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HPO / Human Phenotype Ontology
Provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. HPO is developed using the medical literature, Orphanet, DECIPHER, and OMIM. HPO contains approximately 11,000 terms and over 115,000 annotations to hereditary diseases. HPO also provides a large set of HPO annotations to approximately 4000 common diseases. HPO can be used for clinical diagnostics in human genetics (Phenomizer), bioinformatics research on the relationships between human phenotypic abnormalities and cellular and biochemical networks, for mapping between human and model organism phenotypes, and for providing a standardized vocabulary for clinical databases, among many other things.
Uberon
Represents body parts, organs and tissues in a variety of animal species, with a focus on vertebrates. Uberon is an integrated cross-species ontology covering anatomical structures in animals. It has been constructed to integrate seamlessly with other ontologies, such as the OBO Cell Ontology, the Gene Ontology, Trait and Phenotype ontologies, as well as other anatomical ontologies. It includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.
DGA / Disease and Gene Annotations
A collaborative effort aiming to provide a comprehensive and integrative annotation of the human genes in disease network context by integrating computable controlled vocabulary of the Disease Ontology, NCBI Gene Reference Into Function (GeneRIF) and molecular interaction network (MIN). DGA integrates these resources together using semantic mappings to build an integrative set of disease-to-gene and gene-to-gene relationships with excellent coverage based on current knowledge.
MGED Ontology / Microarray Gene Expression Database Ontology
Provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MGED Ontology does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation.
DOSE
Provides semantic similarity computations among Disease Ontology (DO) terms and genes which allows biologists to explore the similarities of diseases and of gene functions in disease perspective. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented to support discovering disease associations of high-throughput biological data. Comparison among gene clusters is also supported. DOSE provides several DO-specific visualization functions to produce highly customizable, publication-quality figures of similarity and enrichment analyses that are not available elsewhere. With these visualization tools, the results obtained by DOSE are more interpretable.
EXPO
Defines over 200 concepts for creating semantic markup about scientific experiments, using the Web Ontology Language OWL. The ontology EXPO aims to formalise generic knowledge about scientific experimental design, methodology, and results representation. Such a common ontology is both feasible and desirable because all the sciences follow the same experimental principles. The formal description of experiments for efficient analysis, annotation, and sharing of results is a fundamental objective of science.
Ontodog
A web system that generates an ontology view with customized annotation. Authors define ‘ontology community view’ as a whole or a portion of the ontology that maintains textual and logical term definitions and provides additional user-specified annotations including user-preferred labels. Ontodog allows users to easily generate community views with minimal ontology knowledge and no programming skills or installation required. Currently >100 ontologies including all OBO Foundry ontologies are available to generate the views based on user needs.
RICORDO / Researching Interoperability using Core Reference Datasets and Ontologies for the virtual physiological human
Gathers functions for real-time reasoning over very large ontologies to express complex ontology concepts. RICORDO is designed for biomedical resources, and related ontologies, relevant to a number of communities including the physiology modeling, the pharmacology modeling, and the medical education community. It permits to find and annotate resources with both terms from reference ontologies and composites of those terms.
ontologyX
A suite of R packages, consisting of ontologyIndex, ontologyPlot and ontologySimilarity, which together formes a consistent interoperable set of tools that is readily extensible with additional ontological functionality. The key advantage of OntologyIndex is that it can read in arbitraryontologies, integrates naturally with R, and provides a solid base forextension. ontologyPlot enables uniquely simple and aesthetically pleasing visualization of ontological terms and ontological annotation with a wide variety of graphical options. ontologySimilarity facilitates fast and flexible semantic similarity functionality for ontological objects including assessment of statistical significance and is suitable for application to high-throughput datasets.
ICEPO / Ion Channel ElectroPhysiology Ontology
An ontological framework to annotate the electrophysiological class of ion channels. ICEPO is the translation of quantitative assertions extracted through text mining to a formal representation that may help in constructing ontology for ion channel events. The ICEPO ontology is an outcome based on three approaches: i) anecdotal and domain knowledge of the authors, ii) relations extracted from the biomedical text both abstracts and full-text articles, and iii) integration of vocabularies from other existing ontologies. ICEPO focuses on the description of the biophysical properties of voltage-gated ion channels. Ion channels are classified according to either the type of ions for which they are permeable, their three-dimensional structure or the type of stimulus that triggers their activation gating.
MELLO
Provides standardized and integrated definitions, descriptions, and their relations for the relevant lifelog concept domain. MELLO is an ontology for representing health-related lifelog data for covering general medical aspects with rich contents that support definitions, synonyms, and semantic relationships. Concepts were identified through a systematic enrichment and manual review process that founds lifelog terms sparsely scattered over standard sources including Systematized Nomenclature of Medicine-Clinical Terms (SNOMED-CT) and Unified Medical Language System(UMLS).
NCI Thesaurus
It is designed to meet the growing need for accurate, comprehensive, and shared terminology, covering topics including: cancers, findings, drugs, therapies, anatomy, genes, pathways, cellular and subcellular processes, proteins, and experimental organisms. The NCI Thesaurus provides a partial model of how these things relate to each other, responding to actual user needs and implemented in a deductive logic framework that can help maintain the integrity and extend the informational power of what is provided.
FMA / Foundational Model of Anatomy
Provides an ontology for the symbolic representation of the phenotypic structure of the human body. FMA is initially based on the anatomical content of Unified Medical Language System (UMLS). This ontology is organized through four interrelated components: anatomy taxonomy (At), anatomical structural abstraction (ASA), anatomical transformation abstraction (ATA) and metaknowledge (Mk). It includes approximately 75 000 and up to 120 000 terms for over 2.1 million relationship instances.
