Provides an ontology for data recording of biomedical procedures. EXACT is designed to be directly integrated with other bio-medical ontologies. It is based on a framework that translate biomedical protocols from natural text to a machine amenable semantically-defined format. It proceeds by detecting and describing experimental actions and their descriptors in protocol texts and gives them unique IDs.
Provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. This ontology supports the consistent annotation of biomedical investigations, regardless of the particular field of study. The ontology represents the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions.
Standardizes, organizes and semantically defines biological assays and screening results. BAO provides a foundation for standardizing assay descriptions and endpoints. The ontology serves as a knowledge model by describing screening experiments and results semantically using description logic. It opens new functionality for querying and analyzing high-throughput screening (HTS) datasets. Users can query PubChem data using BAO terminology and collect sets of results for further analysis.
A biomedical ontology that logically defines and classifies various adverse events occurring after medical interventions. OAE has successfully been applied in several adverse event studies. The OAE ontological framework provides a platform for systematic representation and analysis of adverse events and of the factors (e.g., vaccinee age) important for determining their clinical outcomes.
Gathers more than 100000 terms dealing with biomedical concepts. NCIT provides a controlled vocabulary encompassing the fields of clinical care, public information and topics related to research. This resource displays definitions and linked information related to over 10000 cancers and 8000 single agents and combination therapies. This tool is used by several administrations such as the U.S. Food and Drug Administration (FDA).
Provides classes and relations to describe and relate objects, processes and their attributes with specific extensions in the biomedical domain. SIO’s data concern spatial and temporal qualitative reasoning including location, containment, overlap, parthood and topology; participation and agency, linguistic and symbolic representation, as well as comparative and other information-oriented relations.
A resource for the semantically controlled description of environmental entities. ENVO bridges multiple domains including biomedicine, natural and anthropogenic ecology, omics and socioeconomic development. It provides a vocabulary to characterise sequenced environmental samples, together with an ontological structure to facilitate search, advanced querying, and inference in support of the aims of the genomics standards consortium. ENVO includes some 2159 classes primarily representing biomes, geographic features, and environmental materials, along with 18,791 axioms.
Provides definitions for the foundational entities of biomedicine as a basic vocabulary to unambiguously describe facts in this domain. BIOTOP presents an ontologically sound layer for linking and integrating various specific domain ontologies. It can be used as top-level model for creating new ontologies for more specific domains or as aid for aligning or improving existing ones.
Describes the nature of reference citations in scientific research articles and other scholarly works, both to other such publications and also to Web information resources, and for publishing these descriptions on the Semantic Web. CiTO has been designed with the requirements of biomedical researchers in mind. It enables the citations within a citing work to be recorded and published in machine-readable form as RDF (resource description framework).
Provides an ontology to simplify formally distinctions and commonalities between various sorts of information entities. IAO is an ontology of information entities that covers the same domain but are compiled independently from each other. The main elements of this tool are the representational unit (RU) and the representational artifact (RA). These core elements are designed to give the possibility to bridge between terminologies, concept systems and ontologies.
An application ontology driven by the annotation and query needs of samples in omics datasets. EFO provides an integration framework for ontologies and combines parts of several biological ontologies such as UBERON anatomy, ChEBI chemical compounds, and Cell Ontology. The relationship between ontology descriptions of rare and common diseases and their phenotypes can offer insights into shared biological mechanisms and potential drug targets. The scope of EFO is to support the annotation, analysis and visualization of several domain specific ontologies.
Consists of a terminology designed for RNA sequencing. ORNASEQ is based on the ontology for biomedical investigations (OBI). It supplies a list of about 160 terms, some of the terms are from several existing ontologies, and more than 20 terms that have been added to OBI. This ontology is useful for the annotation of RNA-based next-generation sequencing and DNA-based next-generation sequencing data.
Consists of an ontology that represents pharmacogenomics (PGx) knowledge units and their components. PGxO has two main objectives: reconciling and tracing the PGx knowledge units. This ontology is designed to structure knowledge extracted from various sources such as reference databases (i.e. PharmGKB), literature, clinical guidelines or electronic health records (EHR)+biobank studies.
Consists of an application ontology for microRNAs. miRNAO can be applied to any database, or related tool, that contains or uses information on microRNAs as well as the regulation of gene expression that these mediate. The ontology follows the rules set by the OBO Foundry, in particular, the one of orthogonality. It aims to facilitate interoperability and reusability across different knowledge areas.
Provides a collaborative experiment to establish a set of principles for ontology development. OBO aims to create a suite of orthogonal interoperable reference ontologies in the biomedical domain. In addition to a listing of OBO ontologies, this site also provides a statement of the OBO Foundry principles, discussion fora, technical infrastructure, and other services to facilitate ontology development.
A spin-off of the PRIDE project, which required a centralized query interface for ontology and controlled vocabulary lookup. The OLS provides a web service interface to query multiple ontologies from a single location with a unified output format. The OLS can integrate any ontology available in the Open Biomedical Ontology (OBO) format.
An open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protege frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content by providing features to add notes to ontology terms, mappings between terms and ontology reviews based on criteria such as usability, domain coverage, quality of content, and documentation and support. Thus, BioPortal not only provides investigators, clinicians, and developers 'one-stop shopping' to programmatically access biomedical ontologies, but also provides support to integrate data from a variety of biomedical resources.
