
Chinese Visible Human Database
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The images of CVH will be annotated by using of ontology.Then the CVH database will be built. | yangxl@pumc.edu.cn | Peking Union Medical College | 1 |
CHO Bioprocess Ontology
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Eventually meant to be used for text mining efforts to sort through literature | coherron@udel.edu | 0 | |
Classificação Estatística Internacional de Doenças, versão 10 (CID10)
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Mapping ICD 10 ontology to portuguese version Classificação Estatística Internacional de Doenças, versão 10 (CID10) | Paulo Bandiera-Paiva | Universidade Federal de São Paulo | 1 |
ClassifyDICOMSeries
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The ClassifyDICOMSeries project is using BioPortals to lookup DICOM related terms for biomedical imaging. | Hauke Bartsch | Haukeland University Hospital | 2 |
Clinical Genomicist Workstation
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The advent of genome-wide profiling technologies and their routine use in basic science and translational research is now promoting their... | 1 | ||
Clinical Narrative Temporal Relation Ontology
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CNTRO2.0 is an OWL ontology that can model temporal information found not only in structured databases, but also in natural-language based clinical reports. | Mayo Clinic | 0 | |
Clinical Study Ontology
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Ontology for general clinical studies. | The Rockefeller University | 0 | |
COBrA
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COBrA is a Java-based ontology editor for bio-ontologies that distinguishes itself from other editors by supporting the linking of concepts... | 1 | ||
Common Workflow Language
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The Common Workflow language is a multi-vendor working group consisting of various organizations and individuals that have an interest in... | 1 | ||
COMODI
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An ontology to characterise differences in versions of computational models in biology | 2 | ||
Comparative Toxicogenomics Database
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A public database that enhances understanding about the effects of environmental chemicals on human health. Integrated GO data and a... | 1 | ||
Computational Biology Institute of Montpellier
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Modeling, processing and analysis of large scale data in biology, health, agronomy and environment | Pierre Larmande (pierre.larmande@ird.fr) | University of Montpellier - LIRMM - CNRS | 7 |
Country Ontology
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The ontology for all country in the world | Narong B. | University of Utah | 2 |
COVID Rapid Acceleration of Diagnostics (RADX) Data Hub
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The NIH Rapid Acceleration of Diagnostics Data Hub (RADx® Data Hub) supports researchers in accessing curated and de-identified COVID-19 data, allowing them to find, aggregate, and perform data analyses in a cloud-enabled platform. | radx-datahub@nih.gov | Stanford Center for BioMedical Informatics, RENCI, Booz Allen Hamilton, NIH | 1 |
Creating big data for brain diseases research
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Automatic retrieving of relevant clinical information from EMRs from patients with MS | Pablo Villoslada | IDIBAPS, Barcelona | 1 |
CTSA Inventory Resource Web Presence
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The CTSA Inventory Resource Web Presence (CIRWP) is a federated, inter-institutional project to facilitate resource discovery. The CIRWP project contains... | 1 | ||
Darwin Core
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The Darwin Core is body of standards. It includes a glossary of terms (in other contexts these might be called... | TDWG Darwin Core Task Group | Biodiversity Information Standards (TDWG) | 1 |
Data collection in the general pediatric clinic for students of the 5th year of medicine at the Escola Paulista de Medicina/Unifesp
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At the end of the internship, the students of the 5th year make a presentation on morbidity with data from consultations carried out at the General Pediatrics Clinic. We are using the REDCap for data entry. | Meide Silva Ancao, Paulo Bandiera Paiva | Escola Paulista de Medicina - Unifesp | 1 |
Database of Experimental Biomaterials and their Biological Effect
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The Database of Experimental Biomaterials and their Biological Effect (DEBBIE) is a new open access tool which will enable a... | osnat.hakimi@upc.edu | Universitat Politecnica de Catalunya | 1 |
DataFlex
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Zur Lsung der komplexen Problemstellung von Datenmanagement wurde im Rahmen ihrer Grundlagenforschung das neuartige OpEN.SC-Datenmanagementprinzip (ODMP) fr den Bereich von... | Thomas Schrader | Charit Berlin | 1 |
DECIDE
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DECIDE, a five-year Horizon 2020 project, will develop data-driven decision support tools that offer robust and early signals of disease... | saba.noor@ugent.be | Ghent university | 0 |
DECIDE
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Decide | sabanoor@ugent.be | Gent University | 0 |
DECIDE Project EU2020
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DECIDE, a five-year Horizon 2020 project, will develop data-driven decision support tools that offer robust and early signals of disease... | sabanoor@ugent.be | Ghent University | 1 |
Decision Support System for the Elderly
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The project is the Decision Support System for the Elderly. It uses the Geriatrics ontology on top of BFO to define classes and properties. | Shubhnkar Upadhyay(shubhnkar123988@nitp.ac.in), Kumar Abhishek(kumar.abhishek@nitp.ac.in) | National Institute of Technology, Patna | 1 |
diabeted diagnosis ontology
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developing a diabetes diagnosis ontology for diagnosing complications | SLIIT | 0 | |
dictyBase
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An Online Informatics Resource for Dictyostelium. | 1 | ||
DisGeNET-RDF
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RDF version of the DisGeNET database, which is a database that integrates gene-disease associations from several public, expert, curated data... | Laura I. Furlong (lfurlong@imim.es), Núria Queralt-Rosinach (nqueralt@imim.es) | GRIB-IMIM-UPF | 11 |
Dispedia
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Dispedia is a framework for information brokering and knowledge management in the complex field of rare diseases. On the one... | Romy Elze, Michael Martin, Lars Eidam, Marcus Nitzschke | Institut fr Angewandte Informatik e.V. | 3 |
Drug Repositioning
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Identifying Drug Repositioning Targets in Domain Neglected Disease | Eduardo Barçante | FIOCRUZ | 1 |
Drug Target Ontology
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Drug Target Ontology (DTO) is being developed at the University of Miami in the research group of Stephan Schürer. DTO... | Stephan Schurer | University of Miami | 1 |
DSS
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Decision Support for Arthropod-borne Infectious Diseases. The Ontology portion of our project is still under construction. | David Penhall, Saul Lozano-Fuentes | Colorado State University | 2 |
Dynamic enhancement of drug product labels
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Demonstrate a novel approach to updating and expanding upon information present in drug product labels that is useful for determining... | Scientific Discourse Task Force | W3C Health Care and Life Sciences Interest Group | 1 |
DynGO
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DynGO is a client-server application that provides several advanced functionalities in addition to the standard browsing capability. DynGO allows users... | 1 | ||
eagle-i
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The eagle-i project is building a searchable network of research resources at research institutions nationwide. We are developing an application... | Melissa Haendel, Carlo Torniai | Consortium | 15 |
Educatioal Medical Materials Annotator
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A work in progress for discovering relations between distributed educational medical materials harvested from the web | r.qadan-al-fayez@warwick.ac.uk | Warwick university | 1 |
EFO
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The Experimental Factor Ontology (EFO) is an application focused ontology modelling the experimental factors in ArrayExpress. The ontology has... | James Malone, Helen Parkinson | EBI | 1 |
