Tag: ontology and terminology

The Gene Ontology resource provides a computational representation of our current scientific knowledge about the functions of genes (or, more properly, the protein and non-coding RNA molecules produced by genes) from many different organisms, from hu ...

The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as Atrial septal defect. The HPO is currently being develope ...

Database that aims to advance understanding about how environmental exposures affect human health. It provides manually curated information about chemical–gene/protein interactions, chemical–disease and gene–disease relationships. These data are inte ...

DisGeNET is a discovery platform containing one of the largest collections available of genes and variants involved in human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models, and the scientific liter ...

The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. Releases: https://githu ...

HGNC is responsible for approving unique symbols and names for human loci, including protein coding genes, ncRNA genes and pseudogenes, to allow unambiguous scientific communication.

Protein Ontology (PRO) provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms ...

A bioinformatic database of antimicrobial resistance genes, their products and associated phenotypes.

Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis which was created to improve knowledge of developmental and disease processes. Through curation and automated data provisioning from various sources, Xenbase aims ...

SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.

The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies ...

ViralZone is a web resource for viral genes and families, providing detailed molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives easy access to UniProtKB/Swiss-Prot viral protein entries.

The GO Annotation Database (GOA) provides Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. GOA files contain a mixture of manual annotati ...

A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.

The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.

The Evidence and Conclusion Ontology (ECO) contains terms that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product X has fun ...

The Chemical Effects in Biological Systems (CEBS) database houses data of interest to environmental health scientists. CEBS is a public resource, and has received depositions of data from academic, industrial, and governmental laboratories.

The Progenetix database provides an overview of copy number abnormalities in human cancer from Comparative Genomic Hybridization (CGH) experiments. With 30817 cases from 1016 publications (Oct 2013), Progenetix is the largest curated database for who ...

ICD-10 is the 10th revision of the International Statistical Classification of Diseases and Related Health Problems (ICD), a medical classification list by the World Health Organization. It contains codes for diseases, signs and symptoms, abnormal fi ...

bio.tools is a registry of information about bioinformatics software and data services. It was created to help researchers in biological and biomedical science to find and use such resources.

The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biol ...

Aniseed is a database designed to offer a representation of ascidian embryonic development at the level of the genome (cis-regulatory sequences, spatial gene expression, protein annotation), of the cell (cell shapes, fate, lineage) or of the whole em ...

Sequence, structure and activity of protein toxins from spider venom

Orphanet Rare Diseases Ontology (ORDO) provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.

The EuroPhenome project provides access to raw and annotated mouse phenotyping data generated from primary pipelines such as EMPReSSlim and secondary procedures from specialist centres. Mutants of interest can be identified by searching the gene or t ...

To enable interoperability of genome annotations, we have developed the Genome Biology Ontology Language (GBOL) and associated stack (GBOL stack). GBOL is provenance centered and provides a consistent representation of genome derived automated predic ...

ParameciumDB is a new model organism database for Paramecium, built using components of the Generic Model Organism Database (http://www.gmod.org) construction set (Chado relational database schema, Turnkey generic web framework and Gbrowse). The data ...

FlyTF (v2) is a manually curated catalogue of Drosophila site-specific transcription factors (TFs). It integrates proteins identified as DNA-binding TFs by computational prediction based on structural domain assignments, and experimentally verified T ...

Experimental annotations of localization for Homo sapiens and Arabidopsis thaliana

Experimentally Characterized Protein annotations

FHIR And SSN based Type 1 diabetes Ontology (FASTO) is an OWL 2 ontology for real time management of insulin for diabetes patients especially type 1 diabetics. The ontology is based on BFO as the top-level ontology, SSN sensor ontology, and HL7 FHIR ...

The Clinical Trials Ontology (CTO) is also known as the Clinical Trial Ontology-Neurodegenerative Diseases (CTO-NDD), and describes clinical trials in the field of neurodegeneration. This resource has been created for use in the IMI-funded AETIONOMY ...

Anatomy ontology for planaria and terms specific to the developmental stages of the planarian Schmidtea mediterranea. As the regenerative flatworm Schmidtea mediterranea gains popularity as a developmental research organism the need for standard nome ...

Mutant mouse lines held at MRC Harwell

Framework for automatically accessing information that is annotated with ontologies or contains terms used to label classes in ontologies.

Integrated database of mammalian genomes, phenotypes, strains and cell lines

A database for systems biology of DNA dynamics during the cell life.

FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data.

GoMapMan is an open web-accessible resource for gene functional annotations in the plant sciences. It was developed to facilitate improvement, consolidation and visualization of gene annotations across several plant species.