BAO / BioAssay Ontology
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.
BDO / Bone Dysplasia Ontology
Represents the most comprehensive structured knowledge source for the skeletal dysplasias domain. It provides the means for integrating and annotating clinical and research data, not only at the generic domain knowledge level, but also at the level of individual patient case studies. It enables links between individual cases and publicly available genotype and phenotype resources based on a community-driven curation process that ensures a shared conceptualisation of the domain knowledge and its continuous incremental evolution.
BoWiki
Provides a platform for research communities to collaboratively integrate information and annotate data. BOWiki includes a wiki system that uses a core ontology together with an automated reasoner to maintain a consistent knowledge base. It is specifically targeted at small- to medium-sized communities. It allows users to characterize the entities specified by wikipages as instances of ontological categories, to define new relations within the wiki, to interrelate wikipages and to query for wikipages satisfying selected criteria.
OntoNorm
An open source machine learning framework to automatically map concepts in an ontology to text. OntoNorm maps the protein-protein interaction (PPI) relevant articles with corresponding interaction method nodes in a standardized PSI-MI (Proteomics Standards Initiative-Molecular Interactions) ontology. This framework obtains competitive performance compared with other similar programs when applied on tasks to identify articles that contain PPI data and to identify methods from an ontology that were used to study these interactions.
ENVO / Environment Ontology
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.
DTO / Drug Target Ontology
Provides a standardized ontology for drug targets that aims to facilitate the integration of diverse drug discovery information from various resources. DTO is organized around the class hierarchies of the four Illuminating the Druggable Genome (IDG) protein families, G protein–coupled receptors (GPCRs), kinases, ion channels, and nuclear hormone receptors. This terminology is composed of protein classes related to tissue and disease according to different levels of confidence.
OntoFox / Ontology Fetches ontology terms and axioms
Retrieves ontology terms and axioms. OntoFox supports ontology reuse by following and extending the existing method MIREOT (Minimum Information to Reference an External Ontology Term). It provides options for users to collect terms from external ontologies, making them available for reuse by import into client OWL ontologies. OntoFox uses a RDF triple store and SPARQL for information storage and retrieval, resulting in a system that scales better than in-memory modularization techniques. It dynamically extracts external ontology terms and their chosen annotations from SPARQL endpoint(s). OntoFox's output can be directly imported into a developer's ontology.
CIO / Confidence Information Ontology
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.
IAO / Information Artifact Ontology
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.
MCO / Microbial Conditions Ontology
Aims to standardize the annotation of experimental conditions in microbial data repositories. MCO provides growth conditions terms together with their definitions, synonyms, references, and higher-level relations. The terms offered by the ontology can unambiguously define and tag each attribute of a particular experimental condition in order to systematize the annotation. It was created with simple ontological terms to describe elementary components.
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NeXO / Network-extracted Ontology
Provides structured knowledge about the cellular components, processes, and functions encoded by genes. NeXO is a data-driven gene ontology (GO) inferred directly from omics data. It uses a principled computational approach which integrates evidence from hundreds of thousands of individual gene and protein interactions to construct a complete hierarchy of cellular components and processes. This data-derived ontology aligns with known biological machinery in the GO Database and also uncovers many new structures.
BioPortal
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.
Ontobee
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.
SBO / Systems Biology Ontology
Provides a set of controlled, relational vocabularies of terms commonly used in Systems Biology. Systems Biology Ontology is a database that consists of seven orthogonal vocabularies defining: (i) reaction participants roles, (ii) quantitative parameters, (iii) classification of mathematical expressions describing the system, (iv) modelling framework used, (v) the nature of the entity, (vi) the type of interaction, and (vii) a branch to define the different types of metadata that may be present within a model.
Planteome database
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.
PCOSKB
A manually curated knowledgebase on polycystic ovary syndrome (PCOS). PCOS-related information available through scientific literature is cross-linked with molecular, biochemical and clinical databases. Information on associated genes, SNPs, diseases, gene ontologies and pathways along with supporting reference literature is collated and integrated in PCOSKB. PCOSKB will be useful for scientists and clinicians. The database currently holds information on 241 genes associated with PCOS.
ProbOnto
Provides information about probability distributions. ProbOnto is a knowledge base built from a simple ontological model. The database contains uni- and multivariate distributions and alternative parameterizations, probability density or mass functions and available cumulative distribution, hazard and survival functions, relationships and re-parameterization formulas, related quantities, parameter and support/range definitions and distribution type and latex and R code for mathematical functions. It provides a means for the encoding and annotation of statistical models, thus facilitating their exchange between software tools.
Aber-OWL
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.
Pre_GI / Predicted Genomic Islands database
Stores prokaryotic genomic islands. Pre_GI is a database that contains more than 20 000 islands found in bacterial and archaeal chromosomes and plasmids. The concept of ‘island’ relevant to this database is defined as a horizontally acquired fragment of DNA in a bacterial/archaeal genome, including those which may have been acquired by ancestral organisms and transferred vertically to its progeny. Users can browse current islands or search and compare their newly predicted islands against Pre_GI records.
Cellosaurus
New
Provides information about cell lines. Cellosaurus is composed of immortalized cell lines, naturally immortal cell lines, finite life cell lines when those are distributed and used widely, vertebrate cell line with an emphasis on human, mouse and rat cell lines, and invertebrate cell lines. It contains more than 100 000 cell lines, representing over 550 species. The database furnishes data such as synonyms, cross-references and references to publications, databases or ontologies.
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