Electronic Medical Record Search Engine
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EMERSE (Electronic Medical Record Search Engine) was designed to help everyday users work with the free text documents (i.e., clinical... | EMERSE-team@umich.edu | University of Michigan North Campus | 0 |
Electronic Trial Master File
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The electronic trial master file (eTMF) content model ontology is designed to support clinical trial content management interoperability. ... | Jennifer Alpert Palchak | CareLex - a Non-profit for Content Archive Resource Exchange | 2 |
Electrophysiology Ontology
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The Electrophysiology (EP) Ontology is part of Project 2 of the Cardiovascular Research Grid (CVRG), an NHLBI funded effort to... | Dr. Raimond L. Winslow, Stephen J. Granite | The Johns Hopkins University | 6 |
eleMAP
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Organized by the National Human Genome Research Institute (NHGRI) with additional funding from the National Institute of General Medical Sciences,... | 0 | ||
EMBOSS
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The European Molecular Biology Open Software Suite (EMBOSS) is a well established, high quality package of open source software tools for molecular biology. | Peter Rice, Alan Bleasby, Jon Ison, Mahmut Uludag | EMBL-EBI | 1 |
eNanoMapper
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Project that develops an ontology to support the research within the European NanoSafety Cluster. | Egon Willighagen | eNanoMapper Consortium | 10 |
Epidemic Marketplace
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The Epidemic Marketplace is a data integration platform where epidemiological data and related resources are stored, managed and made available, fostering collaboration. | Fundacao da Faculdade de Ciencias da Universidade de Lisboa | 12 | |
Epidemiology Term Annotation
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This script will map commonly used epidemiology variables to SNOMED or LOINC concepts | 2 | ||
Epilepsiae
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EPILEPSIAE- Evolving Platform for Improving the Living Expectations for Patients Suffering from IctAl Events is developing the European Database on... | partners from 4 countries | EU FP7 | 1 |
eSysbio
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eSysbio is a project for developing an online workbench for collaborative computational biology research. It provides a secure Web-based workspace... | Kidane Tekle, Hakon Sagehaug, Matus Kalas, Siv Midtun Hollup, Michael Dondrup, Anne-Kristin Stavrum, Pawel Sztromwasser, Armin Topfer, Kjell Petersen, Inge Jonassen, Pal Puntervoll | University of Bergen | 2 |
eTOX
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eTOX is a temporary consortium established in 2010 to share and use toxicology data. It is a pre-competitive collaboration which... | Philippe MARC | Innovative Medicines Initiative IMI | 4 |
European Nutritional Phenotype Assessment and Data Sharing Initiative
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The main objective of ENPADASI project is to deliver an open access research infrastructure that will contain data from a... | Jildau Bouwman | a multidisciplinary consortium of scientists from 50 research centres in 9 countries across Europe. | 1 |
EutilsRDF
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Project to produce RDF output for some NCBI E-utilities | Chris Maloney | 0 | |
Evaluation of LOINC Document Ontology
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Use of LOINC Document Ontology to facilitate NLP projects, Health Information Exchange and secondary use of data | National Institute of Health Clinical Center | 1 | |
Evidence Ontology
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The Evidence Ontology (ECO) is a controlled vocabulary that describes types of scientific evidence within the realm of biological research... | Marcus Chibucos & Michelle Giglio | Institute for Genome Sciences | 3 |
Fantom5 Nanopublications
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Fantom5 cage cluster as an nanopublications | LUMC. Leiden, The Netherlands | 2 | |
Fern Ontology
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Fern Ontology (FO) is a controlled and structured vocabulary of fern specific anatomy and lifecycle. | DBCLS | 1 | |
FGED-MGED Ontology
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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. | 2 | ||
Fishmap
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FishMap is a unified and centralized resource for storage, retrieval, and display of genomic information of zebrafish. | 1 | ||
FIT_Thom
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Formal Inherence Theory of Predication from a Scholastic point of view. | Andre Stander | University of Pretoria | 0 |
FlyBase
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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. | The FlyBase Consortium | 8 | |
FlyGlycoDB
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Glyco-genes of Drosophila, their activities, mutants, protein class, etc. | Kiyoko F. Aoki-Kinoshita, Shoko Nishihara, Yuki Ushioda | Soka University | 0 |
Fundamental Biology of Sudden Cardiac Death and Its Application to Identify Patients at Risk
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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. | Gordon Tomaselli (PI) | Johns Hopkins Hospital, Washington Hospital Center, Virginia College of Medicine | 1 |
G PROTEIN-COUPLED RECEPTOR BIOASSAYS
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The G protein-coupled receptors (GPCRs) ontology (http://www.bioassayontology.org/bao_gpcr) describes pharmacology, biochemistry and physiology of these important and therapeutically promising class of... | Przydzial M, Bhhatarai B, Koleti A, Schurer S. | University of Miami | 4 |
Gemma
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Gemma is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data,... | Dr. Paul Pavlidis | University of British Columbia | 9 |
Gene Ontology Browsing Utility
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Gene Ontology Browsing Utility (GOBU). GOBU is a Java-based software program for integrating biological annotation catalogs under an extendable software... | 1 | ||
Gene Ontology Consortium
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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. | Gene Ontology Consortium | 1 | |
Gene Ontology For Functional Analysis
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Gene Ontology For Functional Analysis (GOFFA) is a tool developed for ArrayTrack that takes a list of genes and identifies... | 1 | ||
Gene Ontology Normal Usage Tracking System
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This Gene Ontology Normal Usage Tracking System (GONUTS) is a wiki where users of the Gene Ontology can contribute and... | 1 | ||
GeneInfoViz
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GeneInfoViz is a web based tool for batch retrieval of gene function information, visualization of GO structure and construction of... | 1 | ||
GeneLab
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Omics database for space biology research | NASA | 1 | |
GeneTools
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GeneTools is a collection of web-based tools that brings together information from a broad range of resources, and provides this... | Norwegian University of Science and Technology | 1 | |
GenNav
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GenNav searches GO terms and annotated gene products, and provides a graphical display of a term's position in the GO DAG. | 1 | ||
GFBio
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GFBio ontologies | 0 | ||
gilsnowmed
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Snomed filtering | Ryan Swenson | Gilead | 1 |
Glycoconjugate Ontology
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Glycoconjugate Ontology (GlycoCoO) is a standard ontology for glycoconjugate data (glycoprotein/glycolipid structures, publication information, biological source information, experimental data). | yamadaissaku@gmail.com | GlyCoCoO Project | 2 |
GlycoRDF
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GlycoRDF is a standard representation for storing Glycomcis data in RDF. | rene@ccrc.uga.edu or kkiyoko@soka.ac.jp | Glycoinformatics Consortium (GLIC) | 1 |
GOblet
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GOblet is a software package that performs annotation based on GO terms for anonymous cDNA or protein sequences. It uses... | 1 | ||
GoFish
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The GoFish program, available as a Java applet online or to download, allows the user to construct arbitrary Boolean queries... | University of Toronto; Ontario; Canada, Harvard Medical School; Massachusetts; USA | 1 | |