System for collecting, preserving and providing bioresources for use as experimental materials for life science research.

The Clinical MetaData Ontology is designed to be used to classify Common Data Elements (CDEs) from different studies and clinical documents. CDEs can be efficiently searched, shared and reused by using our ontology.

The COVID-19 ontology covers the role of molecular and cellular entities in virus-host-interactions, in the virus life cycle, as well as a wide spectrum of medical and epidemiological concepts linked to COVID-19.

Repository of protein names and naming rules

PlantCircNet is a database that provides plant circRNA-miRNA-gene regulatory networks, as well as circRNA information and circRNA expression profiles. It provides convenient search functions for circRNA-associated regulatory networks and enables user ...

Semantic web application network that combines a set of algorithms to streamline the creation of new semantic web-based knowledge management systems. In a single package, it provides the tools to create new applications, including advanced integratio ...

the small RNA Expression Atlas web application. Sign in with Google or with you SEA account below. If you have not created an account yet, then please register first. If you have received an eMail from Oasis 2 that the classification or DE analysis ...

The Ontology of Drug Adverse Events (ODAE) is a biomedical ontology in the area of drug adverse events, developed by following OBO Foundry principles (e.g., openness, collaboration).

GlycoConjugate Ontology (GlycoCoO) as a standard semantic framework to describe and represent glycoconjugate data in RDF.

ARGminer is a web platform dedicated to the validation of ARGs by using sequence alignment and evidence from multiple sources.

CellO (Cell Ontology-based classification) is a Python package for performing cell type classification of human RNA-seq data. CellO makes hierarchical predictions against the Cell Ontology. These classifiers were trained on nearly all of the human pr ...

BiPOm is an ontology based on systemic representation of metabolic processes. BiPOm is an ontological model carrying the main biological processes and molecular roles/functions at a high level of genericity where the usual annotated resources are tre ...

Collection of gene and protein names, organized by species that can be used to search for a given gene/protein name, retrieve all synonyms for this entity, and query Medline with a set of user-selected terms.

GenoSurf is a metadata driven semantic search system for integrated genomic datasets. Many valuable resources developed by worldwide research institutions and consortia describe genomic datasets that are open, but their metadata search interfaces ar ...

The Plant Experimental Assay Ontology (PEAO) was created to describe experimental procedures within plant research, regardless of the scientific questions that prompted the assays. This ontology models entities from three distinct realms (biological, ...

CpGDB (Chloroplast Genome Database) is a user friendly, freely available and dynamic relational database which allows search and download of complete chloroplast genome sequences, individual gene sequences and feature records of different plant speci ...

A toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions. GOMCL is a tool to cluster and extract summarized associations of Gene Ontology based functions in omics data. It clusters GO terms using MCL ba ...

FlorItaly is a data portal for the flora of Italy. This portal organises nomenclatural and distributional data from the recent checklists of the Italian native and alien vascular plants (and their subsequent updatings), with links to resources from o ...

Avian Immunome DB is a user-friendly interface for extracting genetic information about the avian immune system. The avian immune system is characterised by a cascade of complex biological processes underlaid by more than 1000 different genes.

Leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms.

Genome database that is purely based on the Semantic Web technology, which enables the integration of heterogeneous data and flexible semantic searches.

A comprehensive database of trained immunity.

Cov19VaxKB: COVID-19 Vaccine Knowledge Base.

The Colorado Richly Annotated Full Text Corpus (CRAFT) is a manually annotated corpus consisting of 67 full-text biomedical journal articles from the PubMed Central Open Access Subset.

WCO-Lite is an online nomenclatural catalogue of harvestmen of the world (Arachnida, Opiliones) curated in TaxonWorks.

Iranian traditional medicine General Ontology (IrGO) and knowledge base. Iranian traditional medicine (also called Persian Medicine), is an elaborate holistic system of healing grounded in a philosophical basis.

A manually curated database of polycystic ovarian syndrome. Nor Afiqah-Aleng, Sarahani Harun, Mohd Rusman Arief A-Rahman, Nor Azlan Nor Muhammad, Zeti-Azura Mohamed-Hussein, PCOSBase: a manually curated database of polycystic ovarian syndrome, Datab ...

COVID-19 preVIEW is a tool for semantic search to explore COVID-19 research preprints.

Berlin-Tübingen-Oncology corpus (BRONCO) is a large and freely available corpus of shuffled sentences from German oncological discharge summaries annotated with diagnosis, treatments, medications, and further attributes including negation and specula ...

Orphadata provides the scientific community with comprehensive, quality datasets related to rare diseases and orphan drugs from the Orphanet knowledge base, in reusable formats.