A linked data server designed for ontologies. Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis. Ontobee dynamically dereferences and presents individual ontology term URIs to (i) HTML web pages for user-friendly web browsing and navigation, and to (ii) RDF source code for Semantic Web applications. Ontobee is the default linked data server for most OBO Foundry library ontologies. Ontobee has also been used for many non-OBO ontologies.
Gathers a suite of interconnected reference ontologies. Planteome database’s terminologies are employed for the annotation of plant gene expression data, traits, phenotypes, genomes and germplasm, across 95 plant taxa. It contains species-specific Crop Ontologies (CO) and phenotype scoring standards. This database can assist in identification of traits of interest, and locates data, including germplasm, quantitative trait locus (QTL) and genes associated with a given trait.
Offers a collection of original, peer-reviewed chapters on the biology of Caenorhabditis elegans and related nematodes. Wormbook provides links between its chapters and its other relevant topics. The in-text citations are linked to their abstracts in PubMed and full-text references, if available. It represents a generic publishing infrastructure and facilitates the dissemination of knowledge in the field thank to its capability of adaptation to other research communities.
Allows structured event extraction from the molecular to the organ system level. MLEE permits the application of the extraction methods at large scale to automatically annotate the entire available literature. It was used to create corpus annotation to recognize spans of text that expressing statements relevant to their interests.
Aims to bring together the efforts of a number of EMBL-EBI resources that provide access to their data using Semantic Web technologies. The EBI RDF platform provides a unified way to query across resources using the W3C SPARQL query language.
Enables retrieval of information about the predicted functions of lncRNAs. LncRNA Ontology is a database that permits users to visualize, analyze, and download long non-coding RNA (lncRNA) putative functions. This resource makes the functions, chromatin, and expression patterns viewable to users across cell types. It supports searches by individual lncRNA or by a specific gene ontology (GO) term.
A collection of 793 PubMed abstracts fully annotated at the mention and concept level to serve as a research resource for the biomedical natural language processing community. Each PubMed abstract was manually annotated by two annotators with disease mentions and their corresponding concepts in Medical Subject Headings (MeSH®) or Online Mendelian Inheritance in Man (OMIM®). Manual curation was performed using PubTator, which allowed the use of pre-annotations as a pre-step to manual annotations.
Serves to search data repositories from several academic disciplines. Re3data provides users repositories for the permanent storage and aims to encourage sharing, giving a better visibility of research data. The research data concerns information objects which was generated by scholar project. The re3data browser permits to base the research on different details: subject, content type or country. This database allows also scientists to drop off their data.
A tool to facilitate obtaining disease surveillance information. BRD contains disease surveillance resources, epidemiological models (previously known as the 'BARD'), and a disease ontology. BRD is based on a comprehensive framework that can be used to characterize an infectious disease model in an operational context. The framework was developed through a consensus among a panel of subject matter experts.
Provides reasoning services for bio-ontologies. Aber-OWL consists of an ontology repository, a set of web services and web interfaces that enable ontology-based semantic access to biological data and literature. Aber-OWL provides a framework for automatically accessing information that is annotated with ontologies or contains terms used to label classes in ontologies. When using Aber-OWL, access to ontologies and data annotated with them is not merely based on class names or identifiers but rather on the knowledge the ontologies contain and the inferences that can be drawn from it.
Provides several types of information on agronomy domain. AgroPortal is an online repository that allows users to perform different tasks such as: ontology hosting, search, versioning, visualization, comment, and recommendation. Moreover, this database enables semantic annotations and interoperation with the semantic web and assists researchers to store and exploit ontology alignments.
Provides an ontology to capture confidence information about annotation assertions in a more systematic manner. The CIO is an ontology created to address the main points identified to provide clear and meaningful information about confidence in annotations. The CIO structure is made of two branches: (i) the confidence information statement branch, that contains the terms to be used by annotators and (ii) the confidence information element branch, that contains terms representing the intrinsic properties of the CI statements. CI statements are simply pre-composed using CI elements.
Provides thesaurus management system which can be employed to build and manage information systems. MC Lexicon provides a comprehensive list of application programming interfaces (APIs) for interaction with external applications for identifying concepts, parent-child relationships, broader/narrower concepts, candidate terms etc.
Develops next generation semantics-aware data management systems that are based on a synthesis of ontological reasoning and database management principles. DBonto incorporate techniques from many other areas of computer science, particularly those that give a complementary view of "Big Data" management, such as algorithms and machine learning, stream processing, and information retrieval. At the same time, this database aims to make important contributions to the career development of the next generation of research leaders.
Offers a platform dedicated to handle biological data, including COBRA models. COBRAdb furnishes a python software that integrates data into relational databases. The application allows users to figure relationships between three main features: computational models, high throughput experimental data and cellular components. It can be used for storing genome annotations as well as genome-scale metabolic models.
Allows automated recognition of disease mentions, and studied the effect of various techniques in improving the normalization results based on the dictionary lookup approach. DiseaseExtract includes two broad stages: (i) extracting disease mentions from free text–a task referred to as disease named entity recognition (DNER) and (ii) normalizing the recognized mentions to standard controlled vocabularies such as MeSH–a task referred to as disease name normalization (DNORM).
1 - 2 of 2