GOProfiler
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GOProfiler provides a summary of the GO annotations available in AgBase. The user provides a species (taxon id) and GOProfiler... | 1 | ||
GOSlimViewer
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GOSlimViewer is used to summarize the GO function associated with a data set using prepared GO Slim sets. The input is a tab separated list of gene product IDs and GO IDs. | 1 | ||
Gramene
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As an information resource, Gramene's purpose is to provide added value to data sets available within the public sector, which... | 6 | ||
GRANATUM
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The vision of the GRANATUM project is to bridge the information, knowledge and collaboration gap among biomedical researchers in Europe... | 1 | ||
Health Ontology Mapper
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HOMs open source components provide a key framework for mapping data, requesting data and delivering data to and from data... | Rob Wynden, Prakash Lakshminarayanan, Ketty Mobed | UCSF | 0 |
Hierarchical Event Descriptors
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HED is a hierarchical vocabulary for annotating what happens during an experiment. | kay.robbins@utsa.edu | University of Texas at San Antonio | 0 |
HINCare
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We aim to provide a software platform to suggest and match potential helpers from social network and recommend them to the elderly care organizations involved. | tobias.grubenman@live.com | The University of Hong Kong | 1 |
HiTS
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QB3’s discovery research informatics are centralized within SMDC via HiTS, an in-house web application (Grails 2.4.5) on top of a... | Julia Davies, Michelle Arkin | UCSF | 3 |
HIV
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This is an ontology about HIV | Martin Schiller | University of Nevada Las Vegas | 0 |
HPO - ORDO Ontological Module
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Orphanet provides phenotypic annotations of the rare diseases in the Orphanet nomenclature using the Human Phenotype Ontology (HPO). HOOM is... | Ana Rath, ordo.orphanet@inserm.fr | Inserm | 2 |
HuBMAP CCF EUI
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The CCF EUI represents data across multiple scales, supporting navigation by multiple coordinate systems, including spatial, physiologic, and organ-based browsing.... | katy@indiana.edu, bherr@indiana.edu | Indiana University | 3 |
Human Protein Ontology
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This project aims at developing a protein ontology of human proteins for different semantic queries. Proteins are categorized based on... | Arathi Raghunath, Bharat Bhat, Jignesh Bhate, Usha Mahadevan | Molecular Connections Pvt. Ltd | 0 |
HumanGeneCodonOntology
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The ontology contains the information of the frequency of usage and the relative frequency of usage of codons of human genes, to be used by the Project of HIV Ontology. | hanfeib@gmail.com | BMKI Lab | 0 |
Hypertrophic Cardiomyopathy consortium
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The Hypertrophic Cardiomyopathy Consortium is a network of investigators focused on the research, diagnosis, and treatment of HCM. The Consortium... | Theodore Abraham, MD | Johns Hopkins University | 1 |
iBeetle
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The iBeetle projects is a large scale RNAi screening project in the red flour beetle Tribolium castaneum. Using the RNA... | Gregor Bucher, Martin Klinger | Georg-August University Goettingen, Friedrich-Alexander University Erlangen-Nrnberg | 1 |
ICDmap
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map between snomed and icd10 | 2 | ||
iCyrus
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iCyrus is a Linked biomedical images API | ahmad chan , ahmadchan@gmail.com | University of New Brunswick Canada | 1 |
iCyrus: A Semantic BioMedical Images API
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A Semantic BioMedical Images API | Ahmad Chan and Chris J.O Baker | university of New Brunswick | 0 |
IDMP
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IDMP vocabularies | 0 | ||
Image & Data Quality Assessment
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An ontology for assessment of image and data quality | University of Applied Sciences Brandenburg | 0 | |
Immune Epitope Database
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The IEDB contains data related to antibody and T cell epitopes for humans, non-human primates, rodents, and other animal species. | IEDB Contacts | La Jolla Institute for Allergy & Immunology | 1 |
Immunology Database and Analysis Portal
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ImmPort, the Immunology Database and Analysis Portal, is a one stop shop to access reference and experiment data for immunologists.... | Richard H. Scheuermann, et al. | U.T. Southwestern Medical Center | 5 |
Improving the Automatic Classification of Histological Images using an Ontology of the Human Cardiovascular System
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A method that improves the previous automatic classification using the knowledge contained in the human histological ontology created. This solution increase hits rates and decrease misses of the automatic classification process. | claudia.mazo@correounivalle.edu.co | Universidad del Valle | 1 |
Influenza Ontology
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The Influenza Ontology is an application ontology covering the numerous aspects of influenza virus research and surveillance. The influenza ontology extends the Infectious Disease Ontology (IDO). | R. Burke Squires, Lynn Schriml, Joanne Luciano | NIAID BCBB, Univ of Maryland, MITRE | 8 |
Influenza Research Database
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The mission of the Influenza Research Database (IRD) is to provide a resource for the influenza virus research community that... | Richard H. Scheuermann, et al. | J. Craig Venter Institute | 8 |
Integrative Genomics
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Integration of high-dimensional genomic and phenomic data is challenged with scalability and semantic robustness for intuitive querying. To address these... | James Chen, Arka Pattanayak, Chaitanya Shivade | The Ohio State University | 5 |
Integrative Tools for Protozoan Parasite Research
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The Integrative Tools for Protozoan Parasite Research project is using OBI to develop forms to capture structured meta-data about studies... | Christian Stoeckert | University of Pennsylvania | 1 |
Interactive Argumentation Support for the Scientific Domain of Invasion Biology
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Developing a precise argument is not an easy task. In real-world argumentation scenarios, arguments presented in texts (e.g. scientific publications)... | Tina Heger and Alsayed Algergawy | FSU Jena, Freie Universität Berlin, Institute of Biology, Berlin, Germany, University of Bielefeld, | 1 |
Interestingness in Data
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Ontology-based Interestingness in COVID-19 Data. submitted to : 15th International Conference on Metadata and Semantics Research. (Under review) | Abhilash C B | IIIT Dharwad | 1 |
InterNano
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InterNano supports the information needs of the nanomanufacturing community by bringing together resources about the advances in applications, devices, metrology,... | Jessica Adamick, Jeff Morse, Bob Stevens, Mark Tuominen | University of Massachusetts Amherst | 0 |
InterNano Nanomanufacturing Library
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The InterNano Nanomanufacturing Library is a searchable and openly accessible database of nanomanufacturing research, government reports on nanomanufacturing, and federally-funded education and outreach efforts for nanomanufacturing. | Jessica Adamick, Jeff Morse, Bob Stevens, Mark Tuominen | University of Massachusetts Amherst | 0 |
International Fanconi Anemia Registry
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The International Fanconi Anemia Registry (IFAR) was started in 1982 at The Rockefeller University by Dr. Arleen Auerbach. The... | Erica Sanborn, Agata Smogorzewska, Arleen Auerbach, Francis Lach, Edward Barbour, Shamim Mollah, Sajin Balakrishnan, Ummey Johra | Rockefeller University | 5 |
ISA software suite
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An open source ISA software suite and an extensible hierarchical data structure implemented by a growing number of international public... | International collaborative effort | Multiple institutions; leads at University of Oxford, UK | 36 |