Alzheimer’s disease (AD) pathophysiology is still imperfectly understood and current paradigms have not led to curative outcome. Omics technologies offer great promises for improving our understanding and generating new hypotheses. However, integrati ...

Application ontology for Ocular Immune-mediated Inflammatory Diseases, built from domain experts in ophthalmology, clinical guidelines, and enhanced with patient-preferred terms.

DatumKB is a freely accessible database of experimental results involving the function and regulation of human proteins in cultured cells. The results are manually curated from biological research literature using a shorthand language and stored as d ...

Reference anatomies of the brain and corresponding atlases play a central role in experimental neuroimaging workflows and are the foundation for reporting standardized results. The choice of such references —i.e., templates— and atlases is one releva ...

DDIEM - Drug Database for inborn errors of metabolism is a database on therapeutic strategies for inborn errors of metabolism. These strategies are classified by mechanism and outcome in DDIEM ontology. DDIEM uses this ontology to categorize the expe ...

A web-based tool to access and analyse bacterial pesticidal proteins.

A database of comprehensive miRNA target prediction framework for sugarcane (Saccharum officinarum L.).

Semantic-based detection of redundancies to unify protein-protein interaction databases.

A Database and User Interface for scRNA-seq Marker Genes.

The Organ-Disease Annotations (ODiseA) Database of Hereditary Diseases and Inflicted Tissues.

MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes.

A search tool for finding variants from specific chromosome coordinates. It is possible to integrate the results in NGS pipeline.

Methods for broad-scale plant phenology assessments using citizen scientists’ photographs | iNaturalist.org is a joint initiative of the California Academy of Sciences and the National Geographic Society | Explore and share your observations from the ...

SAMS is a database and phenotyping tool for precision medicine. Physicians can enter clinical signs from the Human Phenotype Ontology as well complete diagnoses, and patients can be involved by sharing the symptoms they encounter.

DNMSO is an ontology for representing de novo sequencing results from Tandem-MS data. For the identification and sequencing of proteins, mass spectrometry (MS) has become the tool of choice and as such drives proteomics.

Diatoms.org represents such a content curation community, providing open, online access to a vast amount of recent and historical information on North American diatom taxonomy and ecology.

COVID-19 Knowledge Extractor (COKE) is a tool and a web portal to extract drug - target protein associations from the CORD-19 corpus of scientific publications on COVID-19.

A renovated knowledgebase for deriving biological and chemical insight from genes, proteins, and metabolites.

EUAdb is database for COVID-19 test development that contains standardized information about Eemergency Use Authorizations-issued tests and is focused on RT-qPCR diagnostic tests, or high complexity molecular-based laboratory developed tests.

MEDI (MEDication Indication) is an ensemble medication indication resource for primary and secondary uses of electronic medical record (EMR) data.

a biomedical relation extraction dataset (BioRED) with multiple entity types (e.g. gene/protein, disease, chemical) and relation pairs (e.g. gene-disease; chemical-chemical) at the document level, on a set of 600 PubMed abstracts.

The CerealESTdb, a user-friendly, searchable, and interactive database has been developed with a primary goal to provide information on assembled and annotated ESTs from four major crop plants, namely wheat, rice, maize, and sorghum under multiple en ...

Biomedical Research Software as a Service that enables biomedical & translational researchers to securely manage and combine datasets, typically for patient cohorts. A suite of cloud enabled & integrated open source applications can be accessed in a ...

The Bibliome Variant Database is a collection of variants mined from open-access primary literature. All variants included in the database have been mapped to the human genome and are presented in a manner ordered by genomic location. The goal of thi ...

COVID Term is constructed by Institute of Medical Information, Chinese Academy of Medical Sciences and consists of the bilingual preferred terms, abbreviations, synonyms and some definitions and sources for concepts related with COVID-19 in disease, ...

DODO is a graph database to facilitate access and interaction with disease and phenotype ontologies. The aim of DODO is to allow an easier way to interact and explore disease ontologies and their identifiers. The database is build on Neo4j and incorp ...

A repository of unique short Open Reading Frames identified by both experimental and computational approaches for gene-level and meta-analysis. MetamORF: A repository of unique short Open Reading Frames identified by both experimental and computatio ...

Gene Ontology Meta Annotator for Plants. Lawrence-Dill Plant Informatics and Computation Lab. Welcome to GOMAP-singularity’s documentation! — GOMAP-Singularity 1.3.2 documentation. All publications and products by the team at Lawrence-Dill Plant I ...

A data-driven social network connecting scientists to genomics datasets. ORSO (Online Resource for Social Omics) is a web application designed to help users find next generation sequencing (NGS) datasets relevant to their research interests. ORSO per ...