Kamonwan
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data management unit | chulabhorn royal academy | 0 | |
Kino
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Kino is an integrated suite of tools that enables scientists to annotate biological related web-based documents. It can annotate documents... | Amit Sheth, Ajith Ranabahu, Maryam Panahiazar | Ohio Center of Excellence in Knowledge-enabled Computing (Kno.e.sis) | 7 |
Knowledge Grid
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The Knowledge Grid is infrastructure to support community-based knowledge management and sharing within the context of the Learning Health System | Dr. Charles P. Friedman, Dr. Allen Flynn | University of Michigan | 3 |
LEcture Rapide en Urgence du Dossier Informatisé du patient
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Home page in french. | ASIP SANTÉ | 2 | |
Lexigram
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Lexigram builds simple, scalable medical entity and context extraction APIs for use with patient data, especially tailored to data scientists and developers | Paul Alexander (paul@lexigram.io) | 9 | |
LinkedDesign
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Linked Knowledge in Manufacturing, Engineering and Design for Next-Generation Production | 0 | ||
Linking Open Data for Rare Diseases
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An integrated ORPHA browser enrich with HPO data and OMIM disease descriptions. The application features: 1. A RDF... | remy.choquet@aphp.fr | AP-HP | 4 |
LogMap
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Logic-based and Scalable Ontology Matching. LogMap is a highly scalable ontology matching system with `built-in' reasoning and diagnosis capabilities. Currently,... | Ernesto Jimenez Ruiz and Bernardo Cuenca Grau | University of Oxford | 4 |
Maggot
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Sharing descriptive Metadata is the first essential step towards the so-called Open Scientific Data. With this in mind, Maggot was... | Daniel Jacob | INRAE | 9 |
Maize Genetics and Genomics Database
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MaizeGDB is a community-oriented, long-term, federally funded informatics service to researchers focused on the crop plant and model organism Zea mays. | carson.andorf@ars.usda.gov | USDA ARS | 4 |
Manatee
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Manatee is a web-based gene evaluation and genome annotation tool; Manatee can store and view annotation for prokaryotic and eukaryotic... | J. Craig Venter Institute, University of Maryland School of Medicine | 1 | |
Mapping of Norwegian national quality registries- Variabelbibliotek for medisinske kvalitetsregistre
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Norway has 52 national quality registers with over 5000 different variables, which each has their own value set. This is a mapping between similar variables and to other ontologies. | Linn Brandt - brandtlinn@gmail.com | Norwegian Institute of Public Health | 5 |
MASYMOS
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MASYMOS is a Neo4J instance containing SBML and CellML Models as well as simulation descriptions in SED-ML and frequently used bio-ontologies (GO, ChEBI, KiSAO, SBO). All data is represented as a Graph and can be queried using Cypher. | Dagmar Waltemath, Ron Henkel | University of Rostock | 4 |
MBGD SPARQL Search
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SPARQL interface to the RDF version of Microbial Genome Database for Comparative Analysis (MBGD) | Hirokazu Chiba, Hiroyo Nishide, Ikuo Uchiyama | National Institute for Basic Biology | 4 |
Mental Functioning Ontology
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The Mental Functioning Ontology is an ontology for mental functioning, including mental processes such as cognition and traits such as... | Janna Hastings, Werner Ceusters, Barry Smith, Kevin Mulligan | University of Geneva, University at Buffalo | 2 |
MeRy-B
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MeRy-B is a plant metabolomics platform allowing the storage and visualisation of Nuclear Magnetic Resonance (NMR) metabolic profiles from plants. This database is involved in the ISA commons project (isacommons.org). | Daniel Jacob, Catherine Deborde, Annick Moing | INRA & Univ. Bordeaux | 21 |
MGI GO Browser
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With the MGI GO Browser, you can search for a GO term and view all mouse genes annotated to the... | Mouse Genome Informatics, The Jackson Laboratory | 1 | |
miRNAO
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An application ontology for microRNAs. | 0 | ||
Mobile Pediatric Consultation and Monitoring System (mPCMS)
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“This research project was funded in 2014 by the National Science Foundation- The Scientific and Technological Research Council of Turkey... | Assoc.Prof.Dr.Duygu Celik Ertugrul | Eastern Mediterranean University | 1 |
Mobile RadLex
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A mobile browser of RadLex for the Android Phone. Free to download on the Android Market. :D | Mantas | 1 | |
Mouse Genome Informatics
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MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the... | 1 | ||
Multiscale Ontology for Skin Physiology
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The purpose of this project is to investigate the representation of physiological processes in the skin across levels of spatial scale. | Tariq Abdulla | Loughborough University | 0 |
NanbyoData
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NanbyoData is a portal to the latest information on rare and intractable diseases called Nanbyo. | fujiwara@dbcls.rois.ac.jp | Database Center for Life Science | 4 |
nano-TAB
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The nano-TAB standard specifies the format for representing and sharing information about nanomaterials, small molecules and biological specimens along with... | 1 | ||
NanoCommons
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NanoCommons will deliver a sustainable and openly accessible nanoinformatics framework (knowledgebase and integrated computational tools, supported by expert advice, data... | 1 | ||
NanoSolveIT
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NanoSolveIT aspires to introduce a ground-breaking in silico Integrated Approach to Testing and Assessment (IATA) for the environmental health and... | 1 | ||
NBTontology
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The NBTontology is used to describe Neurophysiological Biomarkers in the Neurophysiological Biomarker Toolbox (NBT) | 0 | ||
Network Ontology Analysis
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Network Ontology Analysis (NOA) is a freely available collection of Gene Ontology tools aiming to analyze functions of gene network... | Chinese Academy of Sciences | 1 | |
NeuMORE
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Develop an ontology in recovery domain. | University of South Alabama | 1 | |
Neural ElectroMagnetic Ontologies
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NEMO is developing ontologies for representation and integration of event-related brain potentials (ERPs). To support this work, we are developing... | NEMO core (Gwen Frishkoff, Robert Frank, Paea LePendu, Haishan Liu, Dejing Dou, Allen Malony, Jason Sydes, Nathan Dunn); NEMO ERP Consortium (Gwen Frishkoff, Tim Curran, Dennis Molfese, John Connolly, Kerry Kilborn, Chuck Perfetti) | University of Oregon & Georgia State University | 22 |
Neurocarta
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Neurocarta is a knowledgebase that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of... | Dr. Paul Pavlidis | University of British Columbia | 3 |
Neuroimaging Data Model
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The Neuroimaging Data Model (NIDM) is a collection of specification documents that define extensions the the W3C PROV standard for... | Nolan Nichols | INCF | 6 |
NeuroLOG
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Neurolog was a 4 years scientific project (2007-2010) funded by the french ANR (National Agency for Research) under contract number... | Johan Montagnat | collaborative research project | 3 |
Neuronal Morphologies and Species Metadata Classification System
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This is species taxonomy for the data curated in NeuroMorpho.Org. The existing ontologies are re-used as needed as the new... | spolavar@gmu.edu | George Mason University | 4 |
Neuroscience Information Framework
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The Neuroscience Information Framework (NIF; http://nif.nih.gov) is a dynamic inventory of Web-based neuroscience resources, data, and tools accessible via any... | Maryann Martone, Jeffrey Grethe, Amarnath Gupta, Gordon Shepherd, Giorgio Ascoli, Paul Sternberg, David Van Essen | 9 | |
NGS Ontology
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The NGSOnto ontology aims at capturing the workflow of all the processes involved , in order to ensure the reproducibility of the entire process, through the use of a controled and specific vocabulary. | Instituo de Medicina Molecular | 5 | |
NLP for the prediction of chemotherapy response
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NLP for the prediction of chemotherapy response | adrien.coulet@inria.fr | Inserm, Inria, AP-HP | 4 |
Nomenclature for Anatomic Pathology
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Unifying Nomenclature for Anatomic Pathology in Italy | Arrigo Bondi | SIAPEC-IAP | 5 |
Nursing domain expert processes
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This is a group of four ontologies which have been acquired from nursing domain experts. The experts describe their specific practice area. | Phil Shields | Victoria University | 4 |
OBO-Edit
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OBO-Edit is an open source, platform-independent application written in Java for viewing and editing any OBO format ontologies. OBO-Edit is... | Gene Ontology Consortium | 1 | |
oebDatasets
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a dataset ontology | 0 | ||
OMA SPARQL endpoint
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The SPARQL endpoint of the Orthologous Matrix (OMA) database. The RDF serialisation of the OMA Hierarchical Orthologous Groups is based on the ORTH ontology v2 specification. | SIB | 1 | |
One health surRveillance Initiative on harmOnization of data collection and interpretatioN
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The ORION project aims at establishing and strengthening inter-institutional collaboration and transdisciplinary knowledge transfer in the area of surveillance data... | German Federal Institute for Risk Assessment (BfR); Swedish National veterinary Institute (SVA); and partners | 1 | |
Onto-Compare
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Microarrays are at the center of a revolution in biotechnology, allowing researchers to screen tens of thousands of genes simultaneously.... | Wayne State University | 1 | |
Onto-Design
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Many Laboratories chose to design and print their own microarrays. At present, the choice of the genes to include on... | Wayne State University | 1 | |
Onto-Express
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The typical result of a microarray experiment is a list of tens or hundreds of genes found to be differentially... | Wayne State University | 1 | |
OntoCAT
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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. | Tomasz Adamusiak, Helen Parkinson, Natalja Kurbatova, Misha Kapushesky, Morris Swertz | EMBL-EBI, University of Groningen | 0 |
OntoCOG
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Ontology based web service for COG enrichment study by using Fisher's exact test. | Yu Lin, Yongqun He, Zuoshuang Xiang | University of Michigan | 2 |
Ontology Evolution Explorer
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The Ontology Evolution Explorer (OnEx) is a web-based system for exploring ontology changes. It provides access to several versions of... | University of Leipzig | 1 | |
Ontology for Floss
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Ontologies for learning patterns in Floss | mukala@di.unipi.it | University of Pisa | 0 |
Ontology for the obstetric and neonatal domain
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This ontology has been created to provide a consensus representation of salient electronic health record (EHR) data and in order to serve interoperability of the associated data and information systems which deal with obstetric and neonatal care. | fernandafarinelli@eci.ufmg.br | Federal University of Minas Gerais | 7 |
Ontology of Data Mining
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OntoDM is a general-purpose ontology for the domain of data mining. The ontology includes the information processing processes that occur... | Pance Panov, Saso Dzeroski, Larisa Soldatova | Jozef Stefan Institute | 7 |
Ontology Project Progress and Future Plans
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Ontology will face more technical challenges and need more academic support. Therefore, Ontology will start a research institute plan, recruiting... | Lettita | Research Institute and Academic Plans | 0 |
Ontology-based knowledge base model-OntoKBCF
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This is a knowledge base model including both molecular genetic information and health information of cystic fibrosis. Another main component... | Xia Jing, Stephen Kay, Nicholas Hardiker, Tom Marley | The University of Salford | 1 |
OntoMaton
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OntoMaton is a google spreadsheet application allowing for ontology search and tagging directly within google spreadsheets. More information can be found here: https://github.com/ISA-tools/OntoMaton | ISA team | Oxford University | 0 |
OntoVisT
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OntoVisT is a general purpose ontological visualization tool. Ontologies have emerged as a fast growing research topic in the area... | Jawaharlal Nehru University | 1 | |
Open Access Journals Integrated service System Project (GoOA)
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As a precursor aiming to explore the method on discovery, selection, evaluation, conservation, and recycling construction of OA resources, GoOA... | openresources@mail.las.ac.cn | National Science Library,Chinese Academy of Sciences | 5 |
Open European Nephrology Science Center
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Das Open European Nephrology Science Center (OpEN.SC) ist ein europisches Leistungszentrum fr Forschungsinformationen in der Nephrologie und Transplantationsmedizin. In Zusammenarbeit... | Thomas Schrader | University of Applied Sciences Brandenburg & Charit Berlin | 1 |
Open PHACTS
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Open PHACTS (Open Pharmacological Concepts Triple Store) is a knowledge management project of the Innovative Medicines Initiative (IMI), a unique... | 8 | ||
OrphaOnto
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Orphanet is the reference information portal on rare diseases and orphan drugs for healthcare professionals and for general audience. Orphanet... | Ferdinand Dhombres, Pierre-Yves Vandenbussche, Ana Rath, Marc Hanauer, Annie Olry, Bruno Urbero, Rmy Choquet, and Jean Charlet | Inserm, Paris, France | 0 |
Panacea
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Panacea aims to build an intelligent recommendation system to effectively propose drug therapies that will support and facilitate health professionals,... | 5 | Ergobyte Informatics S.A. | 2 |
ParameciumDB
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ParameciumDB is a new model organism database associated with the genome sequencing project. Built with core components of the Generic... | 1 | ||
Parkinson's Disease Ontology
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Here, we introduce the Parkinson’s disease ontology (PDO) as a comprehensive semantic framework covering the whole breadth of the Parkinson’s... | Dr. Erfan Younesi | Fraunhofer SCAI | 0 |
Pathway Portal
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The Pathway Portal is a multi-tier approach offering dynamic graphic representation of pathways along with associated annotations, integration with other... | Victoria Petri | Medical College of Wisconsin | 1 |
Patient/Research Participant Permissions Ontology
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An ontology to capture patients' and research participants' research permissions, consents and routine care permissions. | MUSC | 1 | |
Pediatric Terminology
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Terms associated with pediatrics, representing information related to child health and development from pre-birth through 21 years of age. | Ranjana Srivastava, Daniel Lyman | National Institute of Child Health and Human Development | 1 |
Performed Music Ontology
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Part of the Linked Data for Production grant, a BIBFRAME extension ontology for performed music. | Stanford | 1 | |
Personalised Guidance Services for Optimising lifestyle in teenagers through awareness, motivation and engagement
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PEGASO project, under the EU 7th Framework Programme (Grant No: 610727), aims at promoting a sustainable change towards healthy lifestyles... | 0 | ||
PhenoMiner
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PhenoMiner integrates rat phenotype measurement data | Rajni Nigam, Mary Shimoyama, Melinda Dwinell | RGD | 4 |
Phenoscape
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What are the developmental and genetic bases of evolutionary differences in morphology across species? Currently it is difficult to approach... | Paula Mabee, Monte Westerfield, Todd Vision, Hilmar Lapp, Wasila Dahdul, James Balhoff, Peter Midford | National Evolutionary Synthesis Center, University of South Dakota, University of Oregon, University of North Carolina at Chapel Hill | 9 |
PID PhenomeR
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PID phenomer is a web-based integrated platform for collection, mapping, storage and visualization of observed phenotypic terms for primary immunodeficiency diseases (PIDs). | 0 | ||
Ping
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Try to develop COVID-19 risk detection system for older people in residential aged care using ontology and machine learning technology | ping@uow.edu.au | University of Wollongong | 3 |
Plant Ontology
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The Plant Ontology is a controlled vocabulary (ontology) that describes plant anatomical and morphological structures and growth and developmental stages... | Oregon State University | 18 | |
PMF_Foodmatrix
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Foodmatrix Ontology of "Open food safety model repository" | 2 | ||
PractiKPharma
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PractiKPharma (Practice-based evidences for actioning Knowledge in Pharmacogenomics) aims at validating, or moderating, PGx state-of-the-art (SOTA) knowledge on the basis... | Adrien Coulet (last name at loria dot fr) and collaborators | LORIA, HEGP, CHU-St Etienne, LIRMM | 14 |
Preeclampsia Ontology
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The PEO incorporates a wide range of key concepts and terms of PE from clinical and biomedical research in structuring the knowledge base that is specific to PE. | Tohoku University | 1 | |
Prospective Risk Analysis in Medical Environments
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It is the ontology embedding PRIME (Prospective Risk Analysis in Medical Environments) in related issues of patient safety research and... | thomas.schrader@computer.org | Technische Hochschule Brandenburg | 1 |
Proteasix
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Proteasix Ontology (PxO) is a new application ontology that supports the Proteasix tool (http://www.proteasix.org/). Proteasix is an open-source peptide-centric tool... | Robert Stevens [robert.stevens@manchester.ac.uk] | University of Manchester (UK) | 0 |
Protein ANnotation Diagram ORiented Analysis
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With PANDORA, you can search for any non-uniform sets of proteins and detect subsets of proteins that share unique biological... | Hebrew University of Jerusalem | 1 | |
Protein Ontology Project
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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. | Amandeep S. Sidhu | BIOMAP Project Lab | 0 |
Prov
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The outcome of the W3C Prov group | Helena F. Deus | DERI | 0 |
PubCaseFinder
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PubCaseFinder is a phenotype-driven differential-diagnosis system. | fujiwara@dbcls.rois.ac.jp | Database Center for Life Science | 4 |
PubChem
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Chemical biology resource providing biological activities of small molecules and substances. | NCBI | 7 | |
Pull the Covid-19 replicative catalytic core apart
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The PullCovAppart project is the result of an original collaboration between biologists (Isabelle Imbert, India L’Hote, Marion Peltret, Emeline Grellet)... | isabelle.imbert@univ-amu.fr | LITIS/LIS/AFMB | 1 |
QuickGO
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QuickGO is a fast web-based browser for Gene Ontology terms and annotations, which is provided by the UniProtKB-GOA group at... | European Bioinformatics Institute | 1 | |
R.T. National Drug File Research
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Sustantial assistance documentation solutions. Strategic composed software interconnecting social services internship. | 6013078734 | PMGROUP | 1 |
Radiation Oncology Ontology
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The Radiation Oncology Ontology project aims to develop an ontology convering the field of radiation oncology. | 0 | ||
Radiology Gamuts Ontology
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Imaging findings, interventions, and associated disorders for radiological diagnosis. | C. Kahn | University of Pennsylvania | 6 |
Radiology Quiz
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A randomized multiple choice quiz which tests the players knowledge of different relationships from the RadLex Ontology. | Mantas J | MantasCode | 1 |
RadoNorm: Towards effective radiation protection based on improved scientific evidence and social considerations – focus on Radon and NORM
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The key aim of RadoNorm is to provide answers to open questions related to radon and naturally occurring radioactive materials... | PNS12@cam.ac.uk | Coordinator: Bundesamt fuer Strahlenschutz | 1 |
RCD
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to see RCD ontology | 1 | ||
RDNav
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A tool to help physicians to code with orphanet classifications. | Remy Choquet, Yannick Fonjallaz, Albane de Carrara | APHP, Paris, France | 0 |
Reaction Ontology
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Enzyme Reaction Ontology (ERNO) | 0 | ||
Reference Sequence Annotation
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Provide ontologies to describe sequence annotations, reference sequences, and how to link annotations across references. | Zuotian Tatum, Andrew Gibson, Jeroen F.J. Laros, Marco Roos, Mark Thompson | Leiden University Medical Center | 0 |
Register of CDZ
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Used in collection of medical and hospital information | UZIS | 0 | |
Registry of Vascular Anomalies
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The Registry of Vasculair Anomalies is a FAIR registry for patients with vascular anomalies. | 1 | ||
Rehabilita, Disruptive Technologies for the Rehabilitation of the Future
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The project wants to enhance rehabilitation transforming it to a more personalized, ubiquitous and evidence-based rehabilitation. | Laia Subirats (laia.subirats@gmail.com), Luigi Ceccaroni and Mireia Calvo | Eurecat - Technology Centre of Catalonia | 6 |
Reporting Identifications in MS-based Proteomics Experiments
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specification of cross-linking reagents in mass spectrometry cross-linking results | psidev-pi-dev@lists.sourceforge.net | HUPO-PSI | 2 |
Reporting MS-based Proteomics and Metabolomics Results
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derivatization reagents in GC-MS / LC_MS are documented by XLMOD CV terms | HUPO-PSI | 2 | |
Resource of Asian Primary Immunodeficiency Diseases
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Resource of Asian primary immunodeficiency diseases (RAPID) is a web-based integrated compendium of molecular alterations in primary immunodeficiency disease genes and other pertinent information. | RCAI Immunogenomics group, Immunoinformatics group and IOB group | The Institute of Physical and Chemical Research (RIKEN) Yokohama, Japan & Institute of Bioinformatics (IOB), Bangalore, India | 1 |
Retrospective Analytics System
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The Retrospective Analytics System (RAS) is based on semantic and linguistic information technologies. It empowers German clinics and offices to... | Dr.-Ing. Benedikt Kämpgen | Empolis Information Management GmbH | 5 |
RightField
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RightField is an open-source tool for adding ontology term selection to Excel spreadsheets. For each annotation field, RightField can specify... | Stuart Owen, Katy Wolstencroft, Matthew Horridge, Carole Goble | University of Manchester | 1 |
RiskGONE
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RiskGONE (Science-based Risk Governance of Nano-Technology) is an EU H2020 project aiming at providing solid procedures for consistent risk governance of engineered nanomaterials. | 1 | ||
runBioSimulations
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runBioSimulations is a free tool for executing a wide range of simulations. | info@biosimulations.org | Center for Reproducible Biomedical Modeling | 3 |
SADI
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SADI is a framework to create Semantic Web services using OWL classes as service inputs and outputs | 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 | Multi | 1 |
Safety and Toxicity of Excipients for Paediatrics (STEP) Database
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The Safety and Toxicity of Excipients for Paediatrics (STEP) Database is a user-designed resource that compiles the safety and... | International collaborative effort, admin@eupfi.org | European Paediatric Formulation Initiative (EuPFI) | 3 |
SBGN
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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. | SBGN Editors | COMBINE | 1 |
SBML
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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. | SBML Editors | COMBINE | 1 |
SBO
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Systems Biology Ontology | 0 | ||
Schizosaccharomyces pombe
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This database contains all S. pombe (fission yeast) known and predicted protein coding genes, pseudogenes, transposons, tRNAs, rRNAs, snRNAs, snoRNAs... | 1 | ||
Screening Nonrandomized Studies for Inclusion in Systematic Reviews of Evidence
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The EDDA Study Designs and Publications terminology supports information extraction and summarization of documents screened by systematic reviewers. The focus is on reviews where nonrandomized and observational studies are eligible for inclusion. | Tanja Bekhuis, PhD, MS, MLIS | University of Pittsburgh School of Medicine | 1 |
SED-ML
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The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for encoding simulation experiments, following the requirements defined in... | SED-ML editors | COMBINE | 1 |
SEEK
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A suite of tools for the management and sharing of Systems Biology resources, such as data, models, SOPs and publications | Stuart Owen, Katy Wolstencroft, Olga Krebbs, Quyen Nguyen, Franco du Preeze, Jacky Snoep, Wolfgang Mueller, Carole Goble | University of Machester / HITS, Heidelberg | 1 |
Semantic Enrichment of Biomedical Images
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http://ceur-ws.org/Vol-1320/paper_8.pdf | ahmadchan@gmail.com | University of New Brunswick | 1 |
Semantic Indexing of French Biomedical Data Resources
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The SIFR project proposes to investigate the scientific and technical challenges in building ontology-based services to leverage biomedical ontologies and terminologies in indexing, mining and retrieval of French biomedical data. | Clement Jonquet (jonquet@lirmm.fr) | University of Montpellier - LIRMM | 10 |
Semantic Mining of Activity, Social, and Health data
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The SMASH (Semantic Mining of Activity, Social, and Health data) project develops an ontology to describe concepts and relationships of... | Dejing Dou | University of Oregon | 1 |
semanticscience integrated ontology
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The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for diverse knowledge representation across physical, processual and informational entities. | Michel Dumontier | Carleton University | 0 |
SemGen
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SemGen is a software tool for automating the modular composition and decomposition of biosimulation models. It uses BioPortal web services to provide model annotators access to reference ontology terms. | Maxwell Neal, Daniel Cook, John Gennari | University of Washington | 9 |
Semtools
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The Semantic Tools for Data Management (Semtools) project is tackling critical issues in the management and use of heterogeneous scientific... | Leinfelder, Jones, Schildhauer, O'Brien, Bowers | NCEAS - UCSB | 1 |
SEQwiki
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The SEQanswers wiki (SEQwiki) is a wiki database that provides an extensive catalogue of tools, technologies and tutorials for high-throughput sequencing (HTS), including information about HTS service providers. | Jing-Woei Li1, Keith Robison, Marcel Martin, Andreas Sjdin, Bjrn Usadel, Matthew Young, Eric C. Olivares, and Dan M. Bolser | NA | 1 |
SGD
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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. | 1 | ||
Signaling ADEs from social media
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Detect signals of ADEs from social media | 2 | ||
Simulation Delivery and Documentation Deviations
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The taxonomy was developed to facilitate quality assurance in the delivery of high-fidelity simulation (HFS) scenarios (mannequin-based medical simulations). It... | mcivorwr@anes.upmc.edu | University of Pittsburgh Medical Center and the Winter Institute for Simulation Education and Research (WISER) | 0 |
SKELETOME
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The aim of the SKELETOME project is to develop a community-driven, ontology-based knowledge curation platform for the skeletal dysplasia domain. | Tudor Groza | School of ITEE, The University of Queensland | 6 |
Socrates MD
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... | Jeremy Race | Socrates MD, Inc. | 8 |
Software Tool for Rapid Annotation of Proteins
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The Software Tool for Rapid Annotation of Proteins saves you time by automatically annotating a protein list with information that... | Boston University School of Medicine | 1 | |
Solving the Unsolved Rare Diseases
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"Solve-RD - solving the unsolved rare diseases" is a research project funded by the European Commission for five years (2018-2022).... | 3 | ||
Sorcero Health Equity Analytics
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Working with AWS Health Equity Program to build cross-ontology knowledge structures for Health Equity | Richard Graves | Sorcero | 3 |
STATistics Ontology
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STATO is a general-purpose STATistics Ontology. Its aim is to provide coverage for processes such as statistical tests, their conditions... | Alejandra Gonzalez-Beltran, Philippe Rocca-Serra | University of Oxford | 0 |
Stroke Ontology
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An ontology for stroke | 0 | ||
Stroke ontology
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STO covers the knowledge domain of stroke based on expert views and translational continuum of stroke research. | 0 | ||
Suicide Ontology
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An ontology for suicidology. based on human based text mining | alexander garcia | AGC | 1 |
SYSNPs
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SYSNPs allows the user to compile information about all the SNPs in any human gene or genome region of interest... | Institut de Biologia Evolutiva | 1 | |
Systematic process based on ontological modeling applied to risk stratification in mental health for qualitative and quantitative analysis
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Anxiety affects millions of people around the world. The systematization of different sets of data extracted from instruments that evaluate... | Evaldo de Oliveira da Silva e Marcello Peixto Bax | Universidade Federal de Minas Gerais e Centro Universitário UniAcademia | 1 |
TAIR
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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. | 1 | ||
TAIR Keyword Browser
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TAIR Keyword Browser searches and browses for Gene Ontology, TAIR Anatomy, and TAIR Developmental stage terms, and allows you to... | The Arabidopsis Information Resource | 1 | |
Tao Hoang
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Detect signals of adverse drug events from social media | hoatn002@mymail.unisa.edu.au | University of South Australia | 1 |
TerminologyLinkingService
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Terminology Linking Service | 3 | ||
text mining psychiatric clinical notes
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n/a | 2 | ||
The CardioVascular Research Grid
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The aim of the CardioVascular Research Grid (CVRG) project is to create an infrastructure for sharing cardiovascular data and data... | Raimond Winslow, PhD | Johns Hopkins University, Emory University, | 1 |
The Cigarette Smoke Exposure Ontology
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The CSEO has potential to become a widely used standard within the academic and industrial community. Mainly because of the... | 0 | ||
The Cognitive Atlas
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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. | Russell Poldrack | Stanford | 4 |
The Comparative Data Analysis Ontology
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The objective of this project is to develop an ontology for the description of information relevant to experiments in evolutionary... | Arlin Stoltzfus, Julie Thompson, Francisco Prosdocimi, Brandon Chisham, Enrico Pontelli | NMSU, NIST, University of Strasbourg | 0 |
The Drug Interaction Knowledge Base
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The Drug Interaction Knowledge Base (DIKB) is a clinically-oriented, evidence-based, knowledge base designed to support pharmacoepidemiology and clinical decision support.... | Richard D Boyce | University of Pittsburgh | 1 |
The Exploration Of Data Dynamics Of COVID-19
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The contents of researches include: data streams or circles, knowledge Integration, the certainty or uncertainty etc. in COVID-19 fields. | Hanfeib@gmail.com | BMKI Lab, | 1 |
The Human BioMolecular Atlas Program(HuBMAP)
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HuBMAP, a project by the NIH, aims to map healthy cells in the human body through advanced molecular and cellular... | NIH | 1 | |
The Human Phenotype Ontology
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The human phenotype ontology (HPO) intends to offer a tool that will allow large-scale computational analysis of the human phenome.... | 1 | ||
The MACiE Database, a database of enzyme reaction mechanisms
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MACiE, which stands for Mechanism, Annotation and Classification in Enzymes is a database of enzyme reaction mechanisms, the amino acids and small molecules involved and the roles these components play in the enzyme's mechanism. | Gemma Holliday | EMBL-EBI, UCSF | 2 |
The Monarch Initiative
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Enabling navigation across a rich landscape of phenotypes, diseases, models, and genes for translational research. | Melissa Haendel, Chris Mungall, Maryann Martone, Harry Hochhesier, Damian Smedley, Peter Robinson | 10 | |
The Ontological Discovery Environment
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A web-based environment that discovers ontological structure from empirical data. | Elissa Chesler, Erich Baker, Michael Langston, Jeremy Jay | The Jackson Laboratory | 5 |
The Ontology And The Preliminary Researches On The Data-dynamics Of COVID-19
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A pilot project for the generalized dynamics and the pattern medicines on the COVID-19 | hanfeib@gmail.com | BMKI Lab | 1 |
The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology
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DIDEO is an ontology representing potential drug-drug interactions and their evidence based on a realism-oriented approach. | Mathias Brochhausen, Richard D. Boyce | University of Arkansas for Medical Sciences, University of Pittsburgh, University of Florida, University of Arizona | 0 |
The Structure Function Linkage Database
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The Structure-Function Linkage Database (SFLD) is a hierarchical classification of enzymes that relates specific sequence-structure features to specific chemical capabilities.... | Patricia Babbitt & Gemma Holliday | UCSF | 2 |
Time Event Ontology
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The Time Event Ontology (TEO) is an OWL ontology designed for representing the temporal relations among events and time stamps. | Cui Tao | UTHeath | 0 |
Tk-GO
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Tk-GO is a GUI wrapping the basic functions of the GO AppHandle library from BDGP. GO terms are presented in... | Illuminae | 1 | |
Tools for Comparative Phenomics
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Here, we provide a number of tools for the integration, analysis and exploration of phenotypes across species. We currently provide... | 2 | ||
Toxicological ontology
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toxicological ontology | OpenTox FP7 EU project | 0 | |
UF REDCap
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REDCap is a mature, secure web application for building and managing online surveys and databases. Using REDCap's stream-lined process for... | Taryn Stoffs, Corinne Holman | University of Florida | 0 |
Upper-level Cancer Ontology
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Providing an upper-level ontology for cancer. | Andre Stander | University of Pretoria | 0 |
UW Health HIMC
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Health Information Management Center within UW Health. | Nathan S. Wilson, Keith M Wanta | University of Wisconsin | 0 |
Vector Surveillance and Management Ontology
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Produce candidate ontologies for vector surveillance and vector management with incorporation into a computer system | Saul Lozano-Fuentes, Lars Eisen | Colorado State University | 0 |
VectorBase
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VectorBase is one of four Bioinformatics Resource Centers funded by NIAID to provide web-based resources to scientific community conducting basic and applied research on arthropod vectors of human pathogens. | Daniel Lawson | University of Notre Dame, EMBL-EBI, Imperial College | 6 |
Vertebrate Bridging Ontology
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An ontology of homologies between anatomical structures across species within the subphylum Vertebrata | Ravensara Travillian | European Bioinformatics Institute | 0 |
VIrtual Fly Brain
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A data integration hub for Drosophila neuroanatomy. Functionality includes:- Query brain regions for innervating neurons classes and 3D neuron images.- Query brain regions and neurons for expressed trangenes and phenotypes. | 1 | ||
Virtual Imaging Platform project
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The Virtual Imaging Platform project (VIP) is a french project supported by ANR (ANR-09-COSI-03 grant) aiming at sharing medical image... | Tristan Glatard | collaborative research project | 8 |
Virus Pathogen Resource
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Database and analysis resource for human pathogenic viruses, including sequence, surveillance and host response data. | Richard H. Scheuermann, et al. | J. Craig Venter Institute | 7 |
ViSion™ Multimedia Structured Reporting
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ViSion™ is a multimedia structured reporting solution for image-based medical disciplines that captures key images and voice descriptions, tags images with metadata using an ontology, and generates a multimedia report of image findings. | David J. Vining, MD | VisionSR, Inc. | 0 |
Visualization Tool for Refining Mappings between Biomedical Ontologies
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The task of identifying mappings between ontologies, is a key task for knowledge sharing between applications that use different ontologies.... | Samuel | Biomedical Ontologies Departement | 0 |
VIVO
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VIVO is an open source semantic web application originally developed and implemented at Cornell. When installed and populated with researcher... | (see project homepage) | (see project homepage) | 1 |
Wandora
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Wandora is a general purpose information extraction, management and publishing application based on Topic Maps and Java. Wandora has graphical... | Grip Studios Interactive | 1 | |
wFleaBase
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wFleaBase is a repository of data and an electronic information service provided for the Daphnia Genomics Consortium (DGC) and the general scientific community. | 1 | ||
WikiPathways
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Pathway repository | https://groups.google.com/forum/#!forum/wikipathways-discuss | Maastricht University + Gladstone Institute | 2 |
WormBase
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WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible... | 1 | ||
WPHH (WSMIO)
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The Web security Data Model specification describing a structured model and format to enable annotations to be shared and reused... | 2 | ||
XEML Interactive Designer
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XEML Lab has been created to assist plant biologists in designing and documenting simple or sophisticated experiments in a machine... | Max Planck Institute of Molecular Plant Physiology | 5 | |
Xenbase
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The Xenopus model organism database. | xenbase@ucalgary.ca | University of Calgary/ Cincinnati Children's Hospital Medical Center | 3 |
ZFIN
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The zebrafish model organism database. | zfinadmn@zfin.org | University of Oregon | 